# HG changeset patch
# User marcel
# Date 1310482387 14400
# Node ID bb26168c571599555ed45a1fc81c98556686a2d7
# Parent e343494f18fef0474e86b4c76e23fc8f2311e34b
Uploaded
diff -r e343494f18fe -r bb26168c5715 CADDSuite/AntitargetRescorer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AntitargetRescorer Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/AntitargetRescorer.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/AutoModel
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AutoModel Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/AutoModel.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/BindingDBCleaner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/BindingDBCleaner Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/BindingDBCleaner.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/CADDSuite-description.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CADDSuite-description.txt Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,61 @@
+This package contains tools belonging to
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+
+There are tools for the following tasks:
+
+Get Data:
+ - CombiLibGenerator: generate R-group decorated ligands
+ - DBExporter: fetch (filtered) molecules from DB
+
+Preparation of input:
+ - PDBCutter: separate ligand and receptor
+ - ProteinProtonator: protonate protein structures
+ - BindingDBCleaner: fix data from bindingdb.org
+ - EvenSplit: generate splits w/ equal property range
+ - PropertyModifier: modify property tags
+ - LigandFileSplitter: split molecule files
+ - Ligand3DGenerator: generate 3D coordinates for small molecules
+
+Structure checks and evaluations:
+ - ProteinCheck: evaluate protein quality
+ - LigCheck: chemical sanity check for ligands
+
+QuEasy (QSAR):
+ - InputReader: read molecules and generate features
+ - ModelCreator: create a QSAR model
+ - FeatureSelector: automatically select features of a QSAR model
+ - Validator: evaluate quality of a QSAR model
+ - MolPredictor: predict molecule activities with QSAR model
+ - AutoModel: automatically find best QSAR model
+
+Docking:
+ - WaterFinder: find strongly bound water molecules
+ - SpatialConstraintDefiner: define spatial constraint
+ - InteractionConstraintDefiner: define interaction constraint
+ - ConstraintsFinder: find strongly interacting residues
+ - PocketDetector: detect ligand binding pocket
+ - GridBuilder: precalculate grids for docking
+ - IMGDock: run Iterative Multi-Greedy Docking
+
+Rescoring:
+ - SimpleRescorer: rescore docking results
+ - TaGRes-train: Target-specific Grid-Rescoring, training
+ - TaGRes: Target-specific Grid-Rescoring
+ - AntitargetRescoring: rescore w/ respect to antitarget
+
+Analysis:
+ - ScoreAnalyzer: generate ROC or enrichment plots
+ - SimilarityAnalyzer: analyze similarity between two molecule sets
+ - PropertyPlotter: plot molecule properties
+ - RMSDCalculator: calculate RMSD between conformations
+ - VendorFinder: search vendors for compounds
+
+Convert, combine and store:
+ - DockResultMerger: merge docking output files and/or filter them
+ - MolCombine: combine molecular files
+ - DBImporter: import molecules into DB
+ - Converter: interconvert molecular file-formats
+ - MolDepict: generate structure diagrams
+ - VendorFinder: search vendors for compounds
+
+For more information about an individual tool, please call the tool without any parameters (or with '-help').
diff -r e343494f18fe -r bb26168c5715 CADDSuite/CombiLibGenerator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CombiLibGenerator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/CombiLibGenerator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/ConstraintsFinder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ConstraintsFinder Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ConstraintsFinder.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/Converter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Converter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Converter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/DBExporter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBExporter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/DBExporter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/DBImporter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBImporter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/DBImporter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/DockResultMerger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DockResultMerger Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/DockResultMerger.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/EvenSplit
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/EvenSplit Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/EvenSplit.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/FeatureSelector
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/FeatureSelector Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/FeatureSelector.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/GalaxyConfigGenerator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GalaxyConfigGenerator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/GridBuilder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GridBuilder Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/GridBuilder.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/IMGDock
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/IMGDock Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/IMGDock.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/InputPartitioner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputPartitioner Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/InputPartitioner.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/InputReader
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputReader Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/InputReader.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/InteractionConstraintDefiner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InteractionConstraintDefiner Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/LigCheck
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigCheck Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/LigCheck.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/Ligand3DGenerator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Ligand3DGenerator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Ligand3DGenerator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/LigandFileSplitter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigandFileSplitter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/LigandFileSplitter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/ModelCreator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ModelCreator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ModelCreator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/MolCombine
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolCombine Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolCombine.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/MolDepict
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolDepict Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolDepict.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/MolFilter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolFilter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolFilter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/MolPredictor
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolPredictor Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolPredictor.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/PDBCutter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBCutter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PDBCutter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/PDBDownload
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBDownload Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PDBDownload.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/PartialChargesCopy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PartialChargesCopy Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PartialChargesCopy.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/PocketDetector
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PocketDetector Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PocketDetector.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/Predictor
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Predictor Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Predictor.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/PropertyModifier
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyModifier Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PropertyModifier.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/PropertyPlotter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyPlotter Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PropertyPlotter.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/ProteinCheck
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinCheck Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ProteinCheck.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/ProteinProtonator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinProtonator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ProteinProtonator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/README Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,41 @@
+-----------------------------------------------------------------------
+ CADDSuite - A flexible and open framework and workflow system
+ for computer-aided drug design
+-----------------------------------------------------------------------
+
+This package contains all tools belonging to CADDSuite.
+For an overview over the contained tools, please see CADDSuite-description.txt.
+After extraction the package, you can directly start the applications using the startup-scripts in the base-folder.
+
+For more information about an individual tool, please call the tool without any parameters (or with '-help').
+
+
+
+--------------------------------------------------------------------
+Instructions for integration of CADDSuite into the workflow-system
+Galaxy (http://getgalaxy.org)
+--------------------------------------------------------------------
+
+
+In order to install CADDSuite into your Galaxy installation, please to the following:
+
+Let's assume $galaxybase is the base-folder of your Galaxy installation.
+If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first.
+
+
+-- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination.
+
+After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below:
+
+-- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation.
+
+-- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/
+
+-- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
+
+
+
+Last but not least, restart Galaxy.
+All CADDSuite tools should now appear in your Galaxy webinterface.
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/RMSDCalculator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/RMSDCalculator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/RMSDCalculator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/ScoreAnalyzer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ScoreAnalyzer Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ScoreAnalyzer.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/SimilarityAnalyzer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimilarityAnalyzer Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/SimpleRescorer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimpleRescorer Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/SimpleRescorer.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/SpatialConstraintDefiner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SpatialConstraintDefiner Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/TaGRes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/TaGRes.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/TaGRes-train
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes-train Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/TaGRes-train.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/Validator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Validator Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Validator.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/VendorFinder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/VendorFinder Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/VendorFinder.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/WaterFinder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/WaterFinder Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/WaterFinder.bin "$@"
diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/AntitargetRescorer.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/AutoModel.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/BindingDBCleaner.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/CombiLibGenerator.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/ConstraintsFinder.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/Converter.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/DBExporter.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/DBImporter.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/DockResultMerger.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/EvenSplit.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/FeatureSelector.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/GalaxyConfigGenerator.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/bin/LigandFileSplitter.bin
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/changelog.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/changelog.txt Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,54 @@
+Version 0.95, 07-12-2011:
+ - Let rescoring search for correct LigCheck molecule property-tags
+ - Indicate optional parameters in galaxy interface
+ - Fixed compilation with disabled QuEasyViz
+ - Added missing gnuplot data file to release archive
+ - Set some default values for flags for use in GUIs
+ - Clarified EvenSplit docu
+
+Version 0.94, 06-27-2011:
+ - Fixed tool-startup script for pathes containing whitespaces
+ - New tool SpatialConstraintDefiner
+ - New tool InteractionConstraintDefiner
+ - Removed superficial pathes from startup-script
+ - Slight change in ParamFile format (i.e. the files written with -write_par)
+ - Renamed IMeedyDock to IMGDock
+
+Version 0.93, 05-30-2011:
+ - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
+ - Allow to optionally specify output filenames to LigandFileSplitter
+ - Fixed creation of galaxy-scripts for tools with inputfile-lists
+ - Fixed creation of galaxy-scripts for Converter and DockResultMerger
+ - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
+ - New tool MolFilter
+ - Fixed some gnuplot issues
+ - Added PDBDownload tool
+ - Slight change of format of ParamFile
+ - Added some missing tool-manuals
+ - Disable B-factor check for hydrogens in ProteinCheck
+ - Added safeguards to several tools
+ - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
+ - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
+ - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
+ - Enhanced several tool manuals
+ - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
+
+Version 0.92, 05-17-2011:
+ - Speed-up of ob-mol generation
+ - Support build on Windows
+ - ProteinCheck now generates protein-quality report as pdf
+ - Added info about mandatory parameters and parameter-restrictions to parameter xml-file
+ - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
+ - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
+ - New tool MolDepict. It generates structure diagrams for small molecules by using openbabel's svg-writer and merges them to one pdf-file (3 on 5).
+ - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
+ - Write information about supported file-formats to parameter xml-file
+ - new tool ProteinProtonator
+ - new tool Ligand3DGenerator
+ - new tool GalaxyConfigGenerator
+ - allow to open file that do not have an extension (by searching for format-specific keywords)
+
+Version 0.91, 04-12-2011:
+ - All tools now write a manual text to cout as well as to parameter xml-file (as generated by 'write_par)
+
+Version 0.9
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/Amber/amber96-docking.ini
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/Amber/amber96-docking.ini Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,1666 @@
+; This file contains parameter needed for nonbonded ScoringComponents.
+; The parameters were converted from parm96.dat using amber2ini and all sections for bonded parameters were removed since are not needed for docking.
+; Furthermore, lennard-jones and AtomType parameters for some metal ions were obtained from the sources indicated in the comment column and added to this file.
+
+[Options]
+key:0
+@SCEE=1.2
+; please check the settings for SCEE! AMBER91/89a requires a value of 2.0 here!
+
+
+
+
+[HydrophilicTypes]
+; ignored
+;
+C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2
+
+
+[HydrogenBonds]
+ver:version key:I key:J value:A value:B
+@unit_A=kcal/mol*A^12
+@unit_B=kcal/mol*A^10
+;
+;
+; Rev I J A B
+; --- --- --- ---------- ----------
+ 1.0 HW OW 0.0000 0.0000
+
+
+[AtomTypes]
+value:ver key:type value:mass value:comment
+@unit=g/mol
+;
+;
+; Rev Type mass comment
+; --- ---- ---------- ----------------------------------
+ 1.0 BR 79.90000 "bromine"
+ 1.0 C 12.01000 "sp2 C carbonyl group "
+ 1.0 F 19.00000 "fluorine"
+ 1.0 I 126.90000 "iodine"
+ 1.0 H 1.00800 "H bonded to nitrogen atoms"
+ 1.0 IM 35.45000 "assumed to be Cl-"
+ 1.0 IP 22.99000 "assumed to be Na+"
+ 1.0 IB 131.00000 "'big ion w/ waters' for vacuum (Na+, 6H2O)"
+ 1.0 N 14.01000 "sp2 nitrogen in amide groups"
+ 1.0 O 16.00000 "carbonyl group oxygen"
+ 1.0 P 30.97000 "phosphate"
+ 1.0 S 32.06000 "sulphur in disulfide linkage"
+ 1.0 Cu 63.55000 "copper"
+ 1.0 Fe 55.00000 "iron"
+ 1.0 Li 6.94000 "lithium"
+ 1.0 K 39.10000 "potassium"
+ 1.0 Rb 85.47000 "rubidium"
+ 1.0 Cs 132.91000 "cesium"
+ ant Cl 35.450 "same as cl"
+ 2.0 Ca 40.08000 "calcium"
+ 1.0 Mg 24.30500 "magnesium"
+ ant Zn 65.4 "Zn2+, taken from parm99.dat (antechamber)"
+
+
+[LennardJones]
+ver:version key:I value:R value:epsilon
+@unit_R=Angstrom
+@unit_epsilon=kcal/mol
+@format=RE
+;
+;
+; Rev I R epsilon comment
+; --- --- ---------- ---------- -------------------------
+ 1.0 Ca 1.600000 0.100000 " calcium from parm91.dat"
+ 1.0 H 0.600000 0.015700 " !Ferguson base pair geom."
+ 1.0 O 1.661200 0.210000 " OPLS"
+ 1.0 C 1.908000 0.086000 " OPLS"
+ 1.0 N 1.824000 0.170000 " OPLS"
+ 1.0 S 2.000000 0.250000 " W. Cornell CH3SH and CH3SCH3 FEP's"
+ 1.0 P 2.100000 0.200000 " JCC,7,(1986),230;"
+ 1.0 IM 2.470000 0.100000 " Cl- Smith & Dang, JCP 1994,100:5,3757"
+ 1.0 IB 5.000000 0.100000 " solvated ion for vacuum approximation"
+ 1.0 Li 1.137000 0.018300 " Li+ Aqvist JPC 1990,94,8021. (adapted)"
+ 1.0 IP 1.868000 0.002770 " Na+ Aqvist JPC 1990,94,8021. (adapted)"
+ 1.0 K 2.658000 0.000328 " K+ Aqvist JPC 1990,94,8021. (adapted)"
+ 1.0 Rb 2.956000 0.000170 " Rb+ Aqvist JPC 1990,94,8021. (adapted)"
+ 1.0 Cs 3.395000 0.000081 " Cs+ Aqvist JPC 1990,94,8021. (adapted)"
+ 1.0 I 2.350000 0.400000 " JCC,7,(1986),230;"
+ 1.0 F 1.750000 0.061000 " Gough et al. JCC 13,(1992),963."
+ ant Cl 2.47 0.1 " Cl- Smith & Dang, JCP 1994,100:5,3757, taken from parm99.dat (antechamber)"
+ ant Zn 1.10 0.0125 " Zn2+, Merz,PAK, JACS,113,8262,(1991), taken from parm99.dat (antechamber)"
+ ant Mg 0.7926 0.8947 " Mg2+ Aqvist JPC 1990,94,8021.(adapted), taken from parm99.dat (antechamber)"
+; ant Cl 1.9480 0.2650 "same as cl"
+; 1.0 Mg 1.170000 0.100000 " magnesium from parm91.dat"
+
+
+[ResidueImproperTorsions]
+key:name
+;
+;
+; res:atom
+; -------------
+ ALA:N
+ ALA:C
+ GLY:N
+ GLY:C
+ SER:N
+ SER:C
+ THR:N
+ THR:C
+ LEU:N
+ LEU:C
+ ILE:N
+ ILE:C
+ VAL:N
+ VAL:C
+ ASN:N
+ ASN:C
+ ASN:CG
+ ASN:ND2
+ GLN:N
+ GLN:C
+ GLN:CD
+ GLN:NE2
+ ARG:N
+ ARG:C
+ ARG:CZ
+ ARG:NE
+ ARG:NH1
+ ARG:NH2
+ HIS:N
+ HIS:C
+ HIS:ND1
+ HIS:CD2
+ HIS:CE1
+ HIS:CG
+ HIS:N
+ HIS:C
+ HIS:NE2
+ HIS:CD2
+ HIS:CE1
+ HIS:CG
+ HIS:N
+ HIS:C
+ HIS:ND1
+ HIS:NE2
+ HIS:CD2
+ HIS:CE1
+ HIS:CG
+ TRP:N
+ TRP:C
+ TRP:NE1
+ TRP:CZ2
+ TRP:CH2
+ TRP:CZ3
+ TRP:CE3
+ TRP:CD1
+ TRP:CG
+ PHE:N
+ PHE:C
+ PHE:CD2
+ PHE:CE2
+ PHE:CZ
+ PHE:CE1
+ PHE:CD1
+ PHE:CG
+ TYR:N
+ TYR:C
+ TYR:CD2
+ TYR:CE2
+ TYR:CE1
+ TYR:CD1
+ TYR:CG
+ TYR:CZ
+ GLU:N
+ GLU:C
+ GLU:CD
+ ASP:N
+ ASP:C
+ ASP:CG
+ LYS:N
+ LYS:C
+ LYN:N
+ LYN:C
+ PRO:C
+ PRO:N
+ CYS:N
+ CYS:C
+ CYM:N
+ CYM:C
+ CYS-S:N
+ CYS-S:C
+ MET:N
+ MET:C
+ ACE:C
+ NME:N
+ ASH:N
+ ASH:C
+ ASH:CG
+ GLH:N
+ GLH:C
+ GLH:CD
+ ALA-N:C
+ GLY-N:C
+ SER-N:C
+ THR-N:C
+ LEU-N:C
+ ILE-N:C
+ VAL-N:C
+ ASN-N:C
+ ASN-N:CG
+ ASN-N:ND2
+ GLN-N:C
+ GLN-N:CD
+ GLN-N:NE2
+ ARG-N:C
+ ARG-N:CZ
+ ARG-N:NE
+ ARG-N:NH1
+ ARG-N:NH2
+ HIS-N:C
+ HIS-N:ND1
+ HIS-N:CD2
+ HIS-N:CE1
+ HIS-N:CG
+ HIS-N:C
+ HIS-N:NE2
+ HIS-N:CD2
+ HIS-N:CE1
+ HIS-N:CG
+ HIS-N:C
+ HIS-N:ND1
+ HIS-N:NE2
+ HIS-N:CD2
+ HIS-N:CE1
+ HIS-N:CG
+ TRP-N:C
+ TRP-N:NE1
+ TRP-N:CZ2
+ TRP-N:CH2
+ TRP-N:CZ3
+ TRP-N:CE3
+ TRP-N:CD1
+ TRP-N:CG
+ PHE-N:C
+ PHE-N:CD2
+ PHE-N:CE2
+ PHE-N:CZ
+ PHE-N:CE1
+ PHE-N:CD1
+ PHE-N:CG
+ TYR-N:C
+ TYR-N:CD2
+ TYR-N:CE2
+ TYR-N:CE1
+ TYR-N:CD1
+ TYR-N:CG
+ TYR-N:CZ
+ GLU-N:C
+ GLU-N:CD
+ ASP-N:C
+ ASP-N:CG
+ LYS-N:C
+ PRO-N:C
+ CYS-N:C
+ CYS-NS:C
+ MET-N:C
+ ALA-C:N
+ ALA-C:C
+ GLY-C:N
+ GLY-C:C
+ SER-C:N
+ SER-C:C
+ THR-C:N
+ THR-C:C
+ LEU-C:N
+ LEU-C:C
+ ILE-C:N
+ ILE-C:C
+ VAL-C:N
+ VAL-C:C
+ ASN-C:N
+ ASN-C:C
+ ASN-C:CG
+ ASN-C:ND2
+ GLN-C:N
+ GLN-C:C
+ GLN-C:CD
+ GLN-C:NE2
+ ARG-C:N
+ ARG-C:C
+ ARG-C:CZ
+ ARG-C:NE
+ ARG-C:NH1
+ ARG-C:NH2
+ HIS-C:N
+ HIS-C:C
+ HIS-C:ND1
+ HIS-C:CD2
+ HIS-C:CE1
+ HIS-C:CG
+ HIS-C:N
+ HIS-C:C
+ HIS-C:NE2
+ HIS-C:CD2
+ HIS-C:CE1
+ HIS-C:CG
+ HIS-C:N
+ HIS-C:C
+ HIS-C:ND1
+ HIS-C:NE2
+ HIS-C:CD2
+ HIS-C:CE1
+ HIS-C:CG
+ TRP-C:N
+ TRP-C:C
+ TRP-C:NE1
+ TRP-C:CZ2
+ TRP-C:CH2
+ TRP-C:CZ3
+ TRP-C:CE3
+ TRP-C:CD1
+ TRP-C:CG
+ PHE-C:N
+ PHE-C:C
+ PHE-C:CD2
+ PHE-C:CE2
+ PHE-C:CZ
+ PHE-C:CE1
+ PHE-C:CD1
+ PHE-C:CG
+ TYR-C:N
+ TYR-C:C
+ TYR-C:CD2
+ TYR-C:CE2
+ TYR-C:CE1
+ TYR-C:CD1
+ TYR-C:CG
+ TYR-C:CZ
+ GLU-C:N
+ GLU-C:C
+ GLU-C:CD
+ ASP-C:N
+ ASP-C:C
+ ASP-C:CG
+ LYS-C:N
+ LYS-C:C
+ PRO-C:C
+ PRO-C:N
+ CYS-C:N
+ CYS-C:C
+ CYS-CS:N
+ CYS-CS:C
+ MET-C:N
+ MET-C:C
+
+[ChargesAndTypeNames]
+ver:version key:name value:q value:type
+@unit_q=e0
+ 1.0 ALA:N -0.41570 N
+ 1.0 ALA:H 0.27190 H
+ 1.0 ALA:CA 0.03370 CT
+ 1.0 ALA:HA 0.08230 H1
+ 1.0 ALA:CB -0.18250 CT
+ 1.0 ALA:1HB 0.06030 HC
+ 1.0 ALA:2HB 0.06030 HC
+ 1.0 ALA:3HB 0.06030 HC
+ 1.0 ALA:C 0.59730 C
+ 1.0 ALA:O -0.56790 O
+ 1.0 GLY:N -0.41570 N
+ 1.0 GLY:H 0.27190 H
+ 1.0 GLY:CA -0.02520 CT
+ 1.0 GLY:1HA 0.06980 H1
+ 1.0 GLY:2HA 0.06980 H1
+ 1.0 GLY:C 0.59730 C
+ 1.0 GLY:O -0.56790 O
+ 1.0 SER:N -0.41570 N
+ 1.0 SER:H 0.27190 H
+ 1.0 SER:CA -0.02490 CT
+ 1.0 SER:HA 0.08430 H1
+ 1.0 SER:CB 0.21170 CT
+ 1.0 SER:1HB 0.03520 H1
+ 1.0 SER:2HB 0.03520 H1
+ 1.0 SER:OG -0.65460 OH
+ 1.0 SER:HG 0.42750 HO
+ 1.0 SER:C 0.59730 C
+ 1.0 SER:O -0.56790 O
+ 1.0 THR:N -0.41570 N
+ 1.0 THR:H 0.27190 H
+ 1.0 THR:CA -0.03890 CT
+ 1.0 THR:HA 0.10070 H1
+ 1.0 THR:CB 0.36540 CT
+ 1.0 THR:HB 0.00430 H1
+ 1.0 THR:CG2 -0.24380 CT
+ 1.0 THR:1HG2 0.06420 HC
+ 1.0 THR:2HG2 0.06420 HC
+ 1.0 THR:3HG2 0.06420 HC
+ 1.0 THR:OG1 -0.67610 OH
+ 1.0 THR:HG1 0.41020 HO
+ 1.0 THR:C 0.59730 C
+ 1.0 THR:O -0.56790 O
+ 1.0 LEU:N -0.41570 N
+ 1.0 LEU:H 0.27190 H
+ 1.0 LEU:CA -0.05180 CT
+ 1.0 LEU:HA 0.09220 H1
+ 1.0 LEU:CB -0.11020 CT
+ 1.0 LEU:1HB 0.04570 HC
+ 1.0 LEU:2HB 0.04570 HC
+ 1.0 LEU:CG 0.35310 CT
+ 1.0 LEU:HG -0.03610 HC
+ 1.0 LEU:CD1 -0.41210 CT
+ 1.0 LEU:1HD1 0.10000 HC
+ 1.0 LEU:2HD1 0.10000 HC
+ 1.0 LEU:3HD1 0.10000 HC
+ 1.0 LEU:CD2 -0.41210 CT
+ 1.0 LEU:1HD2 0.10000 HC
+ 1.0 LEU:2HD2 0.10000 HC
+ 1.0 LEU:3HD2 0.10000 HC
+ 1.0 LEU:C 0.59730 C
+ 1.0 LEU:O -0.56790 O
+ 1.0 ILE:N -0.41570 N
+ 1.0 ILE:H 0.27190 H
+ 1.0 ILE:CA -0.05970 CT
+ 1.0 ILE:HA 0.08690 H1
+ 1.0 ILE:CB 0.13030 CT
+ 1.0 ILE:HB 0.01870 HC
+ 1.0 ILE:CG2 -0.32040 CT
+ 1.0 ILE:1HG2 0.08820 HC
+ 1.0 ILE:2HG2 0.08820 HC
+ 1.0 ILE:3HG2 0.08820 HC
+ 1.0 ILE:CG1 -0.04300 CT
+ 1.0 ILE:1HG1 0.02360 HC
+ 1.0 ILE:2HG1 0.02360 HC
+ 1.0 ILE:CD1 -0.06600 CT
+ 1.0 ILE:1HD1 0.01860 HC
+ 1.0 ILE:2HD1 0.01860 HC
+ 1.0 ILE:3HD1 0.01860 HC
+ 1.0 ILE:C 0.59730 C
+ 1.0 ILE:O -0.56790 O
+ 1.0 VAL:N -0.41570 N
+ 1.0 VAL:H 0.27190 H
+ 1.0 VAL:CA -0.08750 CT
+ 1.0 VAL:HA 0.09690 H1
+ 1.0 VAL:CB 0.29850 CT
+ 1.0 VAL:HB -0.02970 HC
+ 1.0 VAL:CG1 -0.31920 CT
+ 1.0 VAL:1HG1 0.07910 HC
+ 1.0 VAL:2HG1 0.07910 HC
+ 1.0 VAL:3HG1 0.07910 HC
+ 1.0 VAL:CG2 -0.31920 CT
+ 1.0 VAL:1HG2 0.07910 HC
+ 1.0 VAL:2HG2 0.07910 HC
+ 1.0 VAL:3HG2 0.07910 HC
+ 1.0 VAL:C 0.59730 C
+ 1.0 VAL:O -0.56790 O
+ 1.0 ASN:N -0.41570 N
+ 1.0 ASN:H 0.27190 H
+ 1.0 ASN:CA 0.01430 CT
+ 1.0 ASN:HA 0.10480 H1
+ 1.0 ASN:CB -0.20410 CT
+ 1.0 ASN:1HB 0.07970 HC
+ 1.0 ASN:2HB 0.07970 HC
+ 1.0 ASN:CG 0.71300 C
+ 1.0 ASN:OD1 -0.59310 O
+ 1.0 ASN:ND2 -0.91910 N
+ 1.0 ASN:1HD2 0.41960 H
+ 1.0 ASN:2HD2 0.41960 H
+ 1.0 ASN:C 0.59730 C
+ 1.0 ASN:O -0.56790 O
+ 1.0 GLN:N -0.41570 N
+ 1.0 GLN:H 0.27190 H
+ 1.0 GLN:CA -0.00310 CT
+ 1.0 GLN:HA 0.08500 H1
+ 1.0 GLN:CB -0.00360 CT
+ 1.0 GLN:1HB 0.01710 HC
+ 1.0 GLN:2HB 0.01710 HC
+ 1.0 GLN:CG -0.06450 CT
+ 1.0 GLN:1HG 0.03520 HC
+ 1.0 GLN:2HG 0.03520 HC
+ 1.0 GLN:CD 0.69510 C
+ 1.0 GLN:OE1 -0.60860 O
+ 1.0 GLN:NE2 -0.94070 N
+ 1.0 GLN:1HE2 0.42510 H
+ 1.0 GLN:2HE2 0.42510 H
+ 1.0 GLN:C 0.59730 C
+ 1.0 GLN:O -0.56790 O
+ 1.0 ARG:N -0.34790 N
+ 1.0 ARG:H 0.27470 H
+ 1.0 ARG:CA -0.26370 CT
+ 1.0 ARG:HA 0.15600 H1
+ 1.0 ARG:CB -0.00070 CT
+ 1.0 ARG:1HB 0.03270 HC
+ 1.0 ARG:2HB 0.03270 HC
+ 1.0 ARG:CG 0.03900 CT
+ 1.0 ARG:1HG 0.02850 HC
+ 1.0 ARG:2HG 0.02850 HC
+ 1.0 ARG:CD 0.04860 CT
+ 1.0 ARG:1HD 0.06870 H1
+ 1.0 ARG:2HD 0.06870 H1
+ 1.0 ARG:NE -0.52950 N2
+ 1.0 ARG:HE 0.34560 H
+ 1.0 ARG:CZ 0.80760 CA
+ 1.0 ARG:NH1 -0.86270 N2
+ 1.0 ARG:1HH1 0.44780 H
+ 1.0 ARG:2HH1 0.44780 H
+ 1.0 ARG:NH2 -0.86270 N2
+ 1.0 ARG:1HH2 0.44780 H
+ 1.0 ARG:2HH2 0.44780 H
+ 1.0 ARG:C 0.73410 C
+ 1.0 ARG:O -0.58940 O
+ 1.0 HIS:N -0.34790 N
+ 1.0 HIS:H 0.27470 H
+ 1.0 HIS:CA -0.13540 CT
+ 1.0 HIS:HA 0.12120 H1
+ 1.0 HIS:CB -0.04140 CT
+ 1.0 HIS:1HB 0.08100 HC
+ 1.0 HIS:2HB 0.08100 HC
+ 1.0 HIS:CG -0.00120 CC
+ 1.0 HIS:ND1 -0.15130 NA
+ 1.0 HIS:HD1 0.38660 H
+ 1.0 HIS:CE1 -0.01700 CR
+ 1.0 HIS:HE1 0.26810 H5
+ 1.0 HIS:NE2 -0.17180 NA
+ 1.0 HIS:CD2 -0.11410 CW
+ 1.0 HIS:HD2 0.23170 H4
+ 1.0 HIS:C 0.73410 C
+ 1.0 HIS:O -0.58940 O
+ 1.0 HIS:N -0.34790 N
+ 1.0 HIS:H 0.27470 H
+ 1.0 HIS:CA -0.13540 CT
+ 1.0 HIS:HA 0.12120 H1
+ 1.0 HIS:CB -0.04140 CT
+ 1.0 HIS:1HB 0.08100 HC
+ 1.0 HIS:2HB 0.08100 HC
+ 1.0 HIS:CG -0.00120 CC
+ 1.0 HIS:ND1 -0.15130 NA
+ 1.0 HIS:CE1 -0.01700 CR
+ 1.0 HIS:HE1 0.26810 H5
+ 1.0 HIS:NE2 -0.17180 NA
+ 1.0 HIS:HE2 0.39110 H
+ 1.0 HIS:CD2 -0.11410 CW
+ 1.0 HIS:HD2 0.23170 H4
+ 1.0 HIS:C 0.73410 C
+ 1.0 HIS:O -0.58940 O
+ 1.0 HIS:N -0.34790 N
+ 1.0 HIS:H 0.27470 H
+ 1.0 HIS:CA -0.13540 CT
+ 1.0 HIS:HA 0.12120 H1
+ 1.0 HIS:CB -0.04140 CT
+ 1.0 HIS:1HB 0.08100 HC
+ 1.0 HIS:2HB 0.08100 HC
+ 1.0 HIS:CG -0.00120 CC
+ 1.0 HIS:ND1 -0.15130 NA
+ 1.0 HIS:HD1 0.38660 H
+ 1.0 HIS:CE1 -0.01700 CR
+ 1.0 HIS:HE1 0.26810 H5
+ 1.0 HIS:NE2 -0.17180 NA
+ 1.0 HIS:HE2 0.39110 H
+ 1.0 HIS:CD2 -0.11410 CW
+ 1.0 HIS:HD2 0.23170 H4
+ 1.0 HIS:C 0.73410 C
+ 1.0 HIS:O -0.58940 O
+ 1.0 TRP:N -0.41570 N
+ 1.0 TRP:H 0.27190 H
+ 1.0 TRP:CA -0.02750 CT
+ 1.0 TRP:HA 0.11230 H1
+ 1.0 TRP:CB -0.00500 CT
+ 1.0 TRP:1HB 0.03390 HC
+ 1.0 TRP:2HB 0.03390 HC
+ 1.0 TRP:CG -0.14150 C*
+ 1.0 TRP:CD1 -0.16380 CW
+ 1.0 TRP:HD1 0.20620 H4
+ 1.0 TRP:NE1 -0.34180 NA
+ 1.0 TRP:HE1 0.34120 H
+ 1.0 TRP:CE2 0.13800 CN
+ 1.0 TRP:CZ2 -0.26010 CA
+ 1.0 TRP:HZ2 0.15720 HA
+ 1.0 TRP:CH2 -0.11340 CA
+ 1.0 TRP:HH2 0.14170 HA
+ 1.0 TRP:CZ3 -0.19720 CA
+ 1.0 TRP:HZ3 0.14470 HA
+ 1.0 TRP:CE3 -0.23870 CA
+ 1.0 TRP:HE3 0.17000 HA
+ 1.0 TRP:CD2 0.12430 CB
+ 1.0 TRP:C 0.59730 C
+ 1.0 TRP:O -0.56790 O
+ 1.0 PHE:N -0.41570 N
+ 1.0 PHE:H 0.27190 H
+ 1.0 PHE:CA -0.00240 CT
+ 1.0 PHE:HA 0.09780 H1
+ 1.0 PHE:CB -0.03430 CT
+ 1.0 PHE:1HB 0.02950 HC
+ 1.0 PHE:2HB 0.02950 HC
+ 1.0 PHE:CG 0.01180 CA
+ 1.0 PHE:CD1 -0.12560 CA
+ 1.0 PHE:HD1 0.13300 HA
+ 1.0 PHE:CE1 -0.17040 CA
+ 1.0 PHE:HE1 0.14300 HA
+ 1.0 PHE:CZ -0.10720 CA
+ 1.0 PHE:HZ 0.12970 HA
+ 1.0 PHE:CE2 -0.17040 CA
+ 1.0 PHE:HE2 0.14300 HA
+ 1.0 PHE:CD2 -0.12560 CA
+ 1.0 PHE:HD2 0.13300 HA
+ 1.0 PHE:C 0.59730 C
+ 1.0 PHE:O -0.56790 O
+ 1.0 TYR:N -0.41570 N
+ 1.0 TYR:H 0.27190 H
+ 1.0 TYR:CA -0.00140 CT
+ 1.0 TYR:HA 0.08760 H1
+ 1.0 TYR:CB -0.01520 CT
+ 1.0 TYR:1HB 0.02950 HC
+ 1.0 TYR:2HB 0.02950 HC
+ 1.0 TYR:CG -0.00110 CA
+ 1.0 TYR:CD1 -0.19060 CA
+ 1.0 TYR:HD1 0.16990 HA
+ 1.0 TYR:CE1 -0.23410 CA
+ 1.0 TYR:HE1 0.16560 HA
+ 1.0 TYR:CZ 0.32260 C
+ 1.0 TYR:OH -0.55790 OH
+ 1.0 TYR:HH 0.39920 HO
+ 1.0 TYR:CE2 -0.23410 CA
+ 1.0 TYR:HE2 0.16560 HA
+ 1.0 TYR:CD2 -0.19060 CA
+ 1.0 TYR:HD2 0.16990 HA
+ 1.0 TYR:C 0.59730 C
+ 1.0 TYR:O -0.56790 O
+ 1.0 GLU:N -0.51630 N
+ 1.0 GLU:H 0.29360 H
+ 1.0 GLU:CA 0.03970 CT
+ 1.0 GLU:HA 0.11050 H1
+ 1.0 GLU:CB 0.05600 CT
+ 1.0 GLU:1HB -0.01730 HC
+ 1.0 GLU:2HB -0.01730 HC
+ 1.0 GLU:CG 0.01360 CT
+ 1.0 GLU:1HG -0.04250 HC
+ 1.0 GLU:2HG -0.04250 HC
+ 1.0 GLU:CD 0.80540 C
+ 1.0 GLU:OE1 -0.81880 O2
+ 1.0 GLU:OE2 -0.81880 O2
+ 1.0 GLU:C 0.53660 C
+ 1.0 GLU:O -0.58190 O
+ 1.0 ASP:N -0.51630 N
+ 1.0 ASP:H 0.29360 H
+ 1.0 ASP:CA 0.03810 CT
+ 1.0 ASP:HA 0.08800 H1
+ 1.0 ASP:CB -0.03030 CT
+ 1.0 ASP:1HB -0.01220 HC
+ 1.0 ASP:2HB -0.01220 HC
+ 1.0 ASP:CG 0.79940 C
+ 1.0 ASP:OD1 -0.80140 O2
+ 1.0 ASP:OD2 -0.80140 O2
+ 1.0 ASP:C 0.53660 C
+ 1.0 ASP:O -0.58190 O
+ 1.0 LYS:N -0.34790 N
+ 1.0 LYS:H 0.27470 H
+ 1.0 LYS:CA -0.24000 CT
+ 1.0 LYS:HA 0.14260 H1
+ 1.0 LYS:CB -0.00940 CT
+ 1.0 LYS:1HB 0.03620 HC
+ 1.0 LYS:2HB 0.03620 HC
+ 1.0 LYS:CG 0.01870 CT
+ 1.0 LYS:1HG 0.01030 HC
+ 1.0 LYS:2HG 0.01030 HC
+ 1.0 LYS:CD -0.04790 CT
+ 1.0 LYS:1HD 0.06210 HC
+ 1.0 LYS:2HD 0.06210 HC
+ 1.0 LYS:CE -0.01430 CT
+ 1.0 LYS:1HE 0.11350 HP
+ 1.0 LYS:2HE 0.11350 HP
+ 1.0 LYS:NZ -0.38540 N3
+ 1.0 LYS:1HZ 0.34000 H
+ 1.0 LYS:2HZ 0.34000 H
+ 1.0 LYS:3HZ 0.34000 H
+ 1.0 LYS:C 0.73410 C
+ 1.0 LYS:O -0.58940 O
+ 1.0 LYN:N -0.41570 N
+ 1.0 LYN:H 0.27190 H
+ 1.0 LYN:CA -0.07206 CT
+ 1.0 LYN:HA 0.09940 H1
+ 1.0 LYN:CB -0.04845 CT
+ 1.0 LYN:HB2 0.03400 HC
+ 1.0 LYN:HB3 0.03400 HC
+ 1.0 LYN:CG 0.06612 CT
+ 1.0 LYN:HG2 0.01041 HC
+ 1.0 LYN:HG3 0.01041 HC
+ 1.0 LYN:CD -0.03768 CT
+ 1.0 LYN:HD2 0.01155 HC
+ 1.0 LYN:HD3 0.01155 HC
+ 1.0 LYN:CE 0.32604 CT
+ 1.0 LYN:HE2 -0.03358 HP
+ 1.0 LYN:HE3 -0.03358 HP
+ 1.0 LYN:NZ -1.03581 N3
+ 1.0 LYN:HZ2 0.38604 H
+ 1.0 LYN:HZ3 0.38604 H
+ 1.0 LYN:C 0.59730 C
+ 1.0 LYN:O -0.56790 O
+ 1.0 PRO:N -0.25480 N
+ 1.0 PRO:CD 0.01920 CT
+ 1.0 PRO:1HD 0.03910 H1
+ 1.0 PRO:2HD 0.03910 H1
+ 1.0 PRO:CG 0.01890 CT
+ 1.0 PRO:1HG 0.02130 HC
+ 1.0 PRO:2HG 0.02130 HC
+ 1.0 PRO:CB -0.00700 CT
+ 1.0 PRO:1HB 0.02530 HC
+ 1.0 PRO:2HB 0.02530 HC
+ 1.0 PRO:CA -0.02660 CT
+ 1.0 PRO:HA 0.06410 H1
+ 1.0 PRO:C 0.58960 C
+ 1.0 PRO:O -0.57480 O
+ 1.0 CYS:N -0.41570 N
+ 1.0 CYS:H 0.27190 H
+ 1.0 CYS:CA 0.02130 CT
+ 1.0 CYS:HA 0.11240 H1
+ 1.0 CYS:CB -0.12310 CT
+ 1.0 CYS:1HB 0.11120 H1
+ 1.0 CYS:2HB 0.11120 H1
+ 1.0 CYS:SG -0.31190 SH
+ 1.0 CYS:HG 0.19330 HS
+ 1.0 CYS:C 0.59730 C
+ 1.0 CYS:O -0.56790 O
+ 1.0 CYM:N -0.46300 N
+ 1.0 CYM:HN 0.25200 H
+ 1.0 CYM:CA 0.03500 CT
+ 1.0 CYM:HA 0.04800 H1
+ 1.0 CYM:CB -0.73600 CT
+ 1.0 CYM:HB3 0.24400 H1
+ 1.0 CYM:HB2 0.24400 H1
+ 1.0 CYM:SG -0.73600 SH
+ 1.0 CYM:C 0.61600 C
+ 1.0 CYM:O -0.50400 O
+ 1.0 CYS-S:N -0.41570 N
+ 1.0 CYS-S:H 0.27190 H
+ 1.0 CYS-S:CA 0.04290 CT
+ 1.0 CYS-S:HA 0.07660 H1
+ 1.0 CYS-S:CB -0.07900 CT
+ 1.0 CYS-S:1HB 0.09100 H1
+ 1.0 CYS-S:2HB 0.09100 H1
+ 1.0 CYS-S:SG -0.10810 S
+ 1.0 CYS-S:C 0.59730 C
+ 1.0 CYS-S:O -0.56790 O
+ 1.0 MET:N -0.41570 N
+ 1.0 MET:H 0.27190 H
+ 1.0 MET:CA -0.02370 CT
+ 1.0 MET:HA 0.08800 H1
+ 1.0 MET:CB 0.03420 CT
+ 1.0 MET:1HB 0.02410 HC
+ 1.0 MET:2HB 0.02410 HC
+ 1.0 MET:CG 0.00180 CT
+ 1.0 MET:1HG 0.04400 H1
+ 1.0 MET:2HG 0.04400 H1
+ 1.0 MET:SD -0.27370 S
+ 1.0 MET:CE -0.05360 CT
+ 1.0 MET:1HE 0.06840 H1
+ 1.0 MET:2HE 0.06840 H1
+ 1.0 MET:3HE 0.06840 H1
+ 1.0 MET:C 0.59730 C
+ 1.0 MET:O -0.56790 O
+ 1.0 ACE:1HH3 0.11230 HC
+ 1.0 ACE:CH3 -0.36620 CT
+ 1.0 ACE:2HH3 0.11230 HC
+ 1.0 ACE:3HH3 0.11230 HC
+ 1.0 ACE:C 0.59720 C
+ 1.0 ACE:O -0.56790 O
+ 1.0 HOH:1H 0.41700 HW
+ 1.0 HOH:O -0.83400 OW
+ 1.0 HOH:2H 0.41700 HW
+ 1.0 HOH:H1 0.41700 HW
+ 1.0 HOH:O -0.83400 OW
+ 1.0 HOH:H2 0.41700 HW
+ 1.0 WAT:1H 0.41700 HW
+ 1.0 WAT:O -0.83400 OW
+ 1.0 WAT:2H 0.41700 HW
+ 1.0 ASH:N -0.41570 N
+ 1.0 ASH:H 0.27190 H
+ 1.0 ASH:CA 0.03410 CT
+ 1.0 ASH:HA 0.08640 H1
+ 1.0 ASH:CB -0.03160 CT
+ 1.0 ASH:HB2 0.04880 HC
+ 1.0 ASH:HB3 0.04880 HC
+ 1.0 ASH:CG 0.64620 C
+ 1.0 ASH:OD1 -0.55540 O
+ 1.0 ASH:OD2 -0.63760 OH
+ 1.0 ASH:HD2 0.47470 HO
+ 1.0 ASH:C 0.59730 C
+ 1.0 ASH:O -0.56790 O
+ 1.0 GLH:N -0.41570 N
+ 1.0 GLH:H 0.27190 H
+ 1.0 GLH:CA 0.01450 CT
+ 1.0 GLH:HA 0.07790 H1
+ 1.0 GLH:CB -0.00710 CT
+ 1.0 GLH:HB2 0.02560 HC
+ 1.0 GLH:HB3 0.02560 HC
+ 1.0 GLH:CG -0.01740 CT
+ 1.0 GLH:HG2 0.04300 HC
+ 1.0 GLH:HG3 0.04300 HC
+ 1.0 GLH:CD 0.68010 C
+ 1.0 GLH:OE1 -0.58380 O
+ 1.0 GLH:OE2 -0.65110 OH
+ 1.0 GLH:HE2 0.46410 HO
+ 1.0 GLH:C 0.59730 C
+ 1.0 GLH:O -0.56790 O
+ 1.0 CIP:NA+ 1.00000 IP
+ 1.0 CIM:CL- -1.00000 IM
+ 1.0 ALA-N:N 0.14140 N3
+ 1.0 ALA-N:1H 0.19970 H
+ 1.0 ALA-N:2H 0.19970 H
+ 1.0 ALA-N:3H 0.19970 H
+ 1.0 ALA-N:CA 0.09620 CT
+ 1.0 ALA-N:HA 0.08890 HP
+ 1.0 ALA-N:CB -0.05970 CT
+ 1.0 ALA-N:1HB 0.03000 HC
+ 1.0 ALA-N:2HB 0.03000 HC
+ 1.0 ALA-N:3HB 0.03000 HC
+ 1.0 ALA-N:C 0.61630 C
+ 1.0 ALA-N:O -0.57220 O
+ 1.0 GLY-N:N 0.29430 N3
+ 1.0 GLY-N:1H 0.16420 H
+ 1.0 GLY-N:2H 0.16420 H
+ 1.0 GLY-N:3H 0.16420 H
+ 1.0 GLY-N:CA -0.01000 CT
+ 1.0 GLY-N:1HA 0.08950 HP
+ 1.0 GLY-N:2HA 0.08950 HP
+ 1.0 GLY-N:C 0.61630 C
+ 1.0 GLY-N:O -0.57220 O
+ 1.0 SER-N:N 0.18490 N3
+ 1.0 SER-N:1H 0.18980 H
+ 1.0 SER-N:2H 0.18980 H
+ 1.0 SER-N:3H 0.18980 H
+ 1.0 SER-N:CA 0.05670 CT
+ 1.0 SER-N:HA 0.07820 HP
+ 1.0 SER-N:CB 0.25960 CT
+ 1.0 SER-N:1HB 0.02730 H1
+ 1.0 SER-N:2HB 0.02730 H1
+ 1.0 SER-N:OG -0.67140 OH
+ 1.0 SER-N:HG 0.42390 HO
+ 1.0 SER-N:C 0.61630 C
+ 1.0 SER-N:O -0.57220 O
+ 1.0 THR-N:N 0.18120 N3
+ 1.0 THR-N:1H 0.19340 H
+ 1.0 THR-N:2H 0.19340 H
+ 1.0 THR-N:3H 0.19340 H
+ 1.0 THR-N:CA 0.00340 CT
+ 1.0 THR-N:HA 0.10870 HP
+ 1.0 THR-N:CB 0.45140 CT
+ 1.0 THR-N:HB -0.03230 H1
+ 1.0 THR-N:CG2 -0.25540 CT
+ 1.0 THR-N:1HG2 0.06270 HC
+ 1.0 THR-N:2HG2 0.06270 HC
+ 1.0 THR-N:3HG2 0.06270 HC
+ 1.0 THR-N:OG1 -0.67640 OH
+ 1.0 THR-N:HG1 0.40700 HO
+ 1.0 THR-N:C 0.61630 C
+ 1.0 THR-N:O -0.57220 O
+ 1.0 LEU-N:N 0.10100 N3
+ 1.0 LEU-N:1H 0.21480 H
+ 1.0 LEU-N:2H 0.21480 H
+ 1.0 LEU-N:3H 0.21480 H
+ 1.0 LEU-N:CA 0.01040 CT
+ 1.0 LEU-N:HA 0.10530 HP
+ 1.0 LEU-N:CB -0.02440 CT
+ 1.0 LEU-N:1HB 0.02560 HC
+ 1.0 LEU-N:2HB 0.02560 HC
+ 1.0 LEU-N:CG 0.34210 CT
+ 1.0 LEU-N:HG -0.03800 HC
+ 1.0 LEU-N:CD1 -0.41060 CT
+ 1.0 LEU-N:1HD1 0.09800 HC
+ 1.0 LEU-N:2HD1 0.09800 HC
+ 1.0 LEU-N:3HD1 0.09800 HC
+ 1.0 LEU-N:CD2 -0.41040 CT
+ 1.0 LEU-N:1HD2 0.09800 HC
+ 1.0 LEU-N:2HD2 0.09800 HC
+ 1.0 LEU-N:3HD2 0.09800 HC
+ 1.0 LEU-N:C 0.61230 C
+ 1.0 LEU-N:O -0.57130 O
+ 1.0 ILE-N:N 0.03110 N3
+ 1.0 ILE-N:1H 0.23290 H
+ 1.0 ILE-N:2H 0.23290 H
+ 1.0 ILE-N:3H 0.23290 H
+ 1.0 ILE-N:CA 0.02570 CT
+ 1.0 ILE-N:HA 0.10310 HP
+ 1.0 ILE-N:CB 0.18850 CT
+ 1.0 ILE-N:HB 0.02130 HC
+ 1.0 ILE-N:CG2 -0.37200 CT
+ 1.0 ILE-N:1HG2 0.09470 HC
+ 1.0 ILE-N:2HG2 0.09470 HC
+ 1.0 ILE-N:3HG2 0.09470 HC
+ 1.0 ILE-N:CG1 -0.03870 CT
+ 1.0 ILE-N:1HG1 0.02010 HC
+ 1.0 ILE-N:2HG1 0.02010 HC
+ 1.0 ILE-N:CD1 -0.09080 CT
+ 1.0 ILE-N:1HD1 0.02260 HC
+ 1.0 ILE-N:2HD1 0.02260 HC
+ 1.0 ILE-N:3HD1 0.02260 HC
+ 1.0 ILE-N:C 0.61230 C
+ 1.0 ILE-N:O -0.57130 O
+ 1.0 VAL-N:N 0.05770 N3
+ 1.0 VAL-N:1H 0.22720 H
+ 1.0 VAL-N:2H 0.22720 H
+ 1.0 VAL-N:3H 0.22720 H
+ 1.0 VAL-N:CA -0.00540 CT
+ 1.0 VAL-N:HA 0.10930 HP
+ 1.0 VAL-N:CB 0.31960 CT
+ 1.0 VAL-N:HB -0.02210 HC
+ 1.0 VAL-N:CG1 -0.31290 CT
+ 1.0 VAL-N:1HG1 0.07350 HC
+ 1.0 VAL-N:2HG1 0.07350 HC
+ 1.0 VAL-N:3HG1 0.07350 HC
+ 1.0 VAL-N:CG2 -0.31290 CT
+ 1.0 VAL-N:1HG2 0.07350 HC
+ 1.0 VAL-N:2HG2 0.07350 HC
+ 1.0 VAL-N:3HG2 0.07350 HC
+ 1.0 VAL-N:C 0.61630 C
+ 1.0 VAL-N:O -0.57220 O
+ 1.0 ASN-N:N 0.18010 N3
+ 1.0 ASN-N:1H 0.19210 H
+ 1.0 ASN-N:2H 0.19210 H
+ 1.0 ASN-N:3H 0.19210 H
+ 1.0 ASN-N:CA 0.03680 CT
+ 1.0 ASN-N:HA 0.12310 HP
+ 1.0 ASN-N:CB -0.02830 CT
+ 1.0 ASN-N:1HB 0.05150 HC
+ 1.0 ASN-N:2HB 0.05150 HC
+ 1.0 ASN-N:CG 0.58330 C
+ 1.0 ASN-N:OD1 -0.57440 O
+ 1.0 ASN-N:ND2 -0.86340 N
+ 1.0 ASN-N:1HD2 0.40970 H
+ 1.0 ASN-N:2HD2 0.40970 H
+ 1.0 ASN-N:C 0.61630 C
+ 1.0 ASN-N:O -0.57220 O
+ 1.0 GLN-N:N 0.14930 N3
+ 1.0 GLN-N:1H 0.19960 H
+ 1.0 GLN-N:2H 0.19960 H
+ 1.0 GLN-N:3H 0.19960 H
+ 1.0 GLN-N:CA 0.05360 CT
+ 1.0 GLN-N:HA 0.10150 HP
+ 1.0 GLN-N:CB 0.06510 CT
+ 1.0 GLN-N:1HB 0.00500 HC
+ 1.0 GLN-N:2HB 0.00500 HC
+ 1.0 GLN-N:CG -0.09030 CT
+ 1.0 GLN-N:1HG 0.03310 HC
+ 1.0 GLN-N:2HG 0.03310 HC
+ 1.0 GLN-N:CD 0.73540 C
+ 1.0 GLN-N:OE1 -0.61330 O
+ 1.0 GLN-N:NE2 -1.00310 N
+ 1.0 GLN-N:1HE2 0.44290 H
+ 1.0 GLN-N:2HE2 0.44290 H
+ 1.0 GLN-N:C 0.61230 C
+ 1.0 GLN-N:O -0.57130 O
+ 1.0 ARG-N:N 0.13050 N3
+ 1.0 ARG-N:1H 0.20830 H
+ 1.0 ARG-N:2H 0.20830 H
+ 1.0 ARG-N:3H 0.20830 H
+ 1.0 ARG-N:CA -0.02230 CT
+ 1.0 ARG-N:HA 0.12420 HP
+ 1.0 ARG-N:CB 0.01180 CT
+ 1.0 ARG-N:1HB 0.02260 HC
+ 1.0 ARG-N:2HB 0.02260 HC
+ 1.0 ARG-N:CG 0.02360 CT
+ 1.0 ARG-N:1HG 0.03090 HC
+ 1.0 ARG-N:2HG 0.03090 HC
+ 1.0 ARG-N:CD 0.09350 CT
+ 1.0 ARG-N:1HD 0.05270 H1
+ 1.0 ARG-N:2HD 0.05270 H1
+ 1.0 ARG-N:NE -0.56500 N2
+ 1.0 ARG-N:HE 0.35920 H
+ 1.0 ARG-N:CZ 0.82810 CA
+ 1.0 ARG-N:NH1 -0.86930 N2
+ 1.0 ARG-N:1HH1 0.44940 H
+ 1.0 ARG-N:2HH1 0.44940 H
+ 1.0 ARG-N:NH2 -0.86930 N2
+ 1.0 ARG-N:1HH2 0.44940 H
+ 1.0 ARG-N:2HH2 0.44940 H
+ 1.0 ARG-N:C 0.72140 C
+ 1.0 ARG-N:O -0.60130 O
+ 1.0 HIS-N:N 0.25600 N3
+ 1.0 HIS-N:1H 0.17040 H
+ 1.0 HIS-N:2H 0.17040 H
+ 1.0 HIS-N:3H 0.17040 H
+ 1.0 HIS-N:CA 0.05810 CT
+ 1.0 HIS-N:HA 0.10470 HP
+ 1.0 HIS-N:CB 0.04840 CT
+ 1.0 HIS-N:1HB 0.05310 HC
+ 1.0 HIS-N:2HB 0.05310 HC
+ 1.0 HIS-N:CG -0.02360 CC
+ 1.0 HIS-N:ND1 -0.15100 NA
+ 1.0 HIS-N:HD1 0.38210 H
+ 1.0 HIS-N:CE1 -0.00110 CR
+ 1.0 HIS-N:HE1 0.26450 H5
+ 1.0 HIS-N:NE2 -0.17390 NA
+ 1.0 HIS-N:CD2 -0.14330 CW
+ 1.0 HIS-N:HD2 0.24950 H4
+ 1.0 HIS-N:C 0.72140 C
+ 1.0 HIS-N:O -0.60130 O
+ 1.0 HIS-N:N 0.25600 N3
+ 1.0 HIS-N:1H 0.17040 H
+ 1.0 HIS-N:2H 0.17040 H
+ 1.0 HIS-N:3H 0.17040 H
+ 1.0 HIS-N:CA 0.05810 CT
+ 1.0 HIS-N:HA 0.10470 HP
+ 1.0 HIS-N:CB 0.04840 CT
+ 1.0 HIS-N:1HB 0.05310 HC
+ 1.0 HIS-N:2HB 0.05310 HC
+ 1.0 HIS-N:CG -0.02360 CC
+ 1.0 HIS-N:ND1 -0.15100 NA
+ 1.0 HIS-N:CE1 -0.00110 CR
+ 1.0 HIS-N:HE1 0.26450 H5
+ 1.0 HIS-N:NE2 -0.17390 NA
+ 1.0 HIS-N:HE2 0.39210 H
+ 1.0 HIS-N:CD2 -0.14330 CW
+ 1.0 HIS-N:HD2 0.24950 H4
+ 1.0 HIS-N:C 0.72140 C
+ 1.0 HIS-N:O -0.60130 O
+ 1.0 HIS-N:N 0.25600 N3
+ 1.0 HIS-N:1H 0.17040 H
+ 1.0 HIS-N:2H 0.17040 H
+ 1.0 HIS-N:3H 0.17040 H
+ 1.0 HIS-N:CA 0.05810 CT
+ 1.0 HIS-N:HA 0.10470 HP
+ 1.0 HIS-N:CB 0.04840 CT
+ 1.0 HIS-N:1HB 0.05310 HC
+ 1.0 HIS-N:2HB 0.05310 HC
+ 1.0 HIS-N:CG -0.02360 CC
+ 1.0 HIS-N:ND1 -0.15100 NA
+ 1.0 HIS-N:HD1 0.38210 H
+ 1.0 HIS-N:CE1 -0.00110 CR
+ 1.0 HIS-N:HE1 0.26450 H5
+ 1.0 HIS-N:NE2 -0.17390 NA
+ 1.0 HIS-N:HE2 0.39210 H
+ 1.0 HIS-N:CD2 -0.14330 CW
+ 1.0 HIS-N:HD2 0.24950 H4
+ 1.0 HIS-N:C 0.72140 C
+ 1.0 HIS-N:O -0.60130 O
+ 1.0 TRP-N:N 0.19130 N3
+ 1.0 TRP-N:1H 0.18880 H
+ 1.0 TRP-N:2H 0.18880 H
+ 1.0 TRP-N:3H 0.18880 H
+ 1.0 TRP-N:CA 0.04210 CT
+ 1.0 TRP-N:HA 0.11620 HP
+ 1.0 TRP-N:CB 0.05430 CT
+ 1.0 TRP-N:1HB 0.02220 HC
+ 1.0 TRP-N:2HB 0.02220 HC
+ 1.0 TRP-N:CG -0.16540 C*
+ 1.0 TRP-N:CD1 -0.17880 CW
+ 1.0 TRP-N:HD1 0.21950 H4
+ 1.0 TRP-N:NE1 -0.34440 NA
+ 1.0 TRP-N:HE1 0.34120 H
+ 1.0 TRP-N:CE2 0.15750 CN
+ 1.0 TRP-N:CZ2 -0.27100 CA
+ 1.0 TRP-N:HZ2 0.15890 HA
+ 1.0 TRP-N:CH2 -0.10800 CA
+ 1.0 TRP-N:HH2 0.14110 HA
+ 1.0 TRP-N:CZ3 -0.20340 CA
+ 1.0 TRP-N:HZ3 0.14580 HA
+ 1.0 TRP-N:CE3 -0.22650 CA
+ 1.0 TRP-N:HE3 0.16460 HA
+ 1.0 TRP-N:CD2 0.11320 CB
+ 1.0 TRP-N:C 0.61230 C
+ 1.0 TRP-N:O -0.57130 O
+ 1.0 PHE-N:N 0.17370 N3
+ 1.0 PHE-N:1H 0.19210 H
+ 1.0 PHE-N:2H 0.19210 H
+ 1.0 PHE-N:3H 0.19210 H
+ 1.0 PHE-N:CA 0.07330 CT
+ 1.0 PHE-N:HA 0.10410 HP
+ 1.0 PHE-N:CB 0.03300 CT
+ 1.0 PHE-N:1HB 0.01040 HC
+ 1.0 PHE-N:2HB 0.01040 HC
+ 1.0 PHE-N:CG 0.00310 CA
+ 1.0 PHE-N:CD1 -0.13920 CA
+ 1.0 PHE-N:HD1 0.13740 HA
+ 1.0 PHE-N:CE1 -0.16020 CA
+ 1.0 PHE-N:HE1 0.14330 HA
+ 1.0 PHE-N:CZ -0.12080 CA
+ 1.0 PHE-N:HZ 0.13290 HA
+ 1.0 PHE-N:CE2 -0.16030 CA
+ 1.0 PHE-N:HE2 0.14330 HA
+ 1.0 PHE-N:CD2 -0.13910 CA
+ 1.0 PHE-N:HD2 0.13740 HA
+ 1.0 PHE-N:C 0.61230 C
+ 1.0 PHE-N:O -0.57130 O
+ 1.0 TYR-N:N 0.19400 N3
+ 1.0 TYR-N:1H 0.18730 H
+ 1.0 TYR-N:2H 0.18730 H
+ 1.0 TYR-N:3H 0.18730 H
+ 1.0 TYR-N:CA 0.05700 CT
+ 1.0 TYR-N:HA 0.09830 HP
+ 1.0 TYR-N:CB 0.06590 CT
+ 1.0 TYR-N:1HB 0.01020 HC
+ 1.0 TYR-N:2HB 0.01020 HC
+ 1.0 TYR-N:CG -0.02050 CA
+ 1.0 TYR-N:CD1 -0.20020 CA
+ 1.0 TYR-N:HD1 0.17200 HA
+ 1.0 TYR-N:CE1 -0.22390 CA
+ 1.0 TYR-N:HE1 0.16500 HA
+ 1.0 TYR-N:CZ 0.31390 C
+ 1.0 TYR-N:OH -0.55780 OH
+ 1.0 TYR-N:HH 0.40010 HO
+ 1.0 TYR-N:CE2 -0.22390 CA
+ 1.0 TYR-N:HE2 0.16500 HA
+ 1.0 TYR-N:CD2 -0.20020 CA
+ 1.0 TYR-N:HD2 0.17200 HA
+ 1.0 TYR-N:C 0.61230 C
+ 1.0 TYR-N:O -0.57130 O
+ 1.0 GLU-N:N 0.00170 N3
+ 1.0 GLU-N:1H 0.23910 H
+ 1.0 GLU-N:2H 0.23910 H
+ 1.0 GLU-N:3H 0.23910 H
+ 1.0 GLU-N:CA 0.05880 CT
+ 1.0 GLU-N:HA 0.12020 HP
+ 1.0 GLU-N:CB 0.09090 CT
+ 1.0 GLU-N:1HB -0.02320 HC
+ 1.0 GLU-N:2HB -0.02320 HC
+ 1.0 GLU-N:CG -0.02360 CT
+ 1.0 GLU-N:1HG -0.03150 HC
+ 1.0 GLU-N:2HG -0.03150 HC
+ 1.0 GLU-N:CD 0.80870 C
+ 1.0 GLU-N:OE1 -0.81890 O2
+ 1.0 GLU-N:OE2 -0.81890 O2
+ 1.0 GLU-N:C 0.56210 C
+ 1.0 GLU-N:O -0.58890 O
+ 1.0 ASP-N:N 0.07820 N3
+ 1.0 ASP-N:1H 0.22000 H
+ 1.0 ASP-N:2H 0.22000 H
+ 1.0 ASP-N:3H 0.22000 H
+ 1.0 ASP-N:CA 0.02920 CT
+ 1.0 ASP-N:HA 0.11410 HP
+ 1.0 ASP-N:CB -0.02350 CT
+ 1.0 ASP-N:1HB -0.01690 HC
+ 1.0 ASP-N:2HB -0.01690 HC
+ 1.0 ASP-N:CG 0.81940 C
+ 1.0 ASP-N:OD1 -0.80840 O2
+ 1.0 ASP-N:OD2 -0.80840 O2
+ 1.0 ASP-N:C 0.56210 C
+ 1.0 ASP-N:O -0.58890 O
+ 1.0 LYS-N:N 0.09660 N3
+ 1.0 LYS-N:1H 0.21650 H
+ 1.0 LYS-N:2H 0.21650 H
+ 1.0 LYS-N:3H 0.21650 H
+ 1.0 LYS-N:CA -0.00150 CT
+ 1.0 LYS-N:HA 0.11800 HP
+ 1.0 LYS-N:CB 0.02120 CT
+ 1.0 LYS-N:1HB 0.02830 HC
+ 1.0 LYS-N:2HB 0.02830 HC
+ 1.0 LYS-N:CG -0.00480 CT
+ 1.0 LYS-N:1HG 0.01210 HC
+ 1.0 LYS-N:2HG 0.01210 HC
+ 1.0 LYS-N:CD -0.06080 CT
+ 1.0 LYS-N:1HD 0.06330 HC
+ 1.0 LYS-N:2HD 0.06330 HC
+ 1.0 LYS-N:CE -0.01810 CT
+ 1.0 LYS-N:1HE 0.11710 HP
+ 1.0 LYS-N:2HE 0.11710 HP
+ 1.0 LYS-N:NZ -0.37640 N3
+ 1.0 LYS-N:1HZ 0.33820 H
+ 1.0 LYS-N:2HZ 0.33820 H
+ 1.0 LYS-N:3HZ 0.33820 H
+ 1.0 LYS-N:C 0.72140 C
+ 1.0 LYS-N:O -0.60130 O
+ 1.0 PRO-N:N -0.20200 N3
+ 1.0 PRO-N:1H 0.31200 H
+ 1.0 PRO-N:2H 0.31200 H
+ 1.0 PRO-N:3H 0.31200 H
+ 1.0 PRO-N:CD -0.01200 CT
+ 1.0 PRO-N:1HD 0.10000 HP
+ 1.0 PRO-N:2HD 0.10000 HP
+ 1.0 PRO-N:CG -0.12100 CT
+ 1.0 PRO-N:1HG 0.10000 HC
+ 1.0 PRO-N:2HG 0.10000 HC
+ 1.0 PRO-N:CB -0.11500 CT
+ 1.0 PRO-N:1HB 0.10000 HC
+ 1.0 PRO-N:2HB 0.10000 HC
+ 1.0 PRO-N:CA 0.10000 CT
+ 1.0 PRO-N:HA 0.10000 HP
+ 1.0 PRO-N:C 0.52600 C
+ 1.0 PRO-N:O -0.50000 O
+ 1.0 CYS-N:N 0.13250 N3
+ 1.0 CYS-N:1H 0.20230 H
+ 1.0 CYS-N:2H 0.20230 H
+ 1.0 CYS-N:3H 0.20230 H
+ 1.0 CYS-N:CA 0.09270 CT
+ 1.0 CYS-N:HA 0.14110 HP
+ 1.0 CYS-N:CB -0.11950 CT
+ 1.0 CYS-N:1HB 0.11880 H1
+ 1.0 CYS-N:2HB 0.11880 H1
+ 1.0 CYS-N:SG -0.32980 SH
+ 1.0 CYS-N:HSG 0.19750 HS
+ 1.0 CYS-N:C 0.61230 C
+ 1.0 CYS-N:O -0.57130 O
+ 1.0 CYS-NS:N 0.20690 N3
+ 1.0 CYS-NS:1H 0.18150 H
+ 1.0 CYS-NS:2H 0.18150 H
+ 1.0 CYS-NS:3H 0.18150 H
+ 1.0 CYS-NS:CA 0.10550 CT
+ 1.0 CYS-NS:HA 0.09220 HP
+ 1.0 CYS-NS:CB -0.02770 CT
+ 1.0 CYS-NS:1HB 0.06800 H1
+ 1.0 CYS-NS:2HB 0.06800 H1
+ 1.0 CYS-NS:SG -0.09840 S
+ 1.0 CYS-NS:C 0.61230 C
+ 1.0 CYS-NS:O -0.57130 O
+ 1.0 MET-N:N 0.15920 N3
+ 1.0 MET-N:1H 0.19840 H
+ 1.0 MET-N:2H 0.19840 H
+ 1.0 MET-N:3H 0.19840 H
+ 1.0 MET-N:CA 0.02210 CT
+ 1.0 MET-N:HA 0.11160 HP
+ 1.0 MET-N:CB 0.08650 CT
+ 1.0 MET-N:1HB 0.01250 HC
+ 1.0 MET-N:2HB 0.01250 HC
+ 1.0 MET-N:CG 0.03340 CT
+ 1.0 MET-N:1HG 0.02920 H1
+ 1.0 MET-N:2HG 0.02920 H1
+ 1.0 MET-N:SD -0.27740 S
+ 1.0 MET-N:CE -0.03410 CT
+ 1.0 MET-N:1HE 0.05970 H1
+ 1.0 MET-N:2HE 0.05970 H1
+ 1.0 MET-N:3HE 0.05970 H1
+ 1.0 MET-N:C 0.61230 C
+ 1.0 MET-N:O -0.57130 O
+ 1.0 ALA-C:N -0.38210 N
+ 1.0 ALA-C:H 0.26810 H
+ 1.0 ALA-C:CA -0.17470 CT
+ 1.0 ALA-C:HA 0.10670 H1
+ 1.0 ALA-C:CB -0.20930 CT
+ 1.0 ALA-C:1HB 0.07640 HC
+ 1.0 ALA-C:2HB 0.07640 HC
+ 1.0 ALA-C:3HB 0.07640 HC
+ 1.0 ALA-C:C 0.77310 C
+ 1.0 ALA-C:O -0.80550 O2
+ 1.0 ALA-C:OXT -0.80550 O2
+ 1.0 GLY-C:N -0.38210 N
+ 1.0 GLY-C:H 0.26810 H
+ 1.0 GLY-C:CA -0.24930 CT
+ 1.0 GLY-C:1HA 0.10560 H1
+ 1.0 GLY-C:2HA 0.10560 H1
+ 1.0 GLY-C:C 0.72310 C
+ 1.0 GLY-C:O -0.78550 O2
+ 1.0 GLY-C:OXT -0.78550 O2
+ 1.0 SER-C:N -0.38210 N
+ 1.0 SER-C:H 0.26810 H
+ 1.0 SER-C:CA -0.27220 CT
+ 1.0 SER-C:HA 0.13040 H1
+ 1.0 SER-C:CB 0.11230 CT
+ 1.0 SER-C:1HB 0.08130 H1
+ 1.0 SER-C:2HB 0.08130 H1
+ 1.0 SER-C:OG -0.65140 OH
+ 1.0 SER-C:HG 0.44740 HO
+ 1.0 SER-C:C 0.81130 C
+ 1.0 SER-C:O -0.81320 O2
+ 1.0 SER-C:OXT -0.81320 O2
+ 1.0 THR-C:N -0.38210 N
+ 1.0 THR-C:H 0.26810 H
+ 1.0 THR-C:CA -0.24200 CT
+ 1.0 THR-C:HA 0.12070 H1
+ 1.0 THR-C:CB 0.30250 CT
+ 1.0 THR-C:HB 0.00780 H1
+ 1.0 THR-C:CG2 -0.18530 CT
+ 1.0 THR-C:1HG2 0.05860 HC
+ 1.0 THR-C:2HG2 0.05860 HC
+ 1.0 THR-C:3HG2 0.05860 HC
+ 1.0 THR-C:OG1 -0.64960 OH
+ 1.0 THR-C:HG1 0.41190 HO
+ 1.0 THR-C:C 0.78100 C
+ 1.0 THR-C:O -0.80440 O2
+ 1.0 THR-C:OXT -0.80440 O2
+ 1.0 LEU-C:N -0.38210 N
+ 1.0 LEU-C:H 0.26810 H
+ 1.0 LEU-C:CA -0.28470 CT
+ 1.0 LEU-C:HA 0.13460 H1
+ 1.0 LEU-C:CB -0.24690 CT
+ 1.0 LEU-C:1HB 0.09740 HC
+ 1.0 LEU-C:2HB 0.09740 HC
+ 1.0 LEU-C:CG 0.37060 CT
+ 1.0 LEU-C:HG -0.03740 HC
+ 1.0 LEU-C:CD1 -0.41630 CT
+ 1.0 LEU-C:1HD1 0.10380 HC
+ 1.0 LEU-C:2HD1 0.10380 HC
+ 1.0 LEU-C:3HD1 0.10380 HC
+ 1.0 LEU-C:CD2 -0.41630 CT
+ 1.0 LEU-C:1HD2 0.10380 HC
+ 1.0 LEU-C:2HD2 0.10380 HC
+ 1.0 LEU-C:3HD2 0.10380 HC
+ 1.0 LEU-C:C 0.83260 C
+ 1.0 LEU-C:O -0.81990 O2
+ 1.0 LEU-C:OXT -0.81990 O2
+ 1.0 ILE-C:N -0.38210 N
+ 1.0 ILE-C:H 0.26810 H
+ 1.0 ILE-C:CA -0.31000 CT
+ 1.0 ILE-C:HA 0.13750 H1
+ 1.0 ILE-C:CB 0.03630 CT
+ 1.0 ILE-C:HB 0.07660 HC
+ 1.0 ILE-C:CG2 -0.34980 CT
+ 1.0 ILE-C:1HG2 0.10210 HC
+ 1.0 ILE-C:2HG2 0.10210 HC
+ 1.0 ILE-C:3HG2 0.10210 HC
+ 1.0 ILE-C:CG1 -0.03230 CT
+ 1.0 ILE-C:1HG1 0.03210 HC
+ 1.0 ILE-C:2HG1 0.03210 HC
+ 1.0 ILE-C:CD1 -0.06990 CT
+ 1.0 ILE-C:1HD1 0.01960 HC
+ 1.0 ILE-C:2HD1 0.01960 HC
+ 1.0 ILE-C:3HD1 0.01960 HC
+ 1.0 ILE-C:C 0.83430 C
+ 1.0 ILE-C:O -0.81900 O2
+ 1.0 ILE-C:OXT -0.81900 O2
+ 1.0 NME-C:N -0.41570 N
+ 1.0 NME-C:H 0.27190 H
+ 1.0 NME-C:CH3 -0.14900 CT
+ 1.0 NME-C:1HH3 0.09760 H1
+ 1.0 NME-C:2HH3 0.09760 H1
+ 1.0 NME-C:3HH3 0.09760 H1
+ 1.0 VAL-C:N -0.38210 N
+ 1.0 VAL-C:H 0.26810 H
+ 1.0 VAL-C:CA -0.34380 CT
+ 1.0 VAL-C:HA 0.14380 H1
+ 1.0 VAL-C:CB 0.19400 CT
+ 1.0 VAL-C:HB 0.03080 HC
+ 1.0 VAL-C:CG1 -0.30640 CT
+ 1.0 VAL-C:1HG1 0.08360 HC
+ 1.0 VAL-C:2HG1 0.08360 HC
+ 1.0 VAL-C:3HG1 0.08360 HC
+ 1.0 VAL-C:CG2 -0.30640 CT
+ 1.0 VAL-C:1HG2 0.08360 HC
+ 1.0 VAL-C:2HG2 0.08360 HC
+ 1.0 VAL-C:3HG2 0.08360 HC
+ 1.0 VAL-C:C 0.83500 C
+ 1.0 VAL-C:O -0.81730 O2
+ 1.0 VAL-C:OXT -0.81730 O2
+ 1.0 ASN-C:N -0.38210 N
+ 1.0 ASN-C:H 0.26810 H
+ 1.0 ASN-C:CA -0.20800 CT
+ 1.0 ASN-C:HA 0.13580 H1
+ 1.0 ASN-C:CB -0.22990 CT
+ 1.0 ASN-C:1HB 0.10230 HC
+ 1.0 ASN-C:2HB 0.10230 HC
+ 1.0 ASN-C:CG 0.71530 C
+ 1.0 ASN-C:OD1 -0.60100 O
+ 1.0 ASN-C:ND2 -0.90840 N
+ 1.0 ASN-C:1HD2 0.41500 H
+ 1.0 ASN-C:2HD2 0.41500 H
+ 1.0 ASN-C:C 0.80500 C
+ 1.0 ASN-C:O -0.81470 O2
+ 1.0 ASN-C:OXT -0.81470 O2
+ 1.0 GLN-C:N -0.38210 N
+ 1.0 GLN-C:H 0.26810 H
+ 1.0 GLN-C:CA -0.22480 CT
+ 1.0 GLN-C:HA 0.12320 H1
+ 1.0 GLN-C:CB -0.06640 CT
+ 1.0 GLN-C:1HB 0.04520 HC
+ 1.0 GLN-C:2HB 0.04520 HC
+ 1.0 GLN-C:CG -0.02100 CT
+ 1.0 GLN-C:1HG 0.02030 HC
+ 1.0 GLN-C:2HG 0.02030 HC
+ 1.0 GLN-C:CD 0.70930 C
+ 1.0 GLN-C:OE1 -0.60980 O
+ 1.0 GLN-C:NE2 -0.95740 N
+ 1.0 GLN-C:1HE2 0.43040 H
+ 1.0 GLN-C:2HE2 0.43040 H
+ 1.0 GLN-C:C 0.77750 C
+ 1.0 GLN-C:O -0.80420 O2
+ 1.0 GLN-C:OXT -0.80420 O2
+ 1.0 ARG-C:N -0.34810 N
+ 1.0 ARG-C:H 0.27640 H
+ 1.0 ARG-C:CA -0.30680 CT
+ 1.0 ARG-C:HA 0.14470 H1
+ 1.0 ARG-C:CB -0.03740 CT
+ 1.0 ARG-C:1HB 0.03710 HC
+ 1.0 ARG-C:2HB 0.03710 HC
+ 1.0 ARG-C:CG 0.07440 CT
+ 1.0 ARG-C:1HG 0.01850 HC
+ 1.0 ARG-C:2HG 0.01850 HC
+ 1.0 ARG-C:CD 0.11140 CT
+ 1.0 ARG-C:1HD 0.04680 H1
+ 1.0 ARG-C:2HD 0.04680 H1
+ 1.0 ARG-C:NE -0.55640 N2
+ 1.0 ARG-C:HE 0.34790 H
+ 1.0 ARG-C:CZ 0.83680 CA
+ 1.0 ARG-C:NH1 -0.87370 N2
+ 1.0 ARG-C:1HH1 0.44930 H
+ 1.0 ARG-C:2HH1 0.44930 H
+ 1.0 ARG-C:NH2 -0.87370 N2
+ 1.0 ARG-C:1HH2 0.44930 H
+ 1.0 ARG-C:2HH2 0.44930 H
+ 1.0 ARG-C:C 0.85570 C
+ 1.0 ARG-C:O -0.82660 O2
+ 1.0 ARG-C:OXT -0.82660 O2
+ 1.0 HIS-C:N -0.34810 N
+ 1.0 HIS-C:H 0.27640 H
+ 1.0 HIS-C:CA -0.14450 CT
+ 1.0 HIS-C:HA 0.11150 H1
+ 1.0 HIS-C:CB -0.08000 CT
+ 1.0 HIS-C:1HB 0.08680 HC
+ 1.0 HIS-C:2HB 0.08680 HC
+ 1.0 HIS-C:CG 0.02980 CC
+ 1.0 HIS-C:ND1 -0.15010 NA
+ 1.0 HIS-C:HD1 0.38830 H
+ 1.0 HIS-C:CE1 -0.02510 CR
+ 1.0 HIS-C:HE1 0.26940 H5
+ 1.0 HIS-C:NE2 -0.16830 NA
+ 1.0 HIS-C:CD2 -0.12560 CW
+ 1.0 HIS-C:HD2 0.23360 H4
+ 1.0 HIS-C:C 0.80320 C
+ 1.0 HIS-C:O -0.81770 O2
+ 1.0 HIS-C:OXT -0.81770 O2
+ 1.0 HIS-C:N -0.34810 N
+ 1.0 HIS-C:H 0.27640 H
+ 1.0 HIS-C:CA -0.14450 CT
+ 1.0 HIS-C:HA 0.11150 H1
+ 1.0 HIS-C:CB -0.08000 CT
+ 1.0 HIS-C:1HB 0.08680 HC
+ 1.0 HIS-C:2HB 0.08680 HC
+ 1.0 HIS-C:CG 0.02980 CC
+ 1.0 HIS-C:ND1 -0.15010 NA
+ 1.0 HIS-C:CE1 -0.02510 CR
+ 1.0 HIS-C:HE1 0.26940 H5
+ 1.0 HIS-C:NE2 -0.16830 NA
+ 1.0 HIS-C:HE2 0.39130 H
+ 1.0 HIS-C:CD2 -0.12560 CW
+ 1.0 HIS-C:HD2 0.23360 H4
+ 1.0 HIS-C:C 0.80320 C
+ 1.0 HIS-C:O -0.81770 O2
+ 1.0 HIS-C:OXT -0.81770 O2
+ 1.0 HIS-C:N -0.34810 N
+ 1.0 HIS-C:H 0.27640 H
+ 1.0 HIS-C:CA -0.14450 CT
+ 1.0 HIS-C:HA 0.11150 H1
+ 1.0 HIS-C:CB -0.08000 CT
+ 1.0 HIS-C:1HB 0.08680 HC
+ 1.0 HIS-C:2HB 0.08680 HC
+ 1.0 HIS-C:CG 0.02980 CC
+ 1.0 HIS-C:ND1 -0.15010 NA
+ 1.0 HIS-C:HD1 0.38830 H
+ 1.0 HIS-C:CE1 -0.02510 CR
+ 1.0 HIS-C:HE1 0.26940 H5
+ 1.0 HIS-C:NE2 -0.16830 NA
+ 1.0 HIS-C:HE2 0.39130 H
+ 1.0 HIS-C:CD2 -0.12560 CW
+ 1.0 HIS-C:HD2 0.23360 H4
+ 1.0 HIS-C:C 0.80320 C
+ 1.0 HIS-C:O -0.81770 O2
+ 1.0 HIS-C:OXT -0.81770 O2
+ 1.0 TRP-C:N -0.38210 N
+ 1.0 TRP-C:H 0.26810 H
+ 1.0 TRP-C:CA -0.20840 CT
+ 1.0 TRP-C:HA 0.12720 H1
+ 1.0 TRP-C:CB -0.07420 CT
+ 1.0 TRP-C:1HB 0.04970 HC
+ 1.0 TRP-C:2HB 0.04970 HC
+ 1.0 TRP-C:CG -0.07960 C*
+ 1.0 TRP-C:CD1 -0.18080 CW
+ 1.0 TRP-C:HD1 0.20430 H4
+ 1.0 TRP-C:NE1 -0.33160 NA
+ 1.0 TRP-C:HE1 0.34130 H
+ 1.0 TRP-C:CE2 0.12220 CN
+ 1.0 TRP-C:CZ2 -0.25940 CA
+ 1.0 TRP-C:HZ2 0.15670 HA
+ 1.0 TRP-C:CH2 -0.10200 CA
+ 1.0 TRP-C:HH2 0.14010 HA
+ 1.0 TRP-C:CZ3 -0.22870 CA
+ 1.0 TRP-C:HZ3 0.15070 HA
+ 1.0 TRP-C:CE3 -0.18370 CA
+ 1.0 TRP-C:HE3 0.14910 HA
+ 1.0 TRP-C:CD2 0.10780 CB
+ 1.0 TRP-C:C 0.76580 C
+ 1.0 TRP-C:O -0.80110 O2
+ 1.0 TRP-C:OXT -0.80110 O2
+ 1.0 PHE-C:N -0.38210 N
+ 1.0 PHE-C:H 0.26810 H
+ 1.0 PHE-C:CA -0.18250 CT
+ 1.0 PHE-C:HA 0.10980 H1
+ 1.0 PHE-C:CB -0.09590 CT
+ 1.0 PHE-C:1HB 0.04430 HC
+ 1.0 PHE-C:2HB 0.04430 HC
+ 1.0 PHE-C:CG 0.05520 CA
+ 1.0 PHE-C:CD1 -0.13000 CA
+ 1.0 PHE-C:HD1 0.14080 HA
+ 1.0 PHE-C:CE1 -0.18470 CA
+ 1.0 PHE-C:HE1 0.14610 HA
+ 1.0 PHE-C:CZ -0.09440 CA
+ 1.0 PHE-C:HZ 0.12800 HA
+ 1.0 PHE-C:CE2 -0.18470 CA
+ 1.0 PHE-C:HE2 0.14610 HA
+ 1.0 PHE-C:CD2 -0.13000 CA
+ 1.0 PHE-C:HD2 0.14080 HA
+ 1.0 PHE-C:C 0.76600 C
+ 1.0 PHE-C:O -0.80260 O2
+ 1.0 PHE-C:OXT -0.80260 O2
+ 1.0 TYR-C:N -0.38210 N
+ 1.0 TYR-C:H 0.26810 H
+ 1.0 TYR-C:CA -0.20150 CT
+ 1.0 TYR-C:HA 0.10920 H1
+ 1.0 TYR-C:CB -0.07520 CT
+ 1.0 TYR-C:1HB 0.04900 HC
+ 1.0 TYR-C:2HB 0.04900 HC
+ 1.0 TYR-C:CG 0.02430 CA
+ 1.0 TYR-C:CD1 -0.19220 CA
+ 1.0 TYR-C:HD1 0.17800 HA
+ 1.0 TYR-C:CE1 -0.24580 CA
+ 1.0 TYR-C:HE1 0.16730 HA
+ 1.0 TYR-C:CZ 0.33950 C
+ 1.0 TYR-C:OH -0.56430 OH
+ 1.0 TYR-C:HH 0.40170 HO
+ 1.0 TYR-C:CE2 -0.24580 CA
+ 1.0 TYR-C:HE2 0.16730 HA
+ 1.0 TYR-C:CD2 -0.19220 CA
+ 1.0 TYR-C:HD2 0.17800 HA
+ 1.0 TYR-C:C 0.78170 C
+ 1.0 TYR-C:O -0.80700 O2
+ 1.0 TYR-C:OXT -0.80700 O2
+ 1.0 GLU-C:N -0.51920 N
+ 1.0 GLU-C:H 0.30550 H
+ 1.0 GLU-C:CA -0.20590 CT
+ 1.0 GLU-C:HA 0.13990 H1
+ 1.0 GLU-C:CB 0.00710 CT
+ 1.0 GLU-C:1HB -0.00780 HC
+ 1.0 GLU-C:2HB -0.00780 HC
+ 1.0 GLU-C:CG 0.06750 CT
+ 1.0 GLU-C:1HG -0.05480 HC
+ 1.0 GLU-C:2HG -0.05480 HC
+ 1.0 GLU-C:CD 0.81830 C
+ 1.0 GLU-C:OE1 -0.82200 O2
+ 1.0 GLU-C:OE2 -0.82200 O2
+ 1.0 GLU-C:C 0.74200 C
+ 1.0 GLU-C:O -0.79300 O2
+ 1.0 GLU-C:OXT -0.79300 O2
+ 1.0 ASP-C:N -0.51920 N
+ 1.0 ASP-C:H 0.30550 H
+ 1.0 ASP-C:CA -0.18170 CT
+ 1.0 ASP-C:HA 0.10460 H1
+ 1.0 ASP-C:CB -0.06770 CT
+ 1.0 ASP-C:1HB -0.02120 HC
+ 1.0 ASP-C:2HB -0.02120 HC
+ 1.0 ASP-C:CG 0.88510 C
+ 1.0 ASP-C:OD1 -0.81620 O2
+ 1.0 ASP-C:OD2 -0.81620 O2
+ 1.0 ASP-C:C 0.72560 C
+ 1.0 ASP-C:O -0.78870 O2
+ 1.0 ASP-C:OXT -0.78870 O2
+ 1.0 LYS-C:N -0.34810 N
+ 1.0 LYS-C:H 0.27640 H
+ 1.0 LYS-C:CA -0.29030 CT
+ 1.0 LYS-C:HA 0.14380 H1
+ 1.0 LYS-C:CB -0.05380 CT
+ 1.0 LYS-C:1HB 0.04820 HC
+ 1.0 LYS-C:2HB 0.04820 HC
+ 1.0 LYS-C:CG 0.02270 CT
+ 1.0 LYS-C:1HG 0.01340 HC
+ 1.0 LYS-C:2HG 0.01340 HC
+ 1.0 LYS-C:CD -0.03920 CT
+ 1.0 LYS-C:1HD 0.06110 HC
+ 1.0 LYS-C:2HD 0.06110 HC
+ 1.0 LYS-C:CE -0.01760 CT
+ 1.0 LYS-C:1HE 0.11210 HP
+ 1.0 LYS-C:2HE 0.11210 HP
+ 1.0 LYS-C:NZ -0.37410 N3
+ 1.0 LYS-C:1HZ 0.33740 H
+ 1.0 LYS-C:2HZ 0.33740 H
+ 1.0 LYS-C:3HZ 0.33740 H
+ 1.0 LYS-C:C 0.84880 C
+ 1.0 LYS-C:O -0.82520 O2
+ 1.0 LYS-C:OXT -0.82520 O2
+ 1.0 PRO-C:N -0.28020 N
+ 1.0 PRO-C:CD 0.04340 CT
+ 1.0 PRO-C:1HD 0.03310 H1
+ 1.0 PRO-C:2HD 0.03310 H1
+ 1.0 PRO-C:CG 0.04660 CT
+ 1.0 PRO-C:1HG 0.01720 HC
+ 1.0 PRO-C:2HG 0.01720 HC
+ 1.0 PRO-C:CB -0.05430 CT
+ 1.0 PRO-C:1HB 0.03810 HC
+ 1.0 PRO-C:2HB 0.03810 HC
+ 1.0 PRO-C:CA -0.13360 CT
+ 1.0 PRO-C:HA 0.07760 H1
+ 1.0 PRO-C:C 0.66310 C
+ 1.0 PRO-C:O -0.76970 O2
+ 1.0 PRO-C:OXT -0.76970 O2
+ 1.0 CYS-C:N -0.38210 N
+ 1.0 CYS-C:H 0.26810 H
+ 1.0 CYS-C:CA -0.16350 CT
+ 1.0 CYS-C:HA 0.13960 H1
+ 1.0 CYS-C:CB -0.19960 CT
+ 1.0 CYS-C:1HB 0.14370 H1
+ 1.0 CYS-C:2HB 0.14370 H1
+ 1.0 CYS-C:SG -0.31020 SH
+ 1.0 CYS-C:HSG 0.20680 HS
+ 1.0 CYS-C:C 0.74970 C
+ 1.0 CYS-C:O -0.79810 O2
+ 1.0 CYS-C:OXT -0.79810 O2
+ 1.0 CYS-CS:N -0.38210 N
+ 1.0 CYS-CS:H 0.26810 H
+ 1.0 CYS-CS:CA -0.13180 CT
+ 1.0 CYS-CS:HA 0.09380 H1
+ 1.0 CYS-CS:CB -0.19430 CT
+ 1.0 CYS-CS:1HB 0.12280 H1
+ 1.0 CYS-CS:2HB 0.12280 H1
+ 1.0 CYS-CS:SG -0.05290 S
+ 1.0 CYS-CS:C 0.76180 C
+ 1.0 CYS-CS:O -0.80410 O2
+ 1.0 CYS-CS:OXT -0.80410 O2
+ 1.0 MET-C:N -0.38210 N
+ 1.0 MET-C:H 0.26810 H
+ 1.0 MET-C:CA -0.25970 CT
+ 1.0 MET-C:HA 0.12770 H1
+ 1.0 MET-C:CB -0.02360 CT
+ 1.0 MET-C:1HB 0.04800 HC
+ 1.0 MET-C:2HB 0.04800 HC
+ 1.0 MET-C:CG 0.04920 CT
+ 1.0 MET-C:1HG 0.03170 H1
+ 1.0 MET-C:2HG 0.03170 H1
+ 1.0 MET-C:SD -0.26920 S
+ 1.0 MET-C:CE -0.03760 CT
+ 1.0 MET-C:1HE 0.06250 H1
+ 1.0 MET-C:2HE 0.06250 H1
+ 1.0 MET-C:3HE 0.06250 H1
+ 1.0 MET-C:C 0.80130 C
+ 1.0 MET-C:O -0.81050 O2
+ 1.0 MET-C:OXT -0.81050 O2
+ 1.0 CA:CA 2.00000 C0
+ 1.0 MG:MG 2.00000 MG
+ 1.0 CH4-M:C 0.00000 CT
+ 1.0 CH4-M:1H 0.00000 H1
+ 1.0 CH4-M:2H 0.00000 H1
+ 1.0 CH4-M:3H 0.00000 H1
+ 1.0 CH4-M:4H 0.00000 H1
+ 1.0 PCA:N -0.720984 N
+ 1.0 PCA:H 0.374677 H
+ 1.0 PCA:CA -0.025874 CT
+ 1.0 PCA:C 0.865161 C
+ 1.0 PCA:O -0.798202 O
+ 1.0 PCA:CB 0.114954 CT
+ 1.0 PCA:CG -0.126748 CT
+ 1.0 PCA:CD 0.770356 C
+ 1.0 PCA:OE -0.682912 O
+ 1.0 PCA:HA 0.039708 H1
+ 1.0 PCA:1HB 0.000266 HC
+ 1.0 PCA:2HB -0.031861 HC
+ 1.0 PCA:1HG 0.034072 HC
+ 1.0 PCA:2HG 0.025655 HC
+ 1.0 PCA:OXT -0.838268 O
+ 1.0 PCA-N:N -0.720984 N
+ 1.0 PCA-N:H 0.374677 H
+ 1.0 PCA-N:CA -0.025874 CT
+ 1.0 PCA-N:C 0.865161 C
+ 1.0 PCA-N:O -0.798202 O
+ 1.0 PCA-N:CB 0.114954 CT
+ 1.0 PCA-N:CG -0.126748 CT
+ 1.0 PCA-N:CD 0.770356 C
+ 1.0 PCA-N:OE -0.682912 O
+ 1.0 PCA-N:HA 0.039708 H1
+ 1.0 PCA-N:1HB 0.000266 HC
+ 1.0 PCA-N:2HB -0.031861 HC
+ 1.0 PCA-N:1HG 0.034072 HC
+ 1.0 PCA-N:2HG 0.025655 HC
+ 1.0 PCA-M:N -0.720984 N
+ 1.0 PCA-M:H 0.374677 H
+ 1.0 PCA-M:CA -0.025874 CT
+ 1.0 PCA-M:C 0.865161 C
+ 1.0 PCA-M:O -0.798202 O
+ 1.0 PCA-M:CB 0.114954 CT
+ 1.0 PCA-M:CG -0.126748 CT
+ 1.0 PCA-M:CD 0.770356 C
+ 1.0 PCA-M:OE -0.682912 O
+ 1.0 PCA-M:HA 0.039708 H1
+ 1.0 PCA-M:1HB 0.000266 HC
+ 1.0 PCA-M:2HB -0.031861 HC
+ 1.0 PCA-M:1HG 0.034072 HC
+ 1.0 PCA-M:2HG 0.025655 HC
+ 1.0 PCA-M:OXT -0.838268 O
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/QSAR/atomic_electron_affinities.data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_electron_affinities.data Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,88 @@
+# atomic electron affinities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998; non-excistant values like unstable ions have 0.0
+0.754593
+0.0
+0.6180
+0.0
+0.277
+1.2629
+0.0
+1.4611103
+3.401190
+0.0
+0.547926
+0.0
+0.441
+1.385
+0.7465
+2.077104
+3.61269
+0.0
+0.50147
+0.02455
+0.188
+0.079
+0.525
+0.666
+0.0
+0.151
+0.662
+1.156
+1.235
+0.0
+0.3
+1.233
+0.81
+2.020670
+3.363590
+0.0
+0.48592
+0.048
+0.307
+0.426
+0.893
+0.748
+0.55
+1.05
+1.137
+0.562
+1.302
+0.0
+0.3
+1.112
+1.046
+1.9708
+3.059038
+0.0
+0.471626
+0.15
+0.5
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.322
+0.815
+0.15
+1.1
+1.5638
+2.128
+2.30863
+0.0
+0.2
+0.364
+0.946
+1.9
+2.8
+0.0
+0.46
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/QSAR/atomic_ionization_potentials.data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_ionization_potentials.data Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,73 @@
+# atomic ionization potentials (neutral atom and +1 ion), CRC Handbook of Chemistry and Physics, 79th edition, 1998
+13.59844 20.02
+24.58741 54.41778
+5.39172 75.64018
+9.3227 18.21116
+8.29803 25.15484
+11.26030 24.38332
+14.53414 29.6013
+13.61806 35.11730
+17.42282 34.97082
+21.5646 40.96328
+5.13908 47.2864
+7.64624 15.03528
+5.98577 18.82856
+8.15169 16.34585
+10.48669 19.7694
+10.36001 23.3379
+12.96764 23.814
+15.75962 27.62967
+4.34066 31.63
+6.11316 11.87172
+6.5615 12.79967
+6.8281 13.5755
+6.7463 14.66
+6.7665 16.4857
+7.43402 15.63999
+7.9024 16.1878
+7.8810 17.083
+7.6398 18.16884
+7.72638 20.29240
+9.3942 17.96440
+5.99930 20.5142
+7.8994 15.93462
+9.7886 18.633
+9.75238 21.19
+11.81381 21.8
+13.99961 24.35985
+4.17713 27.285
+5.6949 11.03013
+6.2171 12.24
+6.63390 13.13
+6.75885 14.32
+7.09243 16.16
+7.28 15.26
+7.36050 16.76
+7.45890 18.08
+8.3369 19.43
+7.5763 21.49
+8.9938 16.90832
+5.78636 18.8698
+7.3439 14.63225
+8.6084 16.53051
+9.0096 18.6
+10.45126 19.1313
+12.1298 21.20979
+3.89390 23.15745
+5.21170 10.00390
+5.770 11.060
+5.5387 10.85
+5.464 10.55
+5.5250 10.73
+5.58 10.9
+5.6436 11.07
+5.6704 11.241
+6.1501 12.09
+5.8638 11.52
+5.9389 11.67
+6.0215 11.80
+6.1077 11.93
+6.18431 12.05
+6.25416 12.1761
+5.4259 13.9
+6.82507 14.9
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/QSAR/atomic_polarizabilities.data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_polarizabilities.data Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,101 @@
+# atomic ground state polarizabilities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998
+0.666793
+0.204956
+24.3
+5.6
+3.03
+1.76
+1.1
+0.802
+0.557
+0.3956
+24.08
+10.6
+6.8
+5.38
+3.63
+2.9
+2.18
+1.6411
+43.4
+22.8
+17.8
+14.6
+12.4
+11.6
+9.4
+8.4
+7.5
+6.8
+6.1
+7.1
+8.12
+6.07
+4.31
+3.77
+3.05
+2.4844
+47.3
+27.6
+22.7
+17.9
+15.7
+12.8
+11.4
+9.6
+8.6
+4.8
+7.2
+7.2
+10.2
+7.7
+6.6
+5.5
+5.35
+4.044
+59.6
+39.7
+31.1
+29.6
+28.2
+31.4
+30.1
+28.8
+27.7
+23.5
+25.5
+24.5
+23.6
+22.7
+21.8
+21.0
+21.9
+16.2
+13.1
+11.1
+9.7
+8.5
+7.6
+6.5
+5.8
+5.7
+7.6
+6.8
+7.4
+6.8
+6.0
+5.3
+48.7
+38.3
+32.1
+32.1
+25.4
+24.9
+24.8
+24.5
+23.3
+23.0
+22.7
+20.5
+19.7
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/QSAR/dragon_descriptors.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/dragon_descriptors.txt Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,1665 @@
+MW molecular weight
+AMW average molecular weight
+Sv sum of atomic van der Waals volumes (scaled on Carbon atom)
+Se sum of atomic Sanderson electronegativities (scaled on Carbon atom)
+Sp sum of atomic polarizabilities (scaled on Carbon atom)
+Ss sum of Kier-Hall electrotopological states
+Mv mean atomic van der Waals volume (scaled on Carbon atom)
+Me mean atomic Sanderson electronegativity (scaled on Carbon atom)
+Mp mean atomic polarizability (scaled on Carbon atom)
+Ms mean electrotopological state
+nAT number of atoms
+nSK number of non-H atoms
+nBT number of bonds
+nBO number of non-H bonds
+nBM number of multiple bonds
+SCBO sum of conventional bond orders (H-depleted)
+ARR aromatic ratio
+nCIC number of rings
+nCIR number of circuits
+RBN number of rotatable bonds
+RBF rotatable bond fraction
+nDB number of double bonds
+nTB number of triple bonds
+nAB number of aromatic bonds
+nH number of Hydrogen atoms
+nC number of Carbon atoms
+nN number of Nitrogen atoms
+nO number of Oxygen atoms
+nP number of Phosphorous atoms
+nS number of Sulfur atoms
+nF number of Fluorine atoms
+nCL number of Chlorine atoms
+nBR number of Bromine atoms
+nI number of Iodine atoms
+nB number of Boron atoms
+nHM number of heavy atoms
+nX number of halogen atoms
+nR03 number of 3-membered rings
+nR04 number of 4-membered rings
+nR05 number of 5-membered rings
+nR06 number of 6-membered rings
+nR07 number of 7-membered rings
+nR08 number of 8-membered rings
+nR09 number of 9-membered rings
+nR10 number of 10-membered rings
+nR11 number of 11-membered rings
+nR12 number of 12-membered rings
+nBnz number of benzene-like rings
+ZM1 first Zagreb index M1
+ZM1V first Zagreb index by valence vertex degrees
+ZM2 second Zagreb index M2
+ZM2V second Zagreb index by valence vertex degrees
+Qindex Quadratic index
+SNar Narumi simple topological index (log)
+HNar Narumi harmonic topological index
+GNar Narumi geometric topological index
+Xt Total structure connectivity index
+Dz Pogliani index
+Ram ramification index
+Pol polarity number
+LPRS log of product of row sums (PRS)
+VDA average vertex distance degree
+MSD mean square distance index (Balaban)
+SMTI Schultz Molecular Topological Index (MTI)
+SMTIV Schultz MTI by valence vertex degrees
+GMTI Gutman Molecular Topological Index
+GMTIV Gutman MTI by valence vertex degrees
+Xu Xu index
+SPI superpendentic index
+W Wiener W index
+WA mean Wiener index
+Har Harary H index
+Har2 square reciprocal distance sum index
+QW quasi-Wiener index (Kirchhoff number)
+TI1 first Mohar index TI1
+TI2 second Mohar index TI2
+STN spanning tree number (log)
+HyDp hyper-distance-path index
+RHyDp reciprocal hyper-distance-path index
+w detour index
+ww hyper-detour index
+Rww reciprocal hyper-detour index
+D/D distance/detour index
+Wap all-path Wiener index
+WhetZ Wiener-type index from Z weighted distance matrix (Barysz matrix)
+Whetm Wiener-type index from mass weighted distance matrix
+Whetv Wiener-type index from van der Waals weighted distance matrix
+Whete Wiener-type index from electronegativity weighted distance matrix
+Whetp Wiener-type index from polarizability weighted distance matrix
+J Balaban distance connectivity index
+JhetZ Balaban-type index from Z weighted distance matrix (Barysz matrix)
+Jhetm Balaban-type index from mass weighted distance matrix
+Jhetv Balaban-type index from van der Waals weighted distance matrix
+Jhete Balaban-type index from electronegativity weighted distance matrix
+Jhetp Balaban-type index from polarizability weighted distance matrix
+MAXDN maximal electrotopological negative variation
+MAXDP maximal electrotopological positive variation
+DELS molecular electrotopological variation
+TIE E-state topological parameter
+S0K Kier symmetry index
+S1K 1-path Kier alpha-modified shape index
+S2K 2-path Kier alpha-modified shape index
+S3K 3-path Kier alpha-modified shape index
+PHI Kier flexibility index
+BLI Kier benzene-likeliness index
+PW2 path/walk 2 - Randic shape index
+PW3 path/walk 3 - Randic shape index
+PW4 path/walk 4 - Randic shape index
+PW5 path/walk 5 - Randic shape index
+PJI2 2D Petitjean shape index
+CSI eccentric connectivity index
+ECC eccentricity
+AECC average eccentricity
+DECC eccentric
+MDDD mean distance degree deviation
+UNIP unipolarity
+CENT centralization
+VAR variation
+BAC Balaban centric index
+Lop Lopping centric index
+ICR radial centric information index
+D/Dr03 distance/detour ring index of order 3
+D/Dr04 distance/detour ring index of order 4
+D/Dr05 distance/detour ring index of order 5
+D/Dr06 distance/detour ring index of order 6
+D/Dr07 distance/detour ring index of order 7
+D/Dr08 distance/detour ring index of order 8
+D/Dr09 distance/detour ring index of order 9
+D/Dr10 distance/detour ring index of order 10
+D/Dr11 distance/detour ring index of order 11
+D/Dr12 distance/detour ring index of order 12
+T(N..N) sum of topological distances between N..N
+T(N..O) sum of topological distances between N..O
+T(N..S) sum of topological distances between N..S
+T(N..P) sum of topological distances between N..P
+T(N..F) sum of topological distances between N..F
+T(N..Cl) sum of topological distances between N..Cl
+T(N..Br) sum of topological distances between N..Br
+T(N..I) sum of topological distances between N..I
+T(O..O) sum of topological distances between O..O
+T(O..S) sum of topological distances between O..S
+T(O..P) sum of topological distances between O..P
+T(O..F) sum of topological distances between O..F
+T(O..Cl) sum of topological distances between O..Cl
+T(O..Br) sum of topological distances between O..Br
+T(O..I) sum of topological distances between O..I
+T(S..S) sum of topological distances between S..S
+T(S..P) sum of topological distances between S..P
+T(S..F) sum of topological distances between S..F
+T(S..Cl) sum of topological distances between S..Cl
+T(S..Br) sum of topological distances between S..Br
+T(S..I) sum of topological distances between S..I
+T(P..P) sum of topological distances between P..P
+T(P..F) sum of topological distances between P..F
+T(P..Cl) sum of topological distances between P..Cl
+T(P..Br) sum of topological distances between P..Br
+T(P..I) sum of topological distances between P..I
+T(F..F) sum of topological distances between F..F
+T(F..Cl) sum of topological distances between F..Cl
+T(F..Br) sum of topological distances between F..Br
+T(F..I) sum of topological distances between F..I
+T(Cl..Cl) sum of topological distances between Cl..Cl
+T(Cl..Br) sum of topological distances between Cl..Br
+T(Cl..I) sum of topological distances between Cl..I
+T(Br..Br) sum of topological distances between Br..Br
+T(Br..I) sum of topological distances between Br..I
+T(I..I) sum of topological distances between I..I
+MWC01 molecular walk count of order 01 (number of non-H bonds, nBO)
+MWC02 molecular walk count of order 02
+MWC03 molecular walk count of order 03
+MWC04 molecular walk count of order 04
+MWC05 molecular walk count of order 05
+MWC06 molecular walk count of order 06
+MWC07 molecular walk count of order 07
+MWC08 molecular walk count of order 08
+MWC09 molecular walk count of order 09
+MWC10 molecular walk count of order 10
+TWC total walk count
+SRW01 self-returning walk count of order 01 (number of non-H atoms, nSK)
+SRW02 self-returning walk count of order 02 (twice the number of non-H bonds)
+SRW03 self-returning walk count of order 03
+SRW04 self-returning walk count of order 04
+SRW05 self-returning walk count of order 05
+SRW06 self-returning walk count of order 06
+SRW07 self-returning walk count of order 07
+SRW08 self-returning walk count of order 08
+SRW09 self-returning walk count of order 09
+SRW10 self-returning walk count of order 10
+MPC01 molecular path count of order 01 (number of non-H bonds, nBO)
+MPC02 molecular path count of order 02 (Gordon-Scantlebury index)
+MPC03 molecular path count of order 03
+MPC04 molecular path count of order 04
+MPC05 molecular path count of order 05
+MPC06 molecular path count of order 06
+MPC07 molecular path count of order 07
+MPC08 molecular path count of order 08
+MPC09 molecular path count of order 09
+MPC10 molecular path count of order 10
+piPC01 molecular multiple path count of order 01 (sum of conventional bond orders, SCBO)
+piPC02 molecular multiple path count of order 02
+piPC03 molecular multiple path count of order 03
+piPC04 molecular multiple path count of order 04
+piPC05 molecular multiple path count of order 05
+piPC06 molecular multiple path count of order 06
+piPC07 molecular multiple path count of order 07
+piPC08 molecular multiple path count of order 08
+piPC09 molecular multiple path count of order 09
+piPC10 molecular multiple path count of order 10
+TPC total path count
+piID conventional bond-order ID number
+PCR ratio of multiple path count over path count
+PCD difference between multiple path count and path count
+CID Randic ID number
+BID Balaban ID number
+ISIZ information index on molecular size
+IAC total information index of atomic composition
+AAC mean information index on atomic composition
+IDE mean information content on the distance equality
+IDM mean information content on the distance magnitude
+IDDE mean information content on the distance degree equality
+IDDM mean information content on the distance degree magnitude
+IDET total information content on the distance equality
+IDMT total information content on the distance magnitude
+IVDE mean information content on the vertex degree equality
+IVDM mean information content on the vertex degree magnitude
+HVcpx graph vertex complexity index
+HDcpx graph distance complexity index (log)
+Uindex Balaban U index
+Vindex Balaban V index
+Xindex Balaban X index
+Yindex Balaban Y index
+IC0 information content index (neighborhood symmetry of 0-order)
+TIC0 total information content index (neighborhood symmetry of 0-order)
+SIC0 structural information content (neighborhood symmetry of 0-order)
+CIC0 complementary information content (neighborhood symmetry of 0-order)
+BIC0 bond information content (neighborhood symmetry of 0-order)
+IC1 information content index (neighborhood symmetry of 1-order)
+TIC1 total information content index (neighborhood symmetry of 1-order)
+SIC1 structural information content (neighborhood symmetry of 1-order)
+CIC1 complementary information content (neighborhood symmetry of 1-order)
+BIC1 bond information content (neighborhood symmetry of 1-order)
+IC2 information content index (neighborhood symmetry of 2-order)
+TIC2 total information content index (neighborhood symmetry of 2-order)
+SIC2 structural information content (neighborhood symmetry of 2-order)
+CIC2 complementary information content (neighborhood symmetry of 2-order)
+BIC2 bond information content (neighborhood symmetry of 2-order)
+IC3 information content index (neighborhood symmetry of 3-order)
+TIC3 total information content index (neighborhood symmetry of 3-order)
+SIC3 structural information content (neighborhood symmetry of 3-order)
+CIC3 complementary information content (neighborhood symmetry of 3-order)
+BIC3 bond information content (neighborhood symmetry of 3-order)
+IC4 information content index (neighborhood symmetry of 4-order)
+TIC4 total information content index (neighborhood symmetry of 4-order)
+SIC4 structural information content (neighborhood symmetry of 4-order)
+CIC4 complementary information content (neighborhood symmetry of 4-order)
+BIC4 bond information content (neighborhood symmetry of 4-order)
+IC5 information content index (neighborhood symmetry of 5-order)
+TIC5 total information content index (neighborhood symmetry of 5-order)
+SIC5 structural information content (neighborhood symmetry of 5-order)
+CIC5 complementary information content (neighborhood symmetry of 5-order)
+BIC5 bond information content (neighborhood symmetry of 5-order)
+ATS1m Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic masses
+ATS2m Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic masses
+ATS3m Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic masses
+ATS4m Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic masses
+ATS5m Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic masses
+ATS6m Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic masses
+ATS7m Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic masses
+ATS8m Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic masses
+ATS1v Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic van der Waals volumes
+ATS2v Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic van der Waals volumes
+ATS3v Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic van der Waals volumes
+ATS4v Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic van der Waals volumes
+ATS5v Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic van der Waals volumes
+ATS6v Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic van der Waals volumes
+ATS7v Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic van der Waals volumes
+ATS8v Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic van der Waals volumes
+ATS1e Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic Sanderson electronegativities
+ATS2e Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic Sanderson electronegativities
+ATS3e Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic Sanderson electronegativities
+ATS4e Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic Sanderson electronegativities
+ATS5e Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic Sanderson electronegativities
+ATS6e Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic Sanderson electronegativities
+ATS7e Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic Sanderson electronegativities
+ATS8e Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic Sanderson electronegativities
+ATS1p Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic polarizabilities
+ATS2p Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic polarizabilities
+ATS3p Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic polarizabilities
+ATS4p Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic polarizabilities
+ATS5p Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic polarizabilities
+ATS6p Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic polarizabilities
+ATS7p Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic polarizabilities
+ATS8p Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic polarizabilities
+MATS1m Moran autocorrelation - lag 1 / weighted by atomic masses
+MATS2m Moran autocorrelation - lag 2 / weighted by atomic masses
+MATS3m Moran autocorrelation - lag 3 / weighted by atomic masses
+MATS4m Moran autocorrelation - lag 4 / weighted by atomic masses
+MATS5m Moran autocorrelation - lag 5 / weighted by atomic masses
+MATS6m Moran autocorrelation - lag 6 / weighted by atomic masses
+MATS7m Moran autocorrelation - lag 7 / weighted by atomic masses
+MATS8m Moran autocorrelation - lag 8 / weighted by atomic masses
+MATS1v Moran autocorrelation - lag 1 / weighted by atomic van der Waals volumes
+MATS2v Moran autocorrelation - lag 2 / weighted by atomic van der Waals volumes
+MATS3v Moran autocorrelation - lag 3 / weighted by atomic van der Waals volumes
+MATS4v Moran autocorrelation - lag 4 / weighted by atomic van der Waals volumes
+MATS5v Moran autocorrelation - lag 5 / weighted by atomic van der Waals volumes
+MATS6v Moran autocorrelation - lag 6 / weighted by atomic van der Waals volumes
+MATS7v Moran autocorrelation - lag 7 / weighted by atomic van der Waals volumes
+MATS8v Moran autocorrelation - lag 8 / weighted by atomic van der Waals volumes
+MATS1e Moran autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities
+MATS2e Moran autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities
+MATS3e Moran autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities
+MATS4e Moran autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities
+MATS5e Moran autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities
+MATS6e Moran autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities
+MATS7e Moran autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities
+MATS8e Moran autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities
+MATS1p Moran autocorrelation - lag 1 / weighted by atomic polarizabilities
+MATS2p Moran autocorrelation - lag 2 / weighted by atomic polarizabilities
+MATS3p Moran autocorrelation - lag 3 / weighted by atomic polarizabilities
+MATS4p Moran autocorrelation - lag 4 / weighted by atomic polarizabilities
+MATS5p Moran autocorrelation - lag 5 / weighted by atomic polarizabilities
+MATS6p Moran autocorrelation - lag 6 / weighted by atomic polarizabilities
+MATS7p Moran autocorrelation - lag 7 / weighted by atomic polarizabilities
+MATS8p Moran autocorrelation - lag 8 / weighted by atomic polarizabilities
+GATS1m Geary autocorrelation - lag 1 / weighted by atomic masses
+GATS2m Geary autocorrelation - lag 2 / weighted by atomic masses
+GATS3m Geary autocorrelation - lag 3 / weighted by atomic masses
+GATS4m Geary autocorrelation - lag 4 / weighted by atomic masses
+GATS5m Geary autocorrelation - lag 5 / weighted by atomic masses
+GATS6m Geary autocorrelation - lag 6 / weighted by atomic masses
+GATS7m Geary autocorrelation - lag 7 / weighted by atomic masses
+GATS8m Geary autocorrelation - lag 8 / weighted by atomic masses
+GATS1v Geary autocorrelation - lag 1 / weighted by atomic van der Waals volumes
+GATS2v Geary autocorrelation - lag 2 / weighted by atomic van der Waals volumes
+GATS3v Geary autocorrelation - lag 3 / weighted by atomic van der Waals volumes
+GATS4v Geary autocorrelation - lag 4 / weighted by atomic van der Waals volumes
+GATS5v Geary autocorrelation - lag 5 / weighted by atomic van der Waals volumes
+GATS6v Geary autocorrelation - lag 6 / weighted by atomic van der Waals volumes
+GATS7v Geary autocorrelation - lag 7 / weighted by atomic van der Waals volumes
+GATS8v Geary autocorrelation - lag 8 / weighted by atomic van der Waals volumes
+GATS1e Geary autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities
+GATS2e Geary autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities
+GATS3e Geary autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities
+GATS4e Geary autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities
+GATS5e Geary autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities
+GATS6e Geary autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities
+GATS7e Geary autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities
+GATS8e Geary autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities
+GATS1p Geary autocorrelation - lag 1 / weighted by atomic polarizabilities
+GATS2p Geary autocorrelation - lag 2 / weighted by atomic polarizabilities
+GATS3p Geary autocorrelation - lag 3 / weighted by atomic polarizabilities
+GATS4p Geary autocorrelation - lag 4 / weighted by atomic polarizabilities
+GATS5p Geary autocorrelation - lag 5 / weighted by atomic polarizabilities
+GATS6p Geary autocorrelation - lag 6 / weighted by atomic polarizabilities
+GATS7p Geary autocorrelation - lag 7 / weighted by atomic polarizabilities
+GATS8p Geary autocorrelation - lag 8 / weighted by atomic polarizabilities
+EPS0 edge connectivity index of order 0
+EPS1 edge connectivity index of order 1
+EEig01x Eigenvalue 01from edge adj. matrix weighted by edge degrees
+EEig02x Eigenvalue 02from edge adj. matrix weighted by edge degrees
+EEig03x Eigenvalue 03from edge adj. matrix weighted by edge degrees
+EEig04x Eigenvalue 04from edge adj. matrix weighted by edge degrees
+EEig05x Eigenvalue 05from edge adj. matrix weighted by edge degrees
+EEig06x Eigenvalue 06from edge adj. matrix weighted by edge degrees
+EEig07x Eigenvalue 07from edge adj. matrix weighted by edge degrees
+EEig08x Eigenvalue 08from edge adj. matrix weighted by edge degrees
+EEig09x Eigenvalue 09from edge adj. matrix weighted by edge degrees
+EEig10x Eigenvalue 10from edge adj. matrix weighted by edge degrees
+EEig11x Eigenvalue 11from edge adj. matrix weighted by edge degrees
+EEig12x Eigenvalue 12from edge adj. matrix weighted by edge degrees
+EEig13x Eigenvalue 13from edge adj. matrix weighted by edge degrees
+EEig14x Eigenvalue 14from edge adj. matrix weighted by edge degrees
+EEig15x Eigenvalue 15from edge adj. matrix weighted by edge degrees
+EEig01d Eigenvalue 01 from edge adj. matrix weighted by dipole moments
+EEig02d Eigenvalue 02 from edge adj. matrix weighted by dipole moments
+EEig03d Eigenvalue 03 from edge adj. matrix weighted by dipole moments
+EEig04d Eigenvalue 04 from edge adj. matrix weighted by dipole moments
+EEig05d Eigenvalue 05 from edge adj. matrix weighted by dipole moments
+EEig06d Eigenvalue 06 from edge adj. matrix weighted by dipole moments
+EEig07d Eigenvalue 07 from edge adj. matrix weighted by dipole moments
+EEig08d Eigenvalue 08 from edge adj. matrix weighted by dipole moments
+EEig09d Eigenvalue 09 from edge adj. matrix weighted by dipole moments
+EEig10d Eigenvalue 10 from edge adj. matrix weighted by dipole moments
+EEig11d Eigenvalue 11 from edge adj. matrix weighted by dipole moments
+EEig12d Eigenvalue 12 from edge adj. matrix weighted by dipole moments
+EEig13d Eigenvalue 13 from edge adj. matrix weighted by dipole moments
+EEig14d Eigenvalue 14 from edge adj. matrix weighted by dipole moments
+EEig15d Eigenvalue 15 from edge adj. matrix weighted by dipole moments
+EEig01r Eigenvalue 01 from edge adj. matrix weighted by resonance integrals
+EEig02r Eigenvalue 02 from edge adj. matrix weighted by resonance integrals
+EEig03r Eigenvalue 03 from edge adj. matrix weighted by resonance integrals
+EEig04r Eigenvalue 04 from edge adj. matrix weighted by resonance integrals
+EEig05r Eigenvalue 05 from edge adj. matrix weighted by resonance integrals
+EEig06r Eigenvalue 06 from edge adj. matrix weighted by resonance integrals
+EEig07r Eigenvalue 07 from edge adj. matrix weighted by resonance integrals
+EEig08r Eigenvalue 08 from edge adj. matrix weighted by resonance integrals
+EEig09r Eigenvalue 09 from edge adj. matrix weighted by resonance integrals
+EEig10r Eigenvalue 10 from edge adj. matrix weighted by resonance integrals
+EEig11r Eigenvalue 11 from edge adj. matrix weighted by resonance integrals
+EEig12r Eigenvalue 12 from edge adj. matrix weighted by resonance integrals
+EEig13r Eigenvalue 13 from edge adj. matrix weighted by resonance integrals
+EEig14r Eigenvalue 14 from edge adj. matrix weighted by resonance integrals
+EEig15r Eigenvalue 15 from edge adj. matrix weighted by resonance integrals
+ESpm01u Spectral moment 01 from edge adj. matrix
+ESpm02u Spectral moment 02 from edge adj. matrix
+ESpm03u Spectral moment 03 from edge adj. matrix
+ESpm04u Spectral moment 04 from edge adj. matrix
+ESpm05u Spectral moment 05 from edge adj. matrix
+ESpm06u Spectral moment 06 from edge adj. matrix
+ESpm07u Spectral moment 07 from edge adj. matrix
+ESpm08u Spectral moment 08 from edge adj. matrix
+ESpm09u Spectral moment 09 from edge adj. matrix
+ESpm10u Spectral moment 10 from edge adj. matrix
+ESpm11u Spectral moment 11 from edge adj. matrix
+ESpm12u Spectral moment 12 from edge adj. matrix
+ESpm13u Spectral moment 13 from edge adj. matrix
+ESpm14u Spectral moment 14 from edge adj. matrix
+ESpm15u Spectral moment 15 from edge adj. matrix
+ESpm01x Spectral moment 01 from edge adj. matrix weighted by edge degrees
+ESpm02x Spectral moment 02 from edge adj. matrix weighted by edge degrees
+ESpm03x Spectral moment 03 from edge adj. matrix weighted by edge degrees
+ESpm04x Spectral moment 04 from edge adj. matrix weighted by edge degrees
+ESpm05x Spectral moment 05 from edge adj. matrix weighted by edge degrees
+ESpm06x Spectral moment 06 from edge adj. matrix weighted by edge degrees
+ESpm07x Spectral moment 07 from edge adj. matrix weighted by edge degrees
+ESpm08x Spectral moment 08 from edge adj. matrix weighted by edge degrees
+ESpm09x Spectral moment 09 from edge adj. matrix weighted by edge degrees
+ESpm10x Spectral moment 10 from edge adj. matrix weighted by edge degrees
+ESpm11x Spectral moment 11 from edge adj. matrix weighted by edge degrees
+ESpm12x Spectral moment 12 from edge adj. matrix weighted by edge degrees
+ESpm13x Spectral moment 13 from edge adj. matrix weighted by edge degrees
+ESpm14x Spectral moment 14 from edge adj. matrix weighted by edge degrees
+ESpm15x Spectral moment 15 from edge adj. matrix weighted by edge degrees
+ESpm01d Spectral moment 01 from edge adj. matrix weighted by dipole moments
+ESpm02d Spectral moment 02 from edge adj. matrix weighted by dipole moments
+ESpm03d Spectral moment 03 from edge adj. matrix weighted by dipole moments
+ESpm04d Spectral moment 04 from edge adj. matrix weighted by dipole moments
+ESpm05d Spectral moment 05 from edge adj. matrix weighted by dipole moments
+ESpm06d Spectral moment 06 from edge adj. matrix weighted by dipole moments
+ESpm07d Spectral moment 07 from edge adj. matrix weighted by dipole moments
+ESpm08d Spectral moment 08 from edge adj. matrix weighted by dipole moments
+ESpm09d Spectral moment 09 from edge adj. matrix weighted by dipole moments
+ESpm10d Spectral moment 10 from edge adj. matrix weighted by dipole moments
+ESpm11d Spectral moment 11 from edge adj. matrix weighted by dipole moments
+ESpm12d Spectral moment 12 from edge adj. matrix weighted by dipole moments
+ESpm13d Spectral moment 13 from edge adj. matrix weighted by dipole moments
+ESpm14d Spectral moment 14 from edge adj. matrix weighted by dipole moments
+ESpm15d Spectral moment 15 from edge adj. matrix weighted by dipole moments
+ESpm01r Spectral moment 01 from edge adj. matrix weighted by resonance integrals
+ESpm02r Spectral moment 02 from edge adj. matrix weighted by resonance integrals
+ESpm03r Spectral moment 03 from edge adj. matrix weighted by resonance integrals
+ESpm04r Spectral moment 04 from edge adj. matrix weighted by resonance integrals
+ESpm05r Spectral moment 05 from edge adj. matrix weighted by resonance integrals
+ESpm06r Spectral moment 06 from edge adj. matrix weighted by resonance integrals
+ESpm07r Spectral moment 07 from edge adj. matrix weighted by resonance integrals
+ESpm08r Spectral moment 08 from edge adj. matrix weighted by resonance integrals
+ESpm09r Spectral moment 09 from edge adj. matrix weighted by resonance integrals
+ESpm10r Spectral moment 10 from edge adj. matrix weighted by resonance integrals
+ESpm11r Spectral moment 11 from edge adj. matrix weighted by resonance integrals
+ESpm12r Spectral moment 12 from edge adj. matrix weighted by resonance integrals
+ESpm13r Spectral moment 13 from edge adj. matrix weighted by resonance integrals
+ESpm14r Spectral moment 14 from edge adj. matrix weighted by resonance integrals
+ESpm15r Spectral moment 15 from edge adj. matrix weighted by resonance integrals
+BEHm1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic masses
+BEHm2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic masses
+BEHm3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic masses
+BEHm4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic masses
+BEHm5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic masses
+BEHm6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic masses
+BEHm7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic masses
+BEHm8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic masses
+BELm1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic masses
+BELm2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic masses
+BELm3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic masses
+BELm4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic masses
+BELm5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic masses
+BELm6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic masses
+BELm7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic masses
+BELm8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic masses
+BEHv1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes
+BELv1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes
+BELv2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes
+BELv3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes
+BELv4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes
+BELv5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes
+BELv6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes
+BELv7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes
+BELv8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes
+BEHe1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHp1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities
+BEHp2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities
+BEHp3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities
+BEHp4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities
+BEHp5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities
+BEHp6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities
+BEHp7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities
+BEHp8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities
+BELp1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities
+BELp2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities
+BELp3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities
+BELp4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities
+BELp5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities
+BELp6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities
+BELp7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities
+BELp8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities
+GGI1 topological charge index of order 1
+GGI2 topological charge index of order 2
+GGI3 topological charge index of order 3
+GGI4 topological charge index of order 4
+GGI5 topological charge index of order 5
+GGI6 topological charge index of order 6
+GGI7 topological charge index of order 7
+GGI8 topological charge index of order 8
+GGI9 topological charge index of order 9
+GGI10 topological charge index of order 10
+JGI1 mean topological charge index of order1
+JGI2 mean topological charge index of order2
+JGI3 mean topological charge index of order3
+JGI4 mean topological charge index of order4
+JGI5 mean topological charge index of order5
+JGI6 mean topological charge index of order6
+JGI7 mean topological charge index of order7
+JGI8 mean topological charge index of order8
+JGI9 mean topological charge index of order9
+JGI10 mean topological charge index of order10
+JGT global topological charge index
+LP1 Lovasz-Pelikan index (leading eigenvalue)
+Eig1Z Leading eigenvalue from Z weighted distance matrix (Barysz matrix)
+Eig1m Leading eigenvalue from mass weighted distance matrix
+Eig1v Leading eigenvalue from van der Waals weighted distance matrix
+Eig1e Leading eigenvalue from electronegativity weighted distance matrix
+Eig1p Leading eigenvalue from polarizability weighted distance matrix
+SEigZ Eigenvalue sum from Z weighted distance matrix (Barysz matrix)
+SEigm Eigenvalue sum from mass weighted distance matrix
+SEigv Eigenvalue sum from van der Waals weighted distance matrix
+SEige Eigenvalue sum from electronegativity weighted distance matrix
+SEigp Eigenvalue sum from polarizability weighted distance matrix
+AEigZ Absolute eigenvalue sum from Z weighted distance matrix (Barysz matrix)
+AEigm Absolute eigenvalue sum from mass weighted distance matrix
+AEigv Absolute eigenvalue sum from van der Waals weighted distance matrix
+AEige Absolute eigenvalue sum from electronegativity weighted distance matrix
+AEigp Absolute eigenvalue sum from polarizability weighted distance matrix
+VEA1 eigenvector coefficient sum from adjacency matrix
+VEA2 average eigenvector coefficient sum from adjacency matrix
+VRA1 Randic-type eigenvector-based index from adjacency matrix
+VRA2 average Randic-type eigenvector-based index from adjacency matrix
+VED1 eigenvector coefficient sum from distance matrix
+VED2 average eigenvector coefficient sum from distance matrix
+VRD1 Randic-type eigenvector-based index from distance matrix
+VRD2 average Randic-type eigenvector-based index from distance matrix
+VEZ1 eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix)
+VEZ2 average eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix)
+VRZ1 Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix)
+VRZ2 average Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix)
+VEm1 eigenvector coefficient sum from mass weighted distance matrix
+VEm2 average eigenvector coefficient sum from mass weighted distance matrix
+VRm1 Randic-type eigenvector-based index from mass weighted distance matrix
+VRm2 average Randic-type eigenvector-based index from mass weighted distance matrix
+VEv1 eigenvector coefficient sum from van der Waals weighted distance matrix
+VEv2 average eigenvector coefficient sum from van der Waals weighted distance matrix
+VRv1 Randic-type eigenvector-based index from van der Waals weighted distance matrix
+VRv2 average Randic-type eigenvector-based index from van der Waals weighted distance matrix
+VEe1 eigenvector coefficient sum from electronegativity weighted distance matrix
+VEe2 average eigenvector coefficient sum from electronegativity weighted distance matrix
+VRe1 Randic-type eigenvector-based index from electronegativity weighted distance matrix
+VRe2 average Randic-type eigenvector-based index from electronegativity weighted distance matrix
+VEp1 eigenvector coefficient sum from polarizability weighted distance matrix
+VEp2 average eigenvector coefficient sum from polarizability weighted distance matrix
+VRp1 Randic-type eigenvector-based index from polarizability weighted distance matrix
+VRp2 average Randic-type eigenvector-based index from polarizability weighted distance matrix
+DP01 molecular profile no. 01
+DP02 molecular profile no. 02
+DP03 molecular profile no. 03
+DP04 molecular profile no. 04
+DP05 molecular profile no. 05
+DP06 molecular profile no. 06
+DP07 molecular profile no. 07
+DP08 molecular profile no. 08
+DP09 molecular profile no. 09
+DP10 molecular profile no. 10
+DP11 molecular profile no. 11
+DP12 molecular profile no. 12
+DP13 molecular profile no. 13
+DP14 molecular profile no. 14
+DP15 molecular profile no. 15
+DP16 molecular profile no. 16
+DP17 molecular profile no. 17
+DP18 molecular profile no. 18
+DP19 molecular profile no. 19
+DP20 molecular profile no. 20
+SP01 shape profile no. 01
+SP02 shape profile no. 02
+SP03 shape profile no. 03
+SP04 shape profile no. 04
+SP05 shape profile no. 05
+SP06 shape profile no. 06
+SP07 shape profile no. 07
+SP08 shape profile no. 08
+SP09 shape profile no. 09
+SP10 shape profile no. 10
+SP11 shape profile no. 11
+SP12 shape profile no. 12
+SP13 shape profile no. 13
+SP14 shape profile no. 14
+SP15 shape profile no. 15
+SP16 shape profile no. 16
+SP17 shape profile no. 17
+SP18 shape profile no. 18
+SP19 shape profile no. 19
+SP20 shape profile no. 20
+SHP2 average shape profile index of order 2
+W3D 3D-Wiener index
+J3D 3D-Balaban index
+H3D 3D-Harary index
+AGDD average geometric distance degree
+DDI D/D index
+ADDD average distance/distance degree
+G1 gravitational index G1
+G2 gravitational index G2 (bond-restricted)
+RGyr radius of gyration (mass weighted)
+SPAN span R
+SPAM average span R
+MEcc molecular eccentricity
+SPH spherosity
+ASP asphericity
+FDI folding degree index
+PJI3 3D Petijean shape index
+L/Bw length-to-breadth ratio by WHIM
+SEig absolute eigenvalue sum on geometry matrix
+HOMA Harmonic Oscillator Model of Aromaticity index
+RCI Jug RC index
+AROM aromaticity (trial)
+HOMT HOMA total (trial)
+DISPm d COMMA2 value / weighted by atomic masses
+QXXm Qxx COMMA2 value / weighted by atomic masses
+QYYm Qyy COMMA2 value / weighted by atomic masses
+QZZm Qzz COMMA2 value / weighted by atomic masses
+DISPv d COMMA2 value / weighted by atomic van der Waals volumes
+QXXv Qxx COMMA2 value / weighted by atomic van der Waals volumes
+QYYv Qyy COMMA2 value / weighted by atomic van der Waals volumes
+QZZv Qzz COMMA2 value / weighted by atomic van der Waals volumes
+DISPe d COMMA2 value / weighted by atomic Sanderson electronegativities
+QXXe Qxx COMMA2 value / weighted by atomic Sanderson electronegativities
+QYYe Qyy COMMA2 value / weighted by atomic Sanderson electronegativities
+QZZe Qzz COMMA2 value / weighted by atomic Sanderson electronegativities
+DISPp d COMMA2 value / weighted by atomic polarizabilities
+QXXp Qxx COMMA2 value / weighted by atomic polarizabilities
+QYYp Qyy COMMA2 value / weighted by atomic polarizabilities
+QZZp Qzz COMMA2 value / weighted by atomic polarizabilities
+G(N..N) sum of geometrical distances between N..N
+G(N..O) sum of geometrical distances between N..O
+G(N..S) sum of geometrical distances between N..S
+G(N..P) sum of geometrical distances between N..P
+G(N..F) sum of geometrical distances between N..F
+G(N..Cl) sum of geometrical distances between N..Cl
+G(N..Br) sum of geometrical distances between N..Br
+G(N..I) sum of geometrical distances between N..I
+G(O..O) sum of geometrical distances between O..O
+G(O..S) sum of geometrical distances between O..S
+G(O..P) sum of geometrical distances between O..P
+G(O..F) sum of geometrical distances between O..F
+G(O..Cl) sum of geometrical distances between O..Cl
+G(O..Br) sum of geometrical distances between O..Br
+G(O..I) sum of geometrical distances between O..I
+G(S..S) sum of geometrical distances between S..S
+G(S..P) sum of geometrical distances between S..P
+G(S..F) sum of geometrical distances between S..F
+G(S..Cl) sum of geometrical distances between S..Cl
+G(S..Br) sum of geometrical distances between S..Br
+G(S..I) sum of geometrical distances between S..I
+G(P..P) sum of geometrical distances between P..P
+G(P..F) sum of geometrical distances between P..F
+G(P..Cl) sum of geometrical distances between P..Cl
+G(P..Br) sum of geometrical distances between P..Br
+G(P..I) sum of geometrical distances between P..I
+G(F..F) sum of geometrical distances between F..F
+G(F..Cl) sum of geometrical distances between F..Cl
+G(F..Br) sum of geometrical distances between F..Br
+G(F..I) sum of geometrical distances between F..I
+G(Cl..Cl) sum of geometrical distances between Cl..Cl
+G(Cl..Br) sum of geometrical distances between Cl..Br
+G(Cl..I) sum of geometrical distances between Cl..I
+G(Br..Br) sum of geometrical distances between Br..Br
+G(Br..I) sum of geometrical distances between Br..I
+G(I..I) sum of geometrical distances between I..I
+RDF010u Radial Distribution Function - 1.0 / unweighted
+RDF015u Radial Distribution Function - 1.5 / unweighted
+RDF020u Radial Distribution Function - 2.0 / unweighted
+RDF025u Radial Distribution Function - 2.5 / unweighted
+RDF030u Radial Distribution Function - 3.0 / unweighted
+RDF035u Radial Distribution Function - 3.5 / unweighted
+RDF040u Radial Distribution Function - 4.0 / unweighted
+RDF045u Radial Distribution Function - 4.5 / unweighted
+RDF050u Radial Distribution Function - 5.0 / unweighted
+RDF055u Radial Distribution Function - 5.5 / unweighted
+RDF060u Radial Distribution Function - 6.0 / unweighted
+RDF065u Radial Distribution Function - 6.5 / unweighted
+RDF070u Radial Distribution Function - 7.0 / unweighted
+RDF075u Radial Distribution Function - 7.5 / unweighted
+RDF080u Radial Distribution Function - 8.0 / unweighted
+RDF085u Radial Distribution Function - 8.5 / unweighted
+RDF090u Radial Distribution Function - 9.0 / unweighted
+RDF095u Radial Distribution Function - 9.5 / unweighted
+RDF100u Radial Distribution Function - 10.0 / unweighted
+RDF105u Radial Distribution Function - 10.5 / unweighted
+RDF110u Radial Distribution Function - 11.0 / unweighted
+RDF115u Radial Distribution Function - 11.5 / unweighted
+RDF120u Radial Distribution Function - 12.0 / unweighted
+RDF125u Radial Distribution Function - 12.5 / unweighted
+RDF130u Radial Distribution Function - 13.0 / unweighted
+RDF135u Radial Distribution Function - 13.5 / unweighted
+RDF140u Radial Distribution Function - 14.0 / unweighted
+RDF145u Radial Distribution Function - 14.5 / unweighted
+RDF150u Radial Distribution Function - 15.0 / unweighted
+RDF155u Radial Distribution Function - 15.5 / unweighted
+RDF010m Radial Distribution Function - 1.0 / weighted by atomic masses
+RDF015m Radial Distribution Function - 1.5 / weighted by atomic masses
+RDF020m Radial Distribution Function - 2.0 / weighted by atomic masses
+RDF025m Radial Distribution Function - 2.5 / weighted by atomic masses
+RDF030m Radial Distribution Function - 3.0 / weighted by atomic masses
+RDF035m Radial Distribution Function - 3.5 / weighted by atomic masses
+RDF040m Radial Distribution Function - 4.0 / weighted by atomic masses
+RDF045m Radial Distribution Function - 4.5 / weighted by atomic masses
+RDF050m Radial Distribution Function - 5.0 / weighted by atomic masses
+RDF055m Radial Distribution Function - 5.5 / weighted by atomic masses
+RDF060m Radial Distribution Function - 6.0 / weighted by atomic masses
+RDF065m Radial Distribution Function - 6.5 / weighted by atomic masses
+RDF070m Radial Distribution Function - 7.0 / weighted by atomic masses
+RDF075m Radial Distribution Function - 7.5 / weighted by atomic masses
+RDF080m Radial Distribution Function - 8.0 / weighted by atomic masses
+RDF085m Radial Distribution Function - 8.5 / weighted by atomic masses
+RDF090m Radial Distribution Function - 9.0 / weighted by atomic masses
+RDF095m Radial Distribution Function - 9.5 / weighted by atomic masses
+RDF100m Radial Distribution Function - 10.0 / weighted by atomic masses
+RDF105m Radial Distribution Function - 10.5 / weighted by atomic masses
+RDF110m Radial Distribution Function - 11.0 / weighted by atomic masses
+RDF115m Radial Distribution Function - 11.5 / weighted by atomic masses
+RDF120m Radial Distribution Function - 12.0 / weighted by atomic masses
+RDF125m Radial Distribution Function - 12.5 / weighted by atomic masses
+RDF130m Radial Distribution Function - 13.0 / weighted by atomic masses
+RDF135m Radial Distribution Function - 13.5 / weighted by atomic masses
+RDF140m Radial Distribution Function - 14.0 / weighted by atomic masses
+RDF145m Radial Distribution Function - 14.5 / weighted by atomic masses
+RDF150m Radial Distribution Function - 15.0 / weighted by atomic masses
+RDF155m Radial Distribution Function - 15.5 / weighted by atomic masses
+RDF010v Radial Distribution Function - 1.0 / weighted by atomic van der Waals volumes
+RDF015v Radial Distribution Function - 1.5 / weighted by atomic van der Waals volumes
+RDF020v Radial Distribution Function - 2.0 / weighted by atomic van der Waals volumes
+RDF025v Radial Distribution Function - 2.5 / weighted by atomic van der Waals volumes
+RDF030v Radial Distribution Function - 3.0 / weighted by atomic van der Waals volumes
+RDF035v Radial Distribution Function - 3.5 / weighted by atomic van der Waals volumes
+RDF040v Radial Distribution Function - 4.0 / weighted by atomic van der Waals volumes
+RDF045v Radial Distribution Function - 4.5 / weighted by atomic van der Waals volumes
+RDF050v Radial Distribution Function - 5.0 / weighted by atomic van der Waals volumes
+RDF055v Radial Distribution Function - 5.5 / weighted by atomic van der Waals volumes
+RDF060v Radial Distribution Function - 6.0 / weighted by atomic van der Waals volumes
+RDF065v Radial Distribution Function - 6.5 / weighted by atomic van der Waals volumes
+RDF070v Radial Distribution Function - 7.0 / weighted by atomic van der Waals volumes
+RDF075v Radial Distribution Function - 7.5 / weighted by atomic van der Waals volumes
+RDF080v Radial Distribution Function - 8.0 / weighted by atomic van der Waals volumes
+RDF085v Radial Distribution Function - 8.5 / weighted by atomic van der Waals volumes
+RDF090v Radial Distribution Function - 9.0 / weighted by atomic van der Waals volumes
+RDF095v Radial Distribution Function - 9.5 / weighted by atomic van der Waals volumes
+RDF100v Radial Distribution Function - 10.0 / weighted by atomic van der Waals volumes
+RDF105v Radial Distribution Function - 10.5 / weighted by atomic van der Waals volumes
+RDF110v Radial Distribution Function - 11.0 / weighted by atomic van der Waals volumes
+RDF115v Radial Distribution Function - 11.5 / weighted by atomic van der Waals volumes
+RDF120v Radial Distribution Function - 12.0 / weighted by atomic van der Waals volumes
+RDF125v Radial Distribution Function - 12.5 / weighted by atomic van der Waals volumes
+RDF130v Radial Distribution Function - 13.0 / weighted by atomic van der Waals volumes
+RDF135v Radial Distribution Function - 13.5 / weighted by atomic van der Waals volumes
+RDF140v Radial Distribution Function - 14.0 / weighted by atomic van der Waals volumes
+RDF145v Radial Distribution Function - 14.5 / weighted by atomic van der Waals volumes
+RDF150v Radial Distribution Function - 15.0 / weighted by atomic van der Waals volumes
+RDF155v Radial Distribution Function - 15.5 / weighted by atomic van der Waals volumes
+RDF010e Radial Distribution Function - 1.0 / weighted by atomic Sanderson electronegativities
+RDF015e Radial Distribution Function - 1.5 / weighted by atomic Sanderson electronegativities
+RDF020e Radial Distribution Function - 2.0 / weighted by atomic Sanderson electronegativities
+RDF025e Radial Distribution Function - 2.5 / weighted by atomic Sanderson electronegativities
+RDF030e Radial Distribution Function - 3.0 / weighted by atomic Sanderson electronegativities
+RDF035e Radial Distribution Function - 3.5 / weighted by atomic Sanderson electronegativities
+RDF040e Radial Distribution Function - 4.0 / weighted by atomic Sanderson electronegativities
+RDF045e Radial Distribution Function - 4.5 / weighted by atomic Sanderson electronegativities
+RDF050e Radial Distribution Function - 5.0 / weighted by atomic Sanderson electronegativities
+RDF055e Radial Distribution Function - 5.5 / weighted by atomic Sanderson electronegativities
+RDF060e Radial Distribution Function - 6.0 / weighted by atomic Sanderson electronegativities
+RDF065e Radial Distribution Function - 6.5 / weighted by atomic Sanderson electronegativities
+RDF070e Radial Distribution Function - 7.0 / weighted by atomic Sanderson electronegativities
+RDF075e Radial Distribution Function - 7.5 / weighted by atomic Sanderson electronegativities
+RDF080e Radial Distribution Function - 8.0 / weighted by atomic Sanderson electronegativities
+RDF085e Radial Distribution Function - 8.5 / weighted by atomic Sanderson electronegativities
+RDF090e Radial Distribution Function - 9.0 / weighted by atomic Sanderson electronegativities
+RDF095e Radial Distribution Function - 9.5 / weighted by atomic Sanderson electronegativities
+RDF100e Radial Distribution Function - 10.0 / weighted by atomic Sanderson electronegativities
+RDF105e Radial Distribution Function - 10.5 / weighted by atomic Sanderson electronegativities
+RDF110e Radial Distribution Function - 11.0 / weighted by atomic Sanderson electronegativities
+RDF115e Radial Distribution Function - 11.5 / weighted by atomic Sanderson electronegativities
+RDF120e Radial Distribution Function - 12.0 / weighted by atomic Sanderson electronegativities
+RDF125e Radial Distribution Function - 12.5 / weighted by atomic Sanderson electronegativities
+RDF130e Radial Distribution Function - 13.0 / weighted by atomic Sanderson electronegativities
+RDF135e Radial Distribution Function - 13.5 / weighted by atomic Sanderson electronegativities
+RDF140e Radial Distribution Function - 14.0 / weighted by atomic Sanderson electronegativities
+RDF145e Radial Distribution Function - 14.5 / weighted by atomic Sanderson electronegativities
+RDF150e Radial Distribution Function - 15.0 / weighted by atomic Sanderson electronegativities
+RDF155e Radial Distribution Function - 15.5 / weighted by atomic Sanderson electronegativities
+RDF010p Radial Distribution Function - 1.0 / weighted by atomic polarizabilities
+RDF015p Radial Distribution Function - 1.5 / weighted by atomic polarizabilities
+RDF020p Radial Distribution Function - 2.0 / weighted by atomic polarizabilities
+RDF025p Radial Distribution Function - 2.5 / weighted by atomic polarizabilities
+RDF030p Radial Distribution Function - 3.0 / weighted by atomic polarizabilities
+RDF035p Radial Distribution Function - 3.5 / weighted by atomic polarizabilities
+RDF040p Radial Distribution Function - 4.0 / weighted by atomic polarizabilities
+RDF045p Radial Distribution Function - 4.5 / weighted by atomic polarizabilities
+RDF050p Radial Distribution Function - 5.0 / weighted by atomic polarizabilities
+RDF055p Radial Distribution Function - 5.5 / weighted by atomic polarizabilities
+RDF060p Radial Distribution Function - 6.0 / weighted by atomic polarizabilities
+RDF065p Radial Distribution Function - 6.5 / weighted by atomic polarizabilities
+RDF070p Radial Distribution Function - 7.0 / weighted by atomic polarizabilities
+RDF075p Radial Distribution Function - 7.5 / weighted by atomic polarizabilities
+RDF080p Radial Distribution Function - 8.0 / weighted by atomic polarizabilities
+RDF085p Radial Distribution Function - 8.5 / weighted by atomic polarizabilities
+RDF090p Radial Distribution Function - 9.0 / weighted by atomic polarizabilities
+RDF095p Radial Distribution Function - 9.5 / weighted by atomic polarizabilities
+RDF100p Radial Distribution Function - 10.0 / weighted by atomic polarizabilities
+RDF105p Radial Distribution Function - 10.5 / weighted by atomic polarizabilities
+RDF110p Radial Distribution Function - 11.0 / weighted by atomic polarizabilities
+RDF115p Radial Distribution Function - 11.5 / weighted by atomic polarizabilities
+RDF120p Radial Distribution Function - 12.0 / weighted by atomic polarizabilities
+RDF125p Radial Distribution Function - 12.5 / weighted by atomic polarizabilities
+RDF130p Radial Distribution Function - 13.0 / weighted by atomic polarizabilities
+RDF135p Radial Distribution Function - 13.5 / weighted by atomic polarizabilities
+RDF140p Radial Distribution Function - 14.0 / weighted by atomic polarizabilities
+RDF145p Radial Distribution Function - 14.5 / weighted by atomic polarizabilities
+RDF150p Radial Distribution Function - 15.0 / weighted by atomic polarizabilities
+RDF155p Radial Distribution Function - 15.5 / weighted by atomic polarizabilities
+Mor01u 3D-MoRSE - signal 01 / unweighted
+Mor02u 3D-MoRSE - signal 02 / unweighted
+Mor03u 3D-MoRSE - signal 03 / unweighted
+Mor04u 3D-MoRSE - signal 04 / unweighted
+Mor05u 3D-MoRSE - signal 05 / unweighted
+Mor06u 3D-MoRSE - signal 06 / unweighted
+Mor07u 3D-MoRSE - signal 07 / unweighted
+Mor08u 3D-MoRSE - signal 08 / unweighted
+Mor09u 3D-MoRSE - signal 09 / unweighted
+Mor10u 3D-MoRSE - signal 10 / unweighted
+Mor11u 3D-MoRSE - signal 11 / unweighted
+Mor12u 3D-MoRSE - signal 12 / unweighted
+Mor13u 3D-MoRSE - signal 13 / unweighted
+Mor14u 3D-MoRSE - signal 14 / unweighted
+Mor15u 3D-MoRSE - signal 15 / unweighted
+Mor16u 3D-MoRSE - signal 16 / unweighted
+Mor17u 3D-MoRSE - signal 17 / unweighted
+Mor18u 3D-MoRSE - signal 18 / unweighted
+Mor19u 3D-MoRSE - signal 19 / unweighted
+Mor20u 3D-MoRSE - signal 20 / unweighted
+Mor21u 3D-MoRSE - signal 21 / unweighted
+Mor22u 3D-MoRSE - signal 22 / unweighted
+Mor23u 3D-MoRSE - signal 23 / unweighted
+Mor24u 3D-MoRSE - signal 24 / unweighted
+Mor25u 3D-MoRSE - signal 25 / unweighted
+Mor26u 3D-MoRSE - signal 26 / unweighted
+Mor27u 3D-MoRSE - signal 27 / unweighted
+Mor28u 3D-MoRSE - signal 28 / unweighted
+Mor29u 3D-MoRSE - signal 29 / unweighted
+Mor30u 3D-MoRSE - signal 30 / unweighted
+Mor31u 3D-MoRSE - signal 31 / unweighted
+Mor32u 3D-MoRSE - signal 32 / unweighted
+Mor01m 3D-MoRSE - signal 01 / weighted by atomic masses
+Mor02m 3D-MoRSE - signal 02 / weighted by atomic masses
+Mor03m 3D-MoRSE - signal 03 / weighted by atomic masses
+Mor04m 3D-MoRSE - signal 04 / weighted by atomic masses
+Mor05m 3D-MoRSE - signal 05 / weighted by atomic masses
+Mor06m 3D-MoRSE - signal 06 / weighted by atomic masses
+Mor07m 3D-MoRSE - signal 07 / weighted by atomic masses
+Mor08m 3D-MoRSE - signal 08 / weighted by atomic masses
+Mor09m 3D-MoRSE - signal 09 / weighted by atomic masses
+Mor10m 3D-MoRSE - signal 10 / weighted by atomic masses
+Mor11m 3D-MoRSE - signal 11 / weighted by atomic masses
+Mor12m 3D-MoRSE - signal 12 / weighted by atomic masses
+Mor13m 3D-MoRSE - signal 13 / weighted by atomic masses
+Mor14m 3D-MoRSE - signal 14 / weighted by atomic masses
+Mor15m 3D-MoRSE - signal 15 / weighted by atomic masses
+Mor16m 3D-MoRSE - signal 16 / weighted by atomic masses
+Mor17m 3D-MoRSE - signal 17 / weighted by atomic masses
+Mor18m 3D-MoRSE - signal 18 / weighted by atomic masses
+Mor19m 3D-MoRSE - signal 19 / weighted by atomic masses
+Mor20m 3D-MoRSE - signal 20 / weighted by atomic masses
+Mor21m 3D-MoRSE - signal 21 / weighted by atomic masses
+Mor22m 3D-MoRSE - signal 22 / weighted by atomic masses
+Mor23m 3D-MoRSE - signal 23 / weighted by atomic masses
+Mor24m 3D-MoRSE - signal 24 / weighted by atomic masses
+Mor25m 3D-MoRSE - signal 25 / weighted by atomic masses
+Mor26m 3D-MoRSE - signal 26 / weighted by atomic masses
+Mor27m 3D-MoRSE - signal 27 / weighted by atomic masses
+Mor28m 3D-MoRSE - signal 28 / weighted by atomic masses
+Mor29m 3D-MoRSE - signal 29 / weighted by atomic masses
+Mor30m 3D-MoRSE - signal 30 / weighted by atomic masses
+Mor31m 3D-MoRSE - signal 31 / weighted by atomic masses
+Mor32m 3D-MoRSE - signal 32 / weighted by atomic masses
+Mor01v 3D-MoRSE - signal 01 / weighted by atomic van der Waals volumes
+Mor02v 3D-MoRSE - signal 02 / weighted by atomic van der Waals volumes
+Mor03v 3D-MoRSE - signal 03 / weighted by atomic van der Waals volumes
+Mor04v 3D-MoRSE - signal 04 / weighted by atomic van der Waals volumes
+Mor05v 3D-MoRSE - signal 05 / weighted by atomic van der Waals volumes
+Mor06v 3D-MoRSE - signal 06 / weighted by atomic van der Waals volumes
+Mor07v 3D-MoRSE - signal 07 / weighted by atomic van der Waals volumes
+Mor08v 3D-MoRSE - signal 08 / weighted by atomic van der Waals volumes
+Mor09v 3D-MoRSE - signal 09 / weighted by atomic van der Waals volumes
+Mor10v 3D-MoRSE - signal 10 / weighted by atomic van der Waals volumes
+Mor11v 3D-MoRSE - signal 11 / weighted by atomic van der Waals volumes
+Mor12v 3D-MoRSE - signal 12 / weighted by atomic van der Waals volumes
+Mor13v 3D-MoRSE - signal 13 / weighted by atomic van der Waals volumes
+Mor14v 3D-MoRSE - signal 14 / weighted by atomic van der Waals volumes
+Mor15v 3D-MoRSE - signal 15 / weighted by atomic van der Waals volumes
+Mor16v 3D-MoRSE - signal 16 / weighted by atomic van der Waals volumes
+Mor17v 3D-MoRSE - signal 17 / weighted by atomic van der Waals volumes
+Mor18v 3D-MoRSE - signal 18 / weighted by atomic van der Waals volumes
+Mor19v 3D-MoRSE - signal 19 / weighted by atomic van der Waals volumes
+Mor20v 3D-MoRSE - signal 20 / weighted by atomic van der Waals volumes
+Mor21v 3D-MoRSE - signal 21 / weighted by atomic van der Waals volumes
+Mor22v 3D-MoRSE - signal 22 / weighted by atomic van der Waals volumes
+Mor23v 3D-MoRSE - signal 23 / weighted by atomic van der Waals volumes
+Mor24v 3D-MoRSE - signal 24 / weighted by atomic van der Waals volumes
+Mor25v 3D-MoRSE - signal 25 / weighted by atomic van der Waals volumes
+Mor26v 3D-MoRSE - signal 26 / weighted by atomic van der Waals volumes
+Mor27v 3D-MoRSE - signal 27 / weighted by atomic van der Waals volumes
+Mor28v 3D-MoRSE - signal 28 / weighted by atomic van der Waals volumes
+Mor29v 3D-MoRSE - signal 29 / weighted by atomic van der Waals volumes
+Mor30v 3D-MoRSE - signal 30 / weighted by atomic van der Waals volumes
+Mor31v 3D-MoRSE - signal 31 / weighted by atomic van der Waals volumes
+Mor32v 3D-MoRSE - signal 32 / weighted by atomic van der Waals volumes
+Mor01e 3D-MoRSE - signal 01 / weighted by atomic Sanderson electronegativities
+Mor02e 3D-MoRSE - signal 02 / weighted by atomic Sanderson electronegativities
+Mor03e 3D-MoRSE - signal 03 / weighted by atomic Sanderson electronegativities
+Mor04e 3D-MoRSE - signal 04 / weighted by atomic Sanderson electronegativities
+Mor05e 3D-MoRSE - signal 05 / weighted by atomic Sanderson electronegativities
+Mor06e 3D-MoRSE - signal 06 / weighted by atomic Sanderson electronegativities
+Mor07e 3D-MoRSE - signal 07 / weighted by atomic Sanderson electronegativities
+Mor08e 3D-MoRSE - signal 08 / weighted by atomic Sanderson electronegativities
+Mor09e 3D-MoRSE - signal 09 / weighted by atomic Sanderson electronegativities
+Mor10e 3D-MoRSE - signal 10 / weighted by atomic Sanderson electronegativities
+Mor11e 3D-MoRSE - signal 11 / weighted by atomic Sanderson electronegativities
+Mor12e 3D-MoRSE - signal 12 / weighted by atomic Sanderson electronegativities
+Mor13e 3D-MoRSE - signal 13 / weighted by atomic Sanderson electronegativities
+Mor14e 3D-MoRSE - signal 14 / weighted by atomic Sanderson electronegativities
+Mor15e 3D-MoRSE - signal 15 / weighted by atomic Sanderson electronegativities
+Mor16e 3D-MoRSE - signal 16 / weighted by atomic Sanderson electronegativities
+Mor17e 3D-MoRSE - signal 17 / weighted by atomic Sanderson electronegativities
+Mor18e 3D-MoRSE - signal 18 / weighted by atomic Sanderson electronegativities
+Mor19e 3D-MoRSE - signal 19 / weighted by atomic Sanderson electronegativities
+Mor20e 3D-MoRSE - signal 20 / weighted by atomic Sanderson electronegativities
+Mor21e 3D-MoRSE - signal 21 / weighted by atomic Sanderson electronegativities
+Mor22e 3D-MoRSE - signal 22 / weighted by atomic Sanderson electronegativities
+Mor23e 3D-MoRSE - signal 23 / weighted by atomic Sanderson electronegativities
+Mor24e 3D-MoRSE - signal 24 / weighted by atomic Sanderson electronegativities
+Mor25e 3D-MoRSE - signal 25 / weighted by atomic Sanderson electronegativities
+Mor26e 3D-MoRSE - signal 26 / weighted by atomic Sanderson electronegativities
+Mor27e 3D-MoRSE - signal 27 / weighted by atomic Sanderson electronegativities
+Mor28e 3D-MoRSE - signal 28 / weighted by atomic Sanderson electronegativities
+Mor29e 3D-MoRSE - signal 29 / weighted by atomic Sanderson electronegativities
+Mor30e 3D-MoRSE - signal 30 / weighted by atomic Sanderson electronegativities
+Mor31e 3D-MoRSE - signal 31 / weighted by atomic Sanderson electronegativities
+Mor32e 3D-MoRSE - signal 32 / weighted by atomic Sanderson electronegativities
+Mor01p 3D-MoRSE - signal 01 / weighted by atomic polarizabilities
+Mor02p 3D-MoRSE - signal 02 / weighted by atomic polarizabilities
+Mor03p 3D-MoRSE - signal 03 / weighted by atomic polarizabilities
+Mor04p 3D-MoRSE - signal 04 / weighted by atomic polarizabilities
+Mor05p 3D-MoRSE - signal 05 / weighted by atomic polarizabilities
+Mor06p 3D-MoRSE - signal 06 / weighted by atomic polarizabilities
+Mor07p 3D-MoRSE - signal 07 / weighted by atomic polarizabilities
+Mor08p 3D-MoRSE - signal 08 / weighted by atomic polarizabilities
+Mor09p 3D-MoRSE - signal 09 / weighted by atomic polarizabilities
+Mor10p 3D-MoRSE - signal 10 / weighted by atomic polarizabilities
+Mor11p 3D-MoRSE - signal 11 / weighted by atomic polarizabilities
+Mor12p 3D-MoRSE - signal 12 / weighted by atomic polarizabilities
+Mor13p 3D-MoRSE - signal 13 / weighted by atomic polarizabilities
+Mor14p 3D-MoRSE - signal 14 / weighted by atomic polarizabilities
+Mor15p 3D-MoRSE - signal 15 / weighted by atomic polarizabilities
+Mor16p 3D-MoRSE - signal 16 / weighted by atomic polarizabilities
+Mor17p 3D-MoRSE - signal 17 / weighted by atomic polarizabilities
+Mor18p 3D-MoRSE - signal 18 / weighted by atomic polarizabilities
+Mor19p 3D-MoRSE - signal 19 / weighted by atomic polarizabilities
+Mor20p 3D-MoRSE - signal 20 / weighted by atomic polarizabilities
+Mor21p 3D-MoRSE - signal 21 / weighted by atomic polarizabilities
+Mor22p 3D-MoRSE - signal 22 / weighted by atomic polarizabilities
+Mor23p 3D-MoRSE - signal 23 / weighted by atomic polarizabilities
+Mor24p 3D-MoRSE - signal 24 / weighted by atomic polarizabilities
+Mor25p 3D-MoRSE - signal 25 / weighted by atomic polarizabilities
+Mor26p 3D-MoRSE - signal 26 / weighted by atomic polarizabilities
+Mor27p 3D-MoRSE - signal 27 / weighted by atomic polarizabilities
+Mor28p 3D-MoRSE - signal 28 / weighted by atomic polarizabilities
+Mor29p 3D-MoRSE - signal 29 / weighted by atomic polarizabilities
+Mor30p 3D-MoRSE - signal 30 / weighted by atomic polarizabilities
+Mor31p 3D-MoRSE - signal 31 / weighted by atomic polarizabilities
+Mor32p 3D-MoRSE - signal 32 / weighted by atomic polarizabilities
+L1u 1st component size directional WHIM index / unweighted
+L2u 2nd component size directional WHIM index / unweighted
+L3u 3rd component size directional WHIM index / unweighted
+P1u 1st component shape directional WHIM index / unweighted
+P2u 2nd component shape directional WHIM index / unweighted
+G1u 1st component symmetry directional WHIM index / unweighted
+G2u 2st component symmetry directional WHIM index / unweighted
+G3u 3st component symmetry directional WHIM index / unweighted
+E1u 1st component accessibility directional WHIM index / unweighted
+E2u 2nd component accessibility directional WHIM index / unweighted
+E3u 3rd component accessibility directional WHIM index / unweighted
+L1m 1st component size directional WHIM index / weighted by atomic masses
+L2m 2nd component size directional WHIM index / weighted by atomic masses
+L3m 3rd component size directional WHIM index / weighted by atomic masses
+P1m 1st component shape directional WHIM index / weighted by atomic masses
+P2m 2nd component shape directional WHIM index / weighted by atomic masses
+G1m 1st component symmetry directional WHIM index / weighted by atomic masses
+G2m 2st component symmetry directional WHIM index / weighted by atomic masses
+G3m 3st component symmetry directional WHIM index / weighted by atomic masses
+E1m 1st component accessibility directional WHIM index / weighted by atomic masses
+E2m 2nd component accessibility directional WHIM index / weighted by atomic masses
+E3m 3rd component accessibility directional WHIM index / weighted by atomic masses
+L1v 1st component size directional WHIM index / weighted by atomic van der Waals volumes
+L2v 2nd component size directional WHIM index / weighted by atomic van der Waals volumes
+L3v 3rd component size directional WHIM index / weighted by atomic van der Waals volumes
+P1v 1st component shape directional WHIM index / weighted by atomic van der Waals volumes
+P2v 2nd component shape directional WHIM index / weighted by atomic van der Waals volumes
+G1v 1st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+G2v 2st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+G3v 3st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+E1v 1st component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+E2v 2nd component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+E3v 3rd component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+L1e 1st component size directional WHIM index / weighted by atomic Sanderson electronegativities
+L2e 2nd component size directional WHIM index / weighted by atomic Sanderson electronegativities
+L3e 3rd component size directional WHIM index / weighted by atomic Sanderson electronegativities
+P1e 1st component shape directional WHIM index / weighted by atomic Sanderson electronegativities
+P2e 2nd component shape directional WHIM index / weighted by atomic Sanderson electronegativities
+G1e 1st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+G2e 2st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+G3e 3st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+E1e 1st component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+E2e 2nd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+E3e 3rd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+L1p 1st component size directional WHIM index / weighted by atomic polarizabilities
+L2p 2nd component size directional WHIM index / weighted by atomic polarizabilities
+L3p 3rd component size directional WHIM index / weighted by atomic polarizabilities
+P1p 1st component shape directional WHIM index / weighted by atomic polarizabilities
+P2p 2nd component shape directional WHIM index / weighted by atomic polarizabilities
+G1p 1st component symmetry directional WHIM index / weighted by atomic polarizabilities
+G2p 2st component symmetry directional WHIM index / weighted by atomic polarizabilities
+G3p 3st component symmetry directional WHIM index / weighted by atomic polarizabilities
+E1p 1st component accessibility directional WHIM index / weighted by atomic polarizabilities
+E2p 2nd component accessibility directional WHIM index / weighted by atomic polarizabilities
+E3p 3rd component accessibility directional WHIM index / weighted by atomic polarizabilities
+L1s 1st component size directional WHIM index / weighted by atomic electrotopological states
+L2s 2nd component size directional WHIM index / weighted by atomic electrotopological states
+L3s 3rd component size directional WHIM index / weighted by atomic electrotopological states
+P1s 1st component shape directional WHIM index / weighted by atomic electrotopological states
+P2s 2nd component shape directional WHIM index / weighted by atomic electrotopological states
+G1s 1st component symmetry directional WHIM index / weighted by atomic electrotopological states
+G2s 2st component symmetry directional WHIM index / weighted by atomic electrotopological states
+G3s 3st component symmetry directional WHIM index / weighted by atomic electrotopological states
+E1s 1st component accessibility directional WHIM index / weighted by atomic electrotopological states
+E2s 2nd component accessibility directional WHIM index / weighted by atomic electrotopological states
+E3s 3rd component accessibility directional WHIM index / weighted by atomic electrotopological states
+Tu T total size index / unweighted
+Tm T total size index / weighted by atomic masses
+Tv T total size index / weighted by atomic van der Waals volumes
+Te T total size index / weighted by atomic Sanderson electronegativities
+Tp T total size index / weighted by atomic polarizabilities
+Ts T total size index / weighted by atomic electrotopological states
+Au A total size index / unweighted
+Am A total size index / weighted by atomic masses
+Av A total size index / weighted by atomic van der Waals volumes
+Ae A total size index / weighted by atomic Sanderson electronegativities
+Ap A total size index / weighted by atomic polarizabilities
+As A total size index / weighted by atomic electrotopological states
+Gu G total symmetry index / unweighted
+Gm G total symmetry index / weighted by atomic masses
+Gs G total symmetry index / weighted by atomic electrotopological states
+Ku K global shape index / unweighted
+Km K global shape index / weighted by atomic masses
+Kv K global shape index / weighted by atomic van der Waals volumes
+Ke K global shape index / weighted by atomic Sanderson electronegativities
+Kp K global shape index / weighted by atomic polarizabilities
+Ks K global shape index / weighted by atomic electrotopological states
+Du D total accessibility index / unweighted
+Dm D total accessibility index / weighted by atomic masses
+Dv D total accessibility index / weighted by atomic van der Waals volumes
+De D total accessibility index / weighted by atomic Sanderson electronegativities
+Dp D total accessibility index / weighted by atomic polarizabilities
+Ds D total accessibility index / weighted by atomic electrotopological states
+Vu V total size index / unweighted
+Vm V total size index / weighted by atomic masses
+Vv V total size index / weighted by atomic van der Waals volumes
+Ve V total size index / weighted by atomic Sanderson electronegativities
+Vp V total size index / weighted by atomic polarizabilities
+Vs V total size index / weighted by atomic electrotopological states
+ITH total information content on the leverage equality
+ISH standardized information content on the leverage equality
+HIC mean information content on the leverage magnitude
+HGM geometric mean on the leverage magnitude
+H0u H autocorrelation of lag 0 / unweighted
+H1u H autocorrelation of lag 1 / unweighted
+H2u H autocorrelation of lag 2 / unweighted
+H3u H autocorrelation of lag 3 / unweighted
+H4u H autocorrelation of lag 4 / unweighted
+H5u H autocorrelation of lag 5 / unweighted
+H6u H autocorrelation of lag 6 / unweighted
+H7u H autocorrelation of lag 7 / unweighted
+H8u H autocorrelation of lag 8 / unweighted
+HTu H total index / unweighted
+HATS0u leverage-weighted autocorrelation of lag 0 / unweighted
+HATS1u leverage-weighted autocorrelation of lag 1 / unweighted
+HATS2u leverage-weighted autocorrelation of lag 2 / unweighted
+HATS3u leverage-weighted autocorrelation of lag 3 / unweighted
+HATS4u leverage-weighted autocorrelation of lag 4 / unweighted
+HATS5u leverage-weighted autocorrelation of lag 5 / unweighted
+HATS6u leverage-weighted autocorrelation of lag 6 / unweighted
+HATS7u leverage-weighted autocorrelation of lag 7 / unweighted
+HATS8u leverage-weighted autocorrelation of lag 8 / unweighted
+HATSu leverage-weighted total index / unweighted
+H0m H autocorrelation of lag 0 / weighted by atomic masses
+H1m H autocorrelation of lag 1 / weighted by atomic masses
+H2m H autocorrelation of lag 2 / weighted by atomic masses
+H3m H autocorrelation of lag 3 / weighted by atomic masses
+H4m H autocorrelation of lag 4 / weighted by atomic masses
+H5m H autocorrelation of lag 5 / weighted by atomic masses
+H6m H autocorrelation of lag 6 / weighted by atomic masses
+H7m H autocorrelation of lag 7 / weighted by atomic masses
+H8m H autocorrelation of lag 8 / weighted by atomic masses
+HTm H total index / weighted by atomic masses
+HATS0m leverage-weighted autocorrelation of lag 0 / weighted by atomic masses
+HATS1m leverage-weighted autocorrelation of lag 1 / weighted by atomic masses
+HATS2m leverage-weighted autocorrelation of lag 2 / weighted by atomic masses
+HATS3m leverage-weighted autocorrelation of lag 3 / weighted by atomic masses
+HATS4m leverage-weighted autocorrelation of lag 4 / weighted by atomic masses
+HATS5m leverage-weighted autocorrelation of lag 5 / weighted by atomic masses
+HATS6m leverage-weighted autocorrelation of lag 6 / weighted by atomic masses
+HATS7m leverage-weighted autocorrelation of lag 7 / weighted by atomic masses
+HATS8m leverage-weighted autocorrelation of lag 8 / weighted by atomic masses
+HATSm leverage-weighted total index / weighted by atomic masses
+H0v H autocorrelation of lag 0 / weighted by atomic van der Waals volumes
+H1v H autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+H2v H autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+H3v H autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+H4v H autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+H5v H autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+H6v H autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+H7v H autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+H8v H autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+HTv H total index / weighted by atomic van der Waals volumes
+HATS0v leverage-weighted autocorrelation of lag 0 / weighted by atomic van der Waals volumes
+HATS1v leverage-weighted autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+HATS2v leverage-weighted autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+HATS3v leverage-weighted autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+HATS4v leverage-weighted autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+HATS5v leverage-weighted autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+HATS6v leverage-weighted autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+HATS7v leverage-weighted autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+HATS8v leverage-weighted autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+HATSv leverage-weighted total index / weighted by atomic van der Waals volumes
+H0e H autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities
+H1e H autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+H2e H autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+H3e H autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+H4e H autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+H5e H autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+H6e H autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+H7e H autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+H8e H autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+HTe H total index / weighted by atomic Sanderson electronegativities
+HATS0e leverage-weighted autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities
+HATS1e leverage-weighted autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+HATS2e leverage-weighted autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+HATS3e leverage-weighted autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+HATS4e leverage-weighted autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+HATS5e leverage-weighted autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+HATS6e leverage-weighted autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+HATS7e leverage-weighted autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+HATS8e leverage-weighted autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+HATSe leverage-weighted total index / weighted by atomic Sanderson electronegativities
+H0p H autocorrelation of lag 0 / weighted by atomic polarizabilities
+H1p H autocorrelation of lag 1 / weighted by atomic polarizabilities
+H2p H autocorrelation of lag 2 / weighted by atomic polarizabilities
+H3p H autocorrelation of lag 3 / weighted by atomic polarizabilities
+H4p H autocorrelation of lag 4 / weighted by atomic polarizabilities
+H5p H autocorrelation of lag 5 / weighted by atomic polarizabilities
+H6p H autocorrelation of lag 6 / weighted by atomic polarizabilities
+H7p H autocorrelation of lag 7 / weighted by atomic polarizabilities
+H8p H autocorrelation of lag 8 / weighted by atomic polarizabilities
+HTp H total index / weighted by atomic polarizabilities
+HATS0p leverage-weighted autocorrelation of lag 0 / weighted by atomic polarizabilities
+HATS1p leverage-weighted autocorrelation of lag 1 / weighted by atomic polarizabilities
+HATS2p leverage-weighted autocorrelation of lag 2 / weighted by atomic polarizabilities
+HATS3p leverage-weighted autocorrelation of lag 3 / weighted by atomic polarizabilities
+HATS4p leverage-weighted autocorrelation of lag 4 / weighted by atomic polarizabilities
+HATS5p leverage-weighted autocorrelation of lag 5 / weighted by atomic polarizabilities
+HATS6p leverage-weighted autocorrelation of lag 6 / weighted by atomic polarizabilities
+HATS7p leverage-weighted autocorrelation of lag 7 / weighted by atomic polarizabilities
+HATS8p leverage-weighted autocorrelation of lag 8 / weighted by atomic polarizabilities
+HATSp leverage-weighted total index / weighted by atomic polarizabilities
+RCON Randic-type R matrix connectivity
+RARS R matrix average row sum
+REIG first eigenvalue of the R matrix
+R1u R autocorrelation of lag 1 / unweighted
+R2u R autocorrelation of lag 2 / unweighted
+R3u R autocorrelation of lag 3 / unweighted
+R4u R autocorrelation of lag 4 / unweighted
+R5u R autocorrelation of lag 5 / unweighted
+R6u R autocorrelation of lag 6 / unweighted
+R7u R autocorrelation of lag 7 / unweighted
+R8u R autocorrelation of lag 8 / unweighted
+RTu R total index / unweighted
+R1u+ R maximal autocorrelation of lag 1 / unweighted
+R2u+ R maximal autocorrelation of lag 2 / unweighted
+R3u+ R maximal autocorrelation of lag 3 / unweighted
+R4u+ R maximal autocorrelation of lag 4 / unweighted
+R5u+ R maximal autocorrelation of lag 5 / unweighted
+R6u+ R maximal autocorrelation of lag 6 / unweighted
+R7u+ R maximal autocorrelation of lag 7 / unweighted
+R8u+ R maximal autocorrelation of lag 8 / unweighted
+RTu+ R maximal index / unweighted
+R1m R autocorrelation of lag 1 / weighted by atomic masses
+R2m R autocorrelation of lag 2 / weighted by atomic masses
+R3m R autocorrelation of lag 3 / weighted by atomic masses
+R4m R autocorrelation of lag 4 / weighted by atomic masses
+R5m R autocorrelation of lag 5 / weighted by atomic masses
+R6m R autocorrelation of lag 6 / weighted by atomic masses
+R7m R autocorrelation of lag 7 / weighted by atomic masses
+R8m R autocorrelation of lag 8 / weighted by atomic masses
+RTm R total index / weighted by atomic masses
+R1m+ R maximal autocorrelation of lag 1 / weighted by atomic masses
+R2m+ R maximal autocorrelation of lag 2 / weighted by atomic masses
+R3m+ R maximal autocorrelation of lag 3 / weighted by atomic masses
+R4m+ R maximal autocorrelation of lag 4 / weighted by atomic masses
+R5m+ R maximal autocorrelation of lag 5 / weighted by atomic masses
+R6m+ R maximal autocorrelation of lag 6 / weighted by atomic masses
+R7m+ R maximal autocorrelation of lag 7 / weighted by atomic masses
+R8m+ R maximal autocorrelation of lag 8 / weighted by atomic masses
+RTm+ R maximal index / weighted by atomic masses
+R1v R autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+R2v R autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+R3v R autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+R4v R autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+R5v R autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+R6v R autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+R7v R autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+R8v R autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+RTv R total index / weighted by atomic van der Waals volumes
+R1v+ R maximal autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+R2v+ R maximal autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+R3v+ R maximal autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+R4v+ R maximal autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+R5v+ R maximal autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+R6v+ R maximal autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+R7v+ R maximal autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+R8v+ R maximal autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+RTv+ R maximal index / weighted by atomic van der Waals volumes
+R1e R autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+R2e R autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+R3e R autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+R4e R autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+R5e R autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+R6e R autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+R7e R autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+R8e R autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+RTe R total index / weighted by atomic Sanderson electronegativities
+R1e+ R maximal autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+R2e+ R maximal autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+R3e+ R maximal autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+R4e+ R maximal autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+R5e+ R maximal autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+R6e+ R maximal autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+R7e+ R maximal autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+R8e+ R maximal autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+RTe+ R maximal index / weighted by atomic Sanderson electronegativities
+R1p R autocorrelation of lag 1 / weighted by atomic polarizabilities
+R2p R autocorrelation of lag 2 / weighted by atomic polarizabilities
+R3p R autocorrelation of lag 3 / weighted by atomic polarizabilities
+R4p R autocorrelation of lag 4 / weighted by atomic polarizabilities
+R5p R autocorrelation of lag 5 / weighted by atomic polarizabilities
+R6p R autocorrelation of lag 6 / weighted by atomic polarizabilities
+R7p R autocorrelation of lag 7 / weighted by atomic polarizabilities
+R8p R autocorrelation of lag 8 / weighted by atomic polarizabilities
+RTp R total index / weighted by atomic polarizabilities
+R1p+ R maximal autocorrelation of lag 1 / weighted by atomic polarizabilities
+R2p+ R maximal autocorrelation of lag 2 / weighted by atomic polarizabilities
+R3p+ R maximal autocorrelation of lag 3 / weighted by atomic polarizabilities
+R4p+ R maximal autocorrelation of lag 4 / weighted by atomic polarizabilities
+R5p+ R maximal autocorrelation of lag 5 / weighted by atomic polarizabilities
+R6p+ R maximal autocorrelation of lag 6 / weighted by atomic polarizabilities
+R7p+ R maximal autocorrelation of lag 7 / weighted by atomic polarizabilities
+R8p+ R maximal autocorrelation of lag 8 / weighted by atomic polarizabilities
+RTp+ R maximal index / weighted by atomic polarizabilities
+nCp number of terminal primary C(sp3) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nCs number of total secondary C(sp3) Y = H or any heteroatom
+nCt number of total tertiary C(sp3) Y = H or any heteroatom
+nCq number of total quaternary C(sp3)
+nCrs number of ring secondary C(sp3) Y = H or any heteroatom
+nCrt number of ring tertiary C(sp3) Y = H or any heteroatom
+nCrq number of ring quaternary C(sp3)
+nCar number of aromatic C(sp2)
+nCbH number of unsubstituted benzene C(sp2)
+nCb– number of substituted benzene C(sp2) Y = carbon or any heteroatom
+nCconj number of non-aromatic conjugated C(sp2)
+nR=Cp number of terminal primary C(sp2) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nR=Cs number of aliphatic secondary C(sp2) Y = H or any heteroatom
+nR=Ct number of aliphatic tertiary C(sp2)
+n=C= number of allenes groups
+nR#CH/X number of terminal C(sp) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nR#C– number of non-terminal C(sp) Y = C or any non-terminal heteroatom
+nROCN number of cyanates (aliphatic)
+nArOCN number of cyanates (aromatic)
+nRNCO number of isocyanates (aliphatic)
+nArNCO number of isocyanates (aromatic)
+nRSCN number of thiocyanates (aliphatic)
+nArSCN number of thiocyanates (aromatic)
+nRNCS number of isothiocyanates (aliphatic)
+nArNCS number of isothiocyanates (aromatic)
+nRCOOH number of carboxylic acids (aliphatic)
+nArCOOH number of carboxylic acids (aromatic)
+nRCOOR number of esters (aliphatic) Y = Ar or Al (not H)Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Al = H or aliphatic group linked through C
+nArCOOR number of esters (aromatic) Y = Al or Ar
+nRCONH2 number of primary amides (aliphatic) Al = H or aliphatic group linked through C
+nArCONH2 number of primary amides (aromatic)
+nRCONHR number of secondary amides (aliphatic) Â Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C
+nArCONHR number of secondary amides (aromatic) Y = Ar or Al (not H, not C = O)
+nRCONR2 number of tertiary amides (aliphatic) Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C
+nArCONR2 number of tertiary amides (aromatic) Y = Ar or Al (not H, not C = O)
+nROCON number of (thio-) carbamates (aliphatic) Y = O or S Al = H or aliphatic group linked through any atom
+nArOCON number of (thio-) carbamates (aromatic) Y1 = O or S Y2 = H or aliphatic or aromatic group linked through any atom Ar = aromatic group linked through any atom
+nRCOX number of acyl halogenides (aliphatic)
+nArCOX number of acyl halogenides (aromatic)
+nRCSOH number of thioacids (aliphatic)
+nArCSOH number of thioacids (aromatic)
+nRCSSH number of dithioacids (aliphatic)
+nArCSSH number of dithioacids (aromatic)
+nRCOSR number of thioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C
+nArCOSR number of thioesters (aromatic)
+nRCSSR number of dithioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C
+nArCSSR number of dithioesters (aromatic) Y = Ar or Al (not H)
+nRCHO number of aldehydes (aliphatic)
+nArCHO number of aldehydes (aromatic)
+nRCO number of ketones (aliphatic)
+nArCO number of ketones (aromatic) Y = Al or Ar
+nCONN number of urea (-thio) derivatives Y = O or S
+nC=O(OR)2 number of carbonate (-thio) derivatives Y = O or S
+nN=C-N< number of amidine derivatives Y = C or H
+nC(=N)N2 number of guanidine derivatives
+nRC=N number of imines (aliphatic) Y = H,C or N (two-connected) Al = H or aliphatic group linked through C
+nArC=N number of imines (aromatic) Y = H,C or N (two-connected)
+nRCNO number of oximes (aliphatic) Y = H, Ar or Al
+nArCNO number of oximes (aromatic) Y = H, Ar or Al
+nRNH2 number of primary amines (aliphatic) Al = aliphatic group linked through C (not C = O)
+nArNH2 number of primary amines (aromatic)
+nRNHR number of secondary amines (aliphatic) Al = aliphatic group linked through C (not C = O)
+nArNHR number of secondary amines (aromatic) Y = Ar or Al (not C = O)
+nRNR2 number of tertiary amines (aliphatic) Al = aliphatic group linked through C (not C = O)
+nArNR2 number of tertiary amines (aromatic) Y = Ar or Al (not C = O)
+nN-N number of N hydrazines Y = C or H
+nN=N number of N azo-derivatives Y = C or H
+nRCN number of nitriles (aliphatic)
+nArCN number of nitriles (aromatic)
+nN+ number of positive charged N
+nNq number of quaternary N
+nRNHO number of hydroxylamines (aliphatic) Y = H, Al or Ar
+nArNHO number of hydroxylamines (aromatic) Y = H, Al or Ar
+nRNNOx number of N-nitroso groups (aliphatic) Al = H or aliphatic group linked through C
+nArNNOx number of N-nitroso groups (aromatic) Y = H, Al or Ar
+nRNO number of nitroso groups (aliphatic)
+nArNO number of nitroso groups (aromatic)
+nRNO2 number of nitro groups (aliphatic) Al = H or aliphatic group linked through carbon
+nArNO2 number of nitro groups (aromatic) Al = aromatic group linked through carbon
+nN(CO)2 number of imides (thio-) Y = H or CÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Y1 = O or S
+nC=N-N< number of hydrazones Y = C or H
+nROH number of hydroxyl groups Al = aliphatic group linked through any atom
+nArOH number of aromatic hydroxyls Ar = aromatic group linked through any atom
+nOHp number of primary alcohols
+nOHs number of secondary alcohols
+nOHt number of tertiary alcohols
+nROR number of ethers (aliphatic) Al = aliphatic group linked through C (not CÂ =Â O, not CÂ #Â N)
+nArOR number of ethers (aromatic) Y = Ar or Al (not CÂ =Â O, not CÂ #Â N)
+nROX number of hypohalogenides (aliphatic)
+nArOX number of hypohalogenides (aromatic)
+nO(C=O)2 number of anhydrides (thio-) Y = O or S
+nH2O number of water molecules
+nSH number of thiols
+nC=S number of thioketones
+nRSR number of sulfides
+nRSSR number of disulfides
+nSO number of sulfoxides
+nS(=O)2 number of sulfones
+nSOH number of sulfenic (thio-) acids Y = O or S
+nSOOH number of sulfinic (thio-/dithio-)acids Y = O or S
+nSO2OH number of sulfonic (thio-/dithio-) acids Y = O or S
+nSO3OH number of sulfuric (thio-/dithio-) acids Y = O or S
+nSO2 number of sulfites (thio-/ dithio-) Y = O or S
+nSO3 number of sulfonates (thio- / dithio-) Y = O or S
+nSO4 number of sulfates (thio- / dithio-) Y = O or S
+nSO2N number of sulfonamides / sulfinamides / sulfenamides (thio- / dithio-)
+nPO3 number of phosphites / thiophosphites Y = O or S
+nPO4 number of phosphates / thiophosphates Y = O or S
+nPR3 number of phosphanes Y = H, C, halogens
+nP(=O)O2R number of phosphonates / thiophosphonates Y = O or S Y1 = H, C, halogens
+nP(=O)R3/nPR5 number of phosphoranes / thiophosphoranes Y = O or S
+nCH2RX number of CH2RX
+nCHR2X number of CHR2X
+nCR3X number of CR3X
+nR=CHX number of R=CHX
+nR=CRX number of R=CRX
+nR#CX number of R#CX
+nCHRX2 number of CHRX2
+nCR2X2 number of CR2X2
+nR=CX2 number of R=CX2
+nCRX3 number of CRX3
+nArX number of X on aromatic ring
+nCXr number of X on ring C(sp3)
+nCXr= number of X on ring C(sp2)
+nCconjX number of X on exo-conjugated C
+nAziridines number of Aziridines
+nOxiranes number of Oxiranes
+nThiranes number of Thiranes
+nAzetidines number of Azetidines
+nOxetanes number of Oxetanes
+nThioethanes number of Thioethanes
+nBeta-Lactams number of Beta-Lactams
+nPyrrolidines number of Pyrrolidines
+nOxolanes number of Oxolanes
+nth-Thiophenes number of tetrahydro-Thiophenes
+nPyrroles number of Pyrroles
+nPyrazoles number of Pyrazoles
+nImidazoles number of Imidazoles
+nFuranes number of Furanes
+nThiophenes number of Thiophenes
+nOxazoles number of Oxazoles
+nIsoxazoles number of Isoxazoles
+nThiazoles number of Thiazoles
+nIsothiazoles number of Isothiazoles
+nTriazoles number of Triazoles
+nPyridines number of Pyridines
+nPyridazines number of Pyridazines
+nPyrimidines number of Pyrimidines
+nPyrazines number of Pyrazines
+n135-Triazines number of 135-Triazines
+n124-Triazines number of 124-Triazines
+nHDon number of donor atoms for H-bonds (N and O)
+nHAcc number of acceptor atoms for H-bonds (N, O, F)
+nHBonds number of intramolecular H-bonds Y1 = B, N, O, Al, P, S Y2 = N, O, F The geometric distance between H and Y2 must be in the range 1 - 2,7 A.
+C-001 CH3R / CH4
+C-002 CH2R2
+C-003 CHR3
+C-004 CR4
+C-005 CH3X
+C-006 CH2RX
+C-007 CH2X2
+C-008 CHR2X
+C-009 CHRX2
+C-010 CHX3
+C-011 CR3X
+C-012 CR2X2
+C-013 CRX3
+C-014 CX4
+C-015 =CH2
+C-016 =CHR
+C-017 =CR2
+C-018 =CHX
+C-019 =CRX
+C-020 =CX2
+C-021 #CH
+C-022 #CR / R=C=R
+C-023 #CX
+C-024 R--CH--R
+C-025 R--CR--R
+C-026 R--CX--R
+C-027 R--CH--X
+C-028 R--CR--X
+C-029 R--CX--X
+C-030 X--CH--X
+C-031 X--CR--X
+C-032 X--CX--X
+C-033 R--CH..X
+C-034 R--CR..X
+C-035 R--CX..X
+C-036 Al-CH=X
+C-037 Ar-CH=X
+C-038 Al-C(=X)-Al
+C-039 Ar-C(=X)-R
+C-040 R-C(=X)-X / R-C#X / X=C=X
+C-041 X-C(=X)-X
+C-042 X--CH..X
+C-043 X--CR..X
+C-044 X--CX..X
+U-045 undefined
+H-046 Ha attached to C0(sp3) no X attached to next C
+H-047 Ha attached to C1(sp3) / C0(sp2)
+H-048 Ha attached to C2(sp3) / C1(sp2) / C0(sp)
+H-049 Ha attached to C3(sp3) / C2(sp2) / C3(sp2) / C3(sp)
+H-050 H attached to heteroatom
+H-051 H attached to alpha-Cb
+H-052 Ha attached to C0(sp3) with 1X attached to next C
+H-053 Ha attached to C0(sp3) with 2X attached to next C
+H-054 Ha attached to C0(sp3) with 3X attached to next C
+H-055 Ha attached to C0(sp3) with 4X attached to next C
+O-056 alcohol
+O-057 phenol / enol / carboxyl OH
+O-058 =O
+O-059 Al-O-Al
+O-060 Al-O-Ar / Ar-O-Ar / R..O..R / R-O-C=X
+O-061 O-- c
+O-062 O- (negatively charged)
+O-063 R-O-O-R
+Se-064 Any-Se-Any
+Se-065 =Se
+N-066 Al-NH2
+N-067 Al2-NH
+N-068 Al3-N
+N-069 Ar-NH2 / X-NH2
+N-070 Ar-NH-Al
+N-071 Ar-NAl2
+N-072 RCO-N< / >N-X=X
+N-073 Ar2NH / Ar3N / Ar2N-Al / R..N..Rd
+N-074 R#N / R=N-
+N-075 R--N--Re / R--N--X
+N-076 Ar-NO2 / R--N(--R)--Of / RO-NO
+N-077 Al-NO2
+N-078 Ar-N=X / X-N=X
+N-079 N+ (positively charged)
+U-080 undefined
+F-081 Fa attached to C1(sp3)
+F-082 Fa attached to C2(sp3)
+F-083 Fa attached to C3(sp3)
+F-084 Fa attached to C1(sp2)
+F-085 Fa attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+Cl-086 Cla attached to C1(sp3)
+Cl-087 Cla attached to C2(sp3)
+Cl-088 Cla attached to C3(sp3)
+Cl-089 Cla attached to C1(sp2)
+Cl-090 Cla attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+Br-091 Bra attached to C1(sp3)
+Br-092 Bra attached to C2(sp3)
+Br-093 Bra attached to C3(sp3)
+Br-094 Bra attached to C1(sp2)
+Br-095 Bra attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+I-096 Ia attached to C1(sp3)
+I-097 Ia attached to C2(sp3)
+I-098 Ia attached to C3(sp3)
+I-099 Ia attached to C1(sp2)
+I-100 Ia attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+F-101 fluoride ion
+Cl-102 chloride ion
+Br-103 bromide ion
+I-104 iodide ion
+U-105 undefined
+S-106 R-SH
+S-107 R2S / RS-SR
+S-108 R=S
+S-109 R-SO-R
+S-110 R-SO2-R
+Si-111 >Si<
+B-112 >B- as in boranes
+U-113 undefined
+U-114 undefined
+P-115 P ylids
+P-116 R3-P=X
+P-117 X3-P=X (phosphate)
+P-118 PX3 (phosphite)
+P-119 PR3 (phosphine)
+P-120 C-P(X)2=X (phosphonate)
+qpmax maximum positive charge
+qnmax maximum negative charge
+Qpos total positive charge
+Qneg total negative charge
+Qtot total absolute charge (electronic charge index - ECI)
+Qmean mean absolute charge (charge polarization)
+Q2 total squared charge
+RPCG relative positive charge
+RNCG relative negative charge
+SPP submolecular polarity parameter
+TE1 topological electronic descriptor
+TE2 topological electronic descriptor (bond resctricted)
+PCWTe partial charge weighted topological electronic descriptor
+LDI local dipole index
+Ui unsaturation index
+Hy hydrophilic factor
+AMR molar refractivity
+TPSA(NO) topological polar surface area using N, O polar contributions
+TPSA(tot) topological polar surface area using N, O, S, P polar contributions
+MLogP Moriguchi octanol-water partition coefficient
+MLOGP2 Squared Moriguchi octanol-water partition coeff. (logP^2)
+ALOGP Ghose-Crippen octanol-water partition coeff. (logP)
+ALOGP2 Squared Ghose-Crippen octanol-water partition coeff. (logP^2)
+LAI Lipinski alert index
+GVWAI-80 Ghose-Viswanadhan-Wendoloski drug-like index at 80%
+GVWAI-50 Ghose-Viswanadhan-Wendoloski drug-like index at 50%
+Inflammat-80 Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 80%
+Inflammat-50 Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 50%
+Depressant-80 Ghose-Viswanadhan-Wendoloski antidepressant-like index at 80%
+Depressant-50 Ghose-Viswanadhan-Wendoloski antidepressant-like index at 50%
+Psychotic-80 Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 80%
+Psychotic-50 Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 50%
+Hypertens-80 Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 80%
+Hypertens-50 Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 50%
+Hypnotic-80 Ghose-Viswanadhan-Wendoloski hypnotic-like index at 80%
+Hypnotic-50 Ghose-Viswanadhan-Wendoloski hypnotic-like index at 50%
+Neoplastic-80 Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 80%
+Neoplastic-50 Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 50%
+Infective-80 Ghose-Viswanadhan-Wendoloski antiinfective-like index at 80%
+Infective-50 Ghose-Viswanadhan-Wendoloski antiinfective-like index at 50%
+BLTF96 Verhaar model of Fish base-line toxicity for Fish (96h) from MLOGP (mmol/l)
+BLTD48 Verhaar model of Daphnia base-line toxicity for Daphnia (48h) from MLOGP (mmol/l)
+BLTA96 Verhaar model of Algae base-line toxicity for Algae (96h) from MLOGP (mmol/l)
+B01[C-C] presence/absence of C-C at topological distance 1
+B01[C-N] presence/absence of C-N at topological distance 1
+B01[C-O] presence/absence of C-O at topological distance 1
+B01[C-S] presence/absence of C-S at topological distance 1
+B01[C-P] presence/absence of C-P at topological distance 1
+B01[C-F] presence/absence of C-F at topological distance 1
+B01[C-Cl] presence/absence of C-Cl at topological distance 1
+B01[C-Br] presence/absence of C-Br at topological distance 1
+B01[C-I] presence/absence of C-I at topological distance 1
+B01[C-B] presence/absence of C-B at topological distance 1
+B01[C-Si] presence/absence of C-Si at topological distance 1
+B01[C-X] presence/absence of C-X at topological distance 1
+B01[N-N] presence/absence of N-N at topological distance 1
+B01[N-O] presence/absence of N-O at topological distance 1
+......... ..........................................................
+B10[Si-X] presence/absence of Si-X at topological distance 10
+B10[X-X] presence/absence of X-X at topological distance 10
+F01[C-C] frequency of C-C at topological distance 1
+F01[C-N] frequency of C-N at topological distance 1
+F01[C-O] frequency of C-O at topological distance 1
+F01[C-S] frequency of C-S at topological distance 1
+F01[C-P] frequency of C-P at topological distance 1
+F01[C-F] frequency of C-F at topological distance 1
+F01[C-Cl] frequency of C-Cl at topological distance 1
+F01[C-Br] frequency of C-Br at topological distance 1
+F01[C-I] frequency of C-I at topological distance 1
+F01[C-B] frequency of C-B at topological distance 1
+F01[C-Si] frequency of C-Si at topological distance 1
+F01[C-X] frequency of C-X at topological distance 1
+F01[N-N] frequency of N-N at topological distance 1
+F01[N-O] frequency of N-O at topological distance 1
+......... ..........................................................
+F10[Si-X] frequency of Si-X at topological distance 10
+F10[X-X] frequency of X-X at topological distance 10
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/XRAY/spacegroups.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/XRAY/spacegroups.dat Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,4926 @@
+P 1 1
+(X,Y,Z)
+
+P 1- 2
+(X,Y,Z)
+(-X,-Y,-Z)
+
+P -1 2
+(X,Y,Z)
+(-X,-Y,-Z)
+
+P 2 2
+(X,Y,Z)
+(-X,Y,-Z)
+
+P 1 21 1 2
+(X,Y,Z)
+(-X,Y+1/2,-Z)
+
+P 21 2
+(X,Y,Z)
+(-X,Y+1/2,-Z)
+
+C 1 2 1 4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,1/2+Y,Z)
+(1/2-X,1/2+Y,-Z)
+
+C 2 4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,1/2+Y,Z)
+(1/2-X,1/2+Y,-Z)
+
+P M 2
+(X,Y,Z)
+(X,-Y,Z)
+
+P C 2
+(X,Y,Z)
+(X,-Y,1/2+Z)
+
+C M 4
+(X,Y,Z)
+(X,-Y,Z)
+(1/2+X,1/2+Y,Z)
+(1/2+X,1/2-Y,Z)
+
+C C 4
+(X,Y,Z)
+(X,-Y,1/2+Z)
+(1/2+X,1/2+Y,Z)
+(1/2+X,1/2-Y,1/2+Z)
+
+P 2/M 4
+(X,Y,Z)
+(X,-Y,Z)
+(-X,Y,-Z)
+(-X,-Y,-Z)
+
+P 21/M 4
+(X,Y,Z)
+(-X,1/2+Y,-Z)
+(-X,-Y,-Z)
+(X,1/2-Y,Z)
+
+C 2/M 8
+(X,Y,Z)
+(X,-Y,Z)
+(-X,Y,-Z)
+(-X,-Y,-Z)
+(1/2+X,1/2+Y,Z)
+(1/2+X,1/2-Y,Z)
+(1/2-X,1/2+Y,-Z)
+(1/2-X,1/2-Y,-Z)
+
+P 2/C 4
+(X,Y,Z)
+(-X,Y,1/2-Z)
+(-X,-Y,-Z)
+(X,-Y,1/2+Z)
+
+P 21/C 4
+(X,Y,Z)
+(-X,-Y,-Z)
+(-X,1/2+Y,1/2-Z)
+(X,1/2-Y,1/2+Z)
+
+C 2/C 8
+(X,Y,Z)
+(-X,Y,1/2-Z)
+(-X,-Y,-Z)
+(X,-Y,1/2+Z)
+(1/2+X,1/2+Y,Z)
+(1/2-X,1/2+Y,1/2-Z)
+(1/2-X,1/2-Y,-Z)
+(1/2+X,1/2-Y,1/2+Z)
+
+P 2 2 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(-X,Y,-Z)
+(X,-Y,-Z)
+
+P 2 2 21 4
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+(-X,Y,1/2-Z)
+(X,-Y,-Z)
+
+P 21 21 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(1/2-X,1/2+Y,-Z)
+(1/2+X,1/2-Y,-Z)
+
+P 21 21 21 4
+(X,Y,Z)
+(1/2-X,-Y,1/2+Z)
+(-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,-Z)
+
+C 2 2 21 8
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+(-X,Y,1/2-Z)
+(X,-Y,-Z)
+(1/2+X,1/2+Y,Z)
+(1/2-X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,-Z)
+
+C 2 2 2 8
+(X,Y,Z)
+(-X,-Y,Z)
+(-X,Y,-Z)
+(X,-Y,-Z)
+(1/2+X,1/2+Y,Z)
+(1/2-X,1/2-Y,Z)
+(1/2-X,1/2+Y,-Z)
+(1/2+X,1/2-Y,-Z)
+
+F 2 2 2 16
+(X,Y,Z)
+(-X,-Y,Z)
+(-X,Y,-Z)
+(X,-Y,-Z)
+(X,1/2+Y,1/2+Z)
+(-X,1/2-Y,1/2+Z)
+(-X,1/2+Y,1/2-Z)
+(X,1/2-Y,1/2-Z)
+(1/2+X,Y,1/2+Z)
+(1/2-X,-Y,1/2+Z)
+(1/2-X,Y,1/2-Z)
+(1/2+X,-Y,1/2-Z)
+(1/2+X,1/2+Y,Z)
+(1/2-X,1/2-Y,Z)
+(1/2-X,1/2+Y,-Z)
+(1/2+X,1/2-Y,-Z)
+
+I 2 2 2 8
+(X,Y,Z)
+(-X,-Y,Z)
+(X,-Y,-Z)
+(-X,Y,-Z)
+(X+1/2,Y+1/2,Z+1/2)
+(-X+1/2,-Y+1/2,Z+1/2)
+(X+1/2,-Y+1/2,-Z+1/2)
+(-X+1/2,Y+1/2,-Z+1/2)
+
+I 21 21 21 8
+(X,Y,Z)
+(1/2-X,-Y,1/2+Z)
+(-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,-Z)
+(1/2+X,1/2+Y,1/2+Z)
+(-X,1/2-Y,Z)
+(1/2-X,Y,-Z)
+(X,-Y,1/2-Z)
+
+P M M 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(X,-Y,Z)
+(-X,Y,Z)
+
+P M C 21 4
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+(X,-Y,1/2+Z)
+(-X,Y,Z)
+
+P C C 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(X,-Y,1/2+Z)
+(-X,Y,1/2+Z)
+
+P M A 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(1/2+X,-Y,Z)
+(1/2-X,Y,Z)
+
+P C A 21 4
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+(1/2+X,-Y,Z)
+(1/2-X,Y,1/2+Z)
+
+P N C 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(X,1/2-Y,1/2+Z)
+(-X,1/2+Y,1/2+Z)
+
+P M N 21 4
+(X,Y,Z)
+(1/2-X,-Y,1/2+Z)
+(1/2+X,-Y,1/2+Z)
+(-X,Y,Z)
+
+P B A 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(1/2+X,1/2-Y,Z)
+(1/2-X,1/2+Y,Z)
+
+P N A 21 4
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+(1/2+X,1/2-Y,Z)
+(1/2-X,1/2+Y,1/2+Z)
+
+P N N 2 4
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+(1/4+Y,1/4-X,3/4+Z)
+(1/4-Y,3/4+X,1/4+Z)
+(3/4+X,1/4+Z,1/4-Y)
+(1/4-X,3/4+Z,1/4+Y)
+(3/4-X,3/4-Z,3/4-Y)
+(1/4+X,1/4-Z,3/4+Y)
+(3/4+Z,1/4+Y,1/4-X)
+(1/4+Z,1/4-Y,3/4+X)
+(1/4-Z,3/4+Y,1/4+X)
+(3/4-Z,3/4-Y,3/4-X)
+(-X,-Y,-Z)
+(1/2+X,Y,1/2-Z)
+(X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,Z)
+(-Z,-X,-Y)
+(1/2-Z,1/2+X,Y)
+(1/2+Z,X,1/2-Y)
+(Z,1/2-X,1/2+Y)
+(-Y,-Z,-X)
+(Y,1/2-Z,1/2+X)
+(1/2-Y,1/2+Z,X)
+(1/2+Y,Z,1/2-X)
+(1/4-Y,3/4-X,3/4+Z)
+(1/4+Y,1/4+X,1/4+Z)
+(3/4-Y,3/4+X,1/4-Z)
+(3/4+Y,1/4-X,3/4-Z)
+(1/4-X,3/4-Z,3/4+Y)
+(3/4+X,1/4-Z,3/4-Y)
+(1/4+X,1/4+Z,1/4+Y)
+(3/4-X,3/4+Z,1/4-Y)
+(1/4-Z,3/4-Y,3/4+X)
+(3/4-Z,3/4+Y,1/4-X)
+(3/4+Z,1/4-Y,3/4-X)
+(1/4+Z,1/4+Y,1/4+X)
+(1/2+X,1/2+Y,1/2+Z)
+(-X,1/2-Y,Z)
+(1/2-X,Y,-Z)
+(X,-Y,1/2-Z)
+(1/2+Z,1/2+X,1/2+Y)
+(Z,-X,1/2-Y)
+(-Z,1/2-X,Y)
+(1/2-Z,X,-Y)
+(1/2+Y,1/2+Z,1/2+X)
+(1/2-Y,Z,-X)
+(Y,-Z,1/2-X)
+(-Y,1/2-Z,X)
+(1/4+Y,3/4+X,3/4-Z)
+(1/4-Y,1/4-X,1/4-Z)
+(3/4+Y,3/4-X,1/4+Z)
+(3/4-Y,1/4+X,3/4+Z)
+(1/4+X,3/4+Z,3/4-Y)
+(3/4-X,1/4+Z,3/4+Y)
+(1/4-X,1/4-Z,1/4-Y)
+(3/4+X,3/4-Z,1/4+Y)
+(1/4+Z,3/4+Y,3/4-X)
+(3/4+Z,3/4-Y,1/4+X)
+(3/4-Z,1/4+Y,3/4+X)
+(1/4-Z,1/4-Y,1/4-X)
+(1/2-X,1/2-Y,1/2-Z)
+(X,1/2+Y,-Z)
+(1/2+X,-Y,Z)
+(-X,Y,1/2+Z)
+(1/2-Z,1/2-X,1/2-Y)
+(-Z,X,1/2+Y)
+(Z,1/2+X,-Y)
+(1/2+Z,-X,Y)
+(1/2-Y,1/2-Z,1/2-X)
+(1/2+Y,-Z,X)
+(-Y,Z,1/2+X)
+(Y,1/2+Z,-X)
+(3/4-Y,1/4-X,1/4+Z)
+(3/4+Y,3/4+X,3/4+Z)
+(1/4-Y,1/4+X,3/4-Z)
+(1/4+Y,3/4-X,1/4-Z)
+(3/4-X,1/4-Z,1/4+Y)
+(1/4+X,3/4-Z,1/4-Y)
+(3/4+X,3/4+Z,3/4+Y)
+(1/4-X,1/4+Z,3/4-Y)
+(3/4-Z,1/4-Y,1/4+X)
+(1/4-Z,1/4+Y,3/4-X)
+(1/4+Z,3/4-Y,1/4-X)
+(3/4+Z,3/4+Y,3/4+X)
+
+B 2 4
+(X,Y,Z)
+(-X,-Y,Z)
+(1/2+X,+Y,1/2+Z)
+(1/2-X,-Y,1/2+Z)
+
+P 1 1 21 2
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+
+P 2 21 21 4
+(X,Y,Z)
+(X,-Y,-Z)
+(-X,1/2+Y,1/2-Z)
+(-X,1/2-Y,1/2+Z)
+
+P 21 2 21 4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,-Y,1/2-Z)
+(1/2-X,-Y,1/2+Z)
+
+I 1 2 1 4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,1/2+Y,1/2+Z)
+(1/2-X,1/2+Y,1/2-Z)
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/atomtyping/AMBERTypes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/AMBERTypes.dat Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,61 @@
+CT 6 4 * * * *
+C 6 3 * * * (XA1)
+CN 6 3 * * [RG5,RG6,AR1.AR2.AR3] (C3,C3,N3(H))
+CB 6 3 * * [RG5,RG6,AR1.AR2.AR3] *
+CR 6 3 * * [RG5,AR1.AR2.AR3] (N3,N3)
+CR 6 3 * * [RG5,AR1.AR2.AR3] (N2,N3(H))
+CK 6 3 * * [RG5,AR1.AR2.AR3] (N2,N3)
+CC 6 3 0 * [RG5,AR1.AR2.AR3] (C3,N3(C3,H))
+CC 6 3 0 * [RG5,AR1.AR2.AR3] (C3,N2(C3))
+CW 6 3 * * [RG5,AR1.AR2.AR3] (C3,N3(H))
+CV 6 3 * * [RG5,AR1.AR2.AR3] (C3,N2)
+C* 6 3 * * [RG5,AR1.AR2.AR3] (C3,C3)
+CQ 6 3 * * [RG6,AR1.AR2.AR3] (N2,N2)
+CM 6 3 * * [RG6,AR1.AR2.AR3] (C3,C3(N2(C3(N3(C3)))))
+CM 6 3 * * [RG6,AR1.AR2.AR3] (C3,C3(N3(C3(N3(C3)))))
+CM 6 3 * * [RG6,AR1.AR2.AR3] (C3,N3(C3(N2(C3(C3)))))
+CM 6 3 * * [RG6,AR1.AR2.AR3] (N3,C3(C3(N3(C3(N3)))))
+CA 6 3 * * [AR1.AR2.AR3] *
+CD 6 3 * * * (C3,C3)
+CM 6 3 * * * *
+CZ 6 2 * * * *
+H 1 1 * * * (N)
+HS 1 1 * * * (S)
+HP 1 1 * * * (C(N4))
+HW 1 1 * * * (O(H1))
+HO 1 1 * * * (O)
+H1 1 1 * 1 * (C4)
+H2 1 1 * 2 * (C4)
+H3 1 1 * 3 * (C4)
+HC 1 1 * * * (C4)
+H4 1 1 * 1 * (XX[AR1.AR2.AR3])
+H5 1 1 * 2 * (XX[AR1.AR2.AR3])
+HA 1 1 * * * (XX[AR1.AR2.AR3])
+F 9 1 * * * *
+Cl 17 1 * * * *
+Br 35 1 * * * *
+I 53 1 * * * *
+N1 7 1 * * * *
+NB 7 2 * * [RG5,AR1.AR2.AR3] *
+NC 7 2 * * [RG6,AR1.AR2.AR3] *
+N2 7 -1 * * * (C3(N3,N3))
+NO 7 -1 * * * (O1,O1)
+NA 7 3 1 * [RG5.RG6,AR1.AR2.AR3] *
+N2 7 3 * * [NR] (XX[AR1.AR2.AR3])
+N* 7 3 * * [AR1.AR2.AR3] *
+N 7 3 * * * (C3(XA1))
+NT 7 3 * * * *
+N3 7 4 * * * *
+O2 8 1 * * * (C(O1))
+O2 8 1 * * * (P)
+O 8 1 * * * (C)
+O 8 1 * * * (S)
+OH 8 2 1 * * *
+OW 8 2 2 * * *
+OS 8 2 * * * *
+SH 16 2 1 * * *
+SH 16 2 2 * * *
+S 16 2 * * * *
+SO 16 4 * * * *
+LP 0 -1 * * * *
+DU -1 -1 * * * *
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/atomtyping/GAFFTypes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/GAFFTypes.dat Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,208 @@
+cx 6 4 * * [RG3] *
+cy 6 4 * * [RG4] *
+c3 6 4 * * * *
+c 6 3 * * [2DL] (XA1)
+c 6 3 * * [1DB,0DL] (XA1)
+c 6 3 * * [3sb] (XA1)
+cz 6 3 * * * (N3,N3,N3)
+cp 6 3 * * [AR1,1RG6] (XX[AR1],XX[AR1],XX[AR1])
+ca 6 3 * * [AR1] *
+cc 6 3 * * [sb,db,AR2] (C3(C3))
+cc 6 3 * * [sb,db,AR2] (C3(C2))
+cc 6 3 * * [sb,db,AR2] (C3(XB2))
+cc 6 3 * * [sb,db,AR2] (XB2(XB2))
+cc 6 3 * * [sb,db,AR2] (XB2(C2))
+cc 6 3 * * [sb,db,AR2] (XB2(C3))
+cc 6 3 * * [sb,db,AR2] (C3[sb'])
+cc 6 3 * * [sb,db,AR2] (XB2[sb'])
+cc 6 3 * * [sb,db,AR2] (XD3[sb',db])
+cc 6 3 * * [sb,db,AR2] (XD4[sb',db])
+cc 6 3 * * [sb,db,AR3] (C3(C3))
+cc 6 3 * * [sb,db,AR3] (C3(C2))
+cc 6 3 * * [sb,db,AR3] (C3(XB2))
+cc 6 3 * * [sb,db,AR3] (XB2(XB2))
+cc 6 3 * * [sb,db,AR3] (XB2(C2))
+cc 6 3 * * [sb,db,AR3] (XB2(C3))
+cc 6 3 * * [sb,db,AR3] (C3[sb'])
+cc 6 3 * * [sb,db,AR3] (XB2[sb'])
+cc 6 3 * * [sb,db,AR3] (XD3[sb',db])
+cc 6 3 * * [sb,db,AR3] (XD4[sb',db])
+ce 6 3 * * [sb,db] (C3[SB'])
+ce 6 3 * * [sb,db] (C2[SB'])
+ce 6 3 * * [sb,db] (XB2[SB'])
+ce 6 3 * * [sb,db] (XD3[SB',db])
+ce 6 3 * * [sb,db] (XD4[SB',db])
+cu 6 3 * * [RG3] *
+cv 6 3 * * [RG4] *
+c2 6 3 * * * *
+cg 6 2 * * [sb,tb] (C2[SB'])
+cg 6 2 * * [sb,tb] (C3[SB'])
+cg 6 2 * * [sb,tb] (N1[SB'])
+cg 6 2 * * [sb,tb] (XB2[SB'])
+c1 6 2 * * * *
+c1 6 1 * * * *
+hn 1 1 * * * (N)
+ho 1 1 * * * (O)
+hs 1 1 * * * (S)
+hp 1 1 * * * (P)
+hx 1 1 * * * (C(N4))
+hw 1 1 * * * (O(H1))
+h3 1 1 * 3 * (C4)
+h2 1 1 * 2 * (C4)
+h1 1 1 * 1 * (C4)
+hc 1 1 * * * (C4)
+h5 1 1 * 2 * (C3)
+h4 1 1 * 1 * (C3)
+ha 1 1 * * * *
+f 9 -1 * * * *
+cl 17 -1 * * * *
+br 35 -1 * * * *
+i 53 -1 * * * *
+pc 15 2 * * [sb,db,AR2] (C3(C3))
+pc 15 2 * * [sb,db,AR2] (C3(C2))
+pc 15 2 * * [sb,db,AR2] (C3(XB2))
+pc 15 2 * * [sb,db,AR2] (XB2(C3))
+pc 15 2 * * [sb,db,AR2] (XB2(C2))
+pc 15 2 * * [sb,db,AR2] (XB2(XB2))
+pc 15 2 * * [sb,db,AR2] (C3[sb'])
+pc 15 2 * * [sb,db,AR2] (C2[sb'])
+pc 15 2 * * [sb,db,AR2] (XB2[sb'])
+pc 15 2 * * [sb,db,AR2] (XD3[sb',db])
+pc 15 2 * * [sb,db,AR2] (XD4[sb',db])
+pc 15 2 * * [sb,db,AR3] (C3(C3))
+pc 15 2 * * [sb,db,AR3] (C3(C2))
+pc 15 2 * * [sb,db,AR3] (C3(XB2))
+pc 15 2 * * [sb,db,AR3] (XB2(C3))
+pc 15 2 * * [sb,db,AR3] (XB2(C2))
+pc 15 2 * * [sb,db,AR3] (XB2(XB2))
+pc 15 2 * * [sb,db,AR3] (C3[sb'])
+pc 15 2 * * [sb,db,AR3] (C2[sb'])
+pc 15 2 * * [sb,db,AR3] (XB2[sb'])
+pc 15 2 * * [sb,db,AR3] (XD3[sb',db])
+pc 15 2 * * [sb,db,AR3] (XD4[sb',db])
+pb 15 2 * * [AR1] *
+pe 15 2 * * [sb,db] (C3[sb'])
+pe 15 2 * * [sb,db] (C2[SB'])
+pe 15 2 * * [sb,db] (XA1[SB'])
+pe 15 2 * * [sb,db] (XB2[SB'])
+pe 15 2 * * [sb,db] (XD3[SB',DB])
+pe 15 2 * * [sb,db] (XD4[SB',DB])
+p2 15 2 * * * *
+p2 15 1 * * * *
+px 15 3 * * [db] (XB2[sb'])
+px 15 3 * * [db] (C3[sb'])
+px 15 3 * * [db] (XD3[sb',db])
+px 15 3 * * [db] (XD4[sb',db])
+p4 15 3 * * [db] (XA1)
+p3 15 3 * * * *
+py 15 4 * * [db] (XB2[sb'])
+py 15 4 * * [db] (C3[sb'])
+py 15 4 * * [db] (XD3[sb',db])
+py 15 4 * * [db] (XD4[sb',db])
+p5 15 4 * * * *
+p5 15 5 * * * *
+p5 15 6 * * * *
+n 7 3 * * * (C3(XA1))
+n4 7 4 * * * *
+no 7 3 * * * (O1,O1)
+na 7 3 * * [AR1.AR2.AR3] *
+nh 7 3 * * * (XX[AR1.AR2.AR3])
+nh 7 3 * * * (C3[DB])
+nh 7 3 * * * (N2[DB])
+nh 7 3 * * * (P2[DB])
+n3 7 3 * * * *
+nb 7 2 * * [AR1] *
+nc 7 2 * * [sb,db,AR2] (C3(C3))
+nc 7 2 * * [sb,db,AR2] (C3(C2))
+nc 7 2 * * [sb,db,AR2] (C3(XB2))
+nc 7 2 * * [sb,db,AR2] (XB2(C3))
+nc 7 2 * * [sb,db,AR2] (XB2(C2))
+nc 7 2 * * [sb,db,AR2] (XB2(XB2))
+nc 7 2 * * [sb,db,AR2] (C3[sb'])
+nc 7 2 * * [sb,db,AR2] (XB2[sb'])
+nc 7 2 * * [sb,db,AR2] (XD3[sb',db])
+nc 7 2 * * [sb,db,AR2] (XD4[sb',db])
+nc 7 2 * * [sb,db,AR3] (C3(C3))
+nc 7 2 * * [sb,db,AR3] (C3(C2))
+nc 7 2 * * [sb,db,AR3] (C3(XB2))
+nc 7 2 * * [sb,db,AR3] (XB2(C3))
+nc 7 2 * * [sb,db,AR3] (XB2(C2))
+nc 7 2 * * [sb,db,AR3] (XB2(XB2))
+nc 7 2 * * [sb,db,AR3] (C3[sb'])
+nc 7 2 * * [sb,db,AR3] (XB2[sb'])
+nc 7 2 * * [sb,db,AR3] (XD3[sb',db])
+nc 7 2 * * [sb,db,AR3] (XD4[sb',db])
+ne 7 2 * * [sb,db] (C2[SB'])
+ne 7 2 * * [sb,db] (C3[SB'])
+ne 7 2 * * [sb,db] (XA1[SB'])
+ne 7 2 * * [sb,db] (XB2[SB'])
+ne 7 2 * * [sb,db] (XD3[SB',db])
+ne 7 2 * * [sb,db] (XD4[SB',db])
+n1 7 2 * * [2db] *
+n1 7 2 * * [tb,sb] *
+n2 7 2 * * * *
+n1 7 1 * * * *
+o 8 1 * * * *
+oh 8 2 1 * * *
+oh 8 2 2 * * *
+oh 8 3 1 * * *
+oh 8 3 2 * * *
+oh 8 3 3 * * *
+os 8 2 * * * *
+os 8 3 * * * *
+os 8 -1 * * * *
+s 16 1 * * * *
+s2 16 2 * * [DB] *
+s2 16 2 * * [TB] *
+sh 16 2 1 * * *
+sh 16 2 2 * * *
+ss 16 2 * * * *
+sx 16 3 * * [db] (XB2[sb'])
+sx 16 3 * * [db] (C3[sb'])
+sx 16 3 * * [db] (XD3[sb',db])
+sx 16 3 * * [db] (XD4[sb',db])
+s4 16 3 * * * *
+sy 16 4 * * [db] (XB2[sb'])
+sy 16 4 * * [db] (C3[sb'])
+sy 16 4 * * [db] (XD3[sb',db])
+sy 16 4 * * [db] (XD4[sb',db])
+s6 16 4 * * * *
+s6 16 5 * * * *
+s6 16 6 * * * *
+Li 3 -1 * * * *
+Be 4 -1 * * * *
+B 5 -1 * * * *
+Na 11 -1 * * * *
+Mg 12 -1 * * * *
+Al 13 -1 * * * *
+Si 14 -1 * * * *
+K 19 -1 * * * *
+Ca 20 -1 * * * *
+Sr 38 -1 * * * *
+Ba 56 -1 * * * *
+Sc 21 -1 * * * *
+Ti 22 -1 * * * *
+V 23 -1 * * * *
+Cr 24 -1 * * * *
+Mn 25 -1 * * * *
+Fe 26 -1 * * * *
+Co 27 -1 * * * *
+Ni 28 -1 * * * *
+Cu 29 -1 * * * *
+Zn 30 -1 * * * *
+Ga 31 -1 * * * *
+Ge 32 -1 * * * *
+As 33 -1 * * * *
+Se 34 -1 * * * *
+Ru 44 -1 * * * *
+Rh 45 -1 * * * *
+Pd 46 -1 * * * *
+Ag 47 -1 * * * *
+Cd 48 -1 * * * *
+Pt 78 -1 * * * *
+Au 79 -1 * * * *
+Hg 80 -1 * * * *
+Tl 81 -1 * * * *
+Pb 82 -1 * * * *
+lp 0 1 * * * *
+DU -1 -1 * * * *
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/atomtyping/SYBYLTypes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/SYBYLTypes.dat Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,66 @@
+C.3 6 4 * * * *
+C.cat 6 3 * * * (N3,N3,N3)
+C.ar 6 3 * * [AR1] *
+C.2 6 3 * * * *
+C.1 6 2 * * * *
+C.1 6 1 * * * *
+H 1 -1 * * * *
+F 9 -1 * * * *
+Cl 17 -1 * * * *
+Br 35 -1 * * * *
+I 53 -1 * * * *
+P.3 15 -1 * * * *
+N.4 7 4 * * * *
+N.am 7 3 * * * (C3(XA1))
+N.pl3 7 3 * * * (O1,O1)
+N.pl3 7 3 * * [AR1.AR2.AR3] *
+N.3 7 3 * * * *
+N.ar 7 2 * * [AR1] *
+N.2 7 2 * * * *
+N.1 7 1 * * * *
+O.co2 8 1 * * * (C3(O1))
+O.co2 8 1 * * * (P(O1))
+O.2 8 1 * * * *
+O.3 8 2 * * * *
+S.2 16 1 * * * *
+S.3 16 2 * * * *
+S.o 16 3 * * * (O1[DB'])
+S.o2 16 4 * * * (O1[DB'],O1[DB'])
+s.3 16 -1 * * * *
+Li 3 -1 * * * *
+Be 4 -1 * * * *
+B 5 -1 * * * *
+Na 11 -1 * * * *
+Mg 12 -1 * * * *
+Al 13 -1 * * * *
+Si 14 -1 * * * *
+K 19 -1 * * * *
+Ca 20 -1 * * * *
+Sr 38 -1 * * * *
+Ba 56 -1 * * * *
+Sc 21 -1 * * * *
+Ti 22 -1 * * * *
+V 23 -1 * * * *
+Cr 24 -1 * * * *
+Mn 25 -1 * * * *
+Fe 26 -1 * * * *
+Co 27 -1 * * * *
+Ni 28 -1 * * * *
+Cu 29 -1 * * * *
+Zn 30 -1 * * * *
+Ga 31 -1 * * * *
+Ge 32 -1 * * * *
+As 33 -1 * * * *
+Se 34 -1 * * * *
+Ru 44 -1 * * * *
+Rh 45 -1 * * * *
+Pd 46 -1 * * * *
+Ag 47 -1 * * * *
+Cd 48 -1 * * * *
+Pt 78 -1 * * * *
+Au 79 -1 * * * *
+Hg 80 -1 * * * *
+Tl 81 -1 * * * *
+Pb 82 -1 * * * *
+lp 0 1 * * * *
+ANY -1 -1 * * * * *
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/bond_lengths/BondOrder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrder.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,366 @@
+
+
+
+
+
+ H
+ SMARTS([#1+])
+ 0
+
+
+ H
+ SMARTS([#1])
+ 0
+
+
+ F
+ SMARTS(F)
+ 64
+ 0
+ 64
+
+
+ Br
+ SMARTS(Br)
+ 64
+ 0
+ 64
+
+
+ I
+ SMARTS(I)
+ 64
+ 0
+ 64
+
+
+ C
+ SMARTS([$([#6D1](~[#7D2]))])
+ 0
+ 1
+ 32
+
+
+ C
+ SMARTS([#6D1])
+ 1
+ 0
+ 32
+
+
+ C
+ SMARTS([#6])
+ 64
+ 32
+ 0
+ 32
+ 64
+
+
+ Si
+ SMARTS(Si)
+ 0
+
+
+ N
+ SMARTS([$([#7D1](~[#7D2]))])
+ 0
+ 0
+
+
+ N
+ SMARTS([#7D1])
+ 3
+ 0
+ 32
+
+
+ N
+ SMARTS([$([#7D2](~[#7D1]))])
+ 1
+ 0
+
+
+ N
+ SMARTS([#7D2])
+ 4
+ 0
+ 2
+
+
+ N
+ SMARTS([$([#7D3](~[#8D1-,#16D1-])~[#8D1,#16D1])])
+ 32
+ 0
+ 32
+ 64
+
+
+ N
+ SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])
+ 64
+ 32
+ 0
+ 32
+
+
+ N
+
+ SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])
+ 1
+ 0
+
+
+ N
+ SMARTS([#7D3])
+ 32
+ 0
+ 1
+ 2
+
+
+ N
+ SMARTS([#7D4+])
+ 32
+ 0
+
+
+ N
+ SMARTS([#7D4])
+ 64
+ 0
+ 64
+
+
+ N
+ SMARTS([#7D5])
+ 0
+
+
+ O
+ SMARTS([#8D1-])
+ 0
+ 32
+
+
+ O
+ SMARTS([$([#8D1](~[#6D3]~[#8D1,#16D1]))])
+ 0
+ 0
+
+
+ O
+ SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(O)
+ 0
+ 1
+
+
+ O
+ SMARTS([#8D1])
+ 1
+ 0
+ 64
+
+
+ O
+ SMARTS([#8D2])
+ 32
+ 0
+ 64
+
+
+ O
+ SMARTS([#8D3])
+ 0
+
+
+ P
+ SMARTS(#15D1)
+ 2
+ 0
+ 32
+
+
+ P
+ SMARTS(#15D2)
+ 4
+ 0
+ 2
+
+
+ P
+ SMARTS(#15D3)
+ 32
+ 0
+ 1
+ 2
+
+
+ P
+
+ SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1,#8D1-,#16D1-])(~[#8D1-,#16D1-]))])
+ 0
+ 32
+
+
+ P
+
+ SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])
+ 32
+ 0
+ 32
+
+
+ P
+ SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])
+ 32
+ 0
+
+
+ P
+
+ SMARTS(#15D4)
+ 64
+ 1
+ 0
+ 32
+
+
+ S
+ SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)
+ 0
+ 1
+
+
+ S
+ SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])
+ 0
+ 0
+
+
+ S
+ SMARTS([#16D1])
+ 2
+ 0
+ 64
+
+
+ S
+ SMARTS([#16D2])
+ 2
+ 0
+ 64
+
+
+ S
+ SMARTS([#16D3])
+ 1
+ 0
+ 2
+ 2
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])
+ 0
+ 32
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1-,#16D1-])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])
+ 0
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])
+ 32
+ 0
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])
+ 32
+ 0
+
+
+ S
+ SMARTS([#16D4])
+ 4
+ 2
+ 0
+
+
+ S
+ SMARTS([#16D5])
+ 2
+ 0
+
+
+
+ Li
+ SMARTS([#3])
+ 0
+
+
+ Na
+ SMARTS([#11])
+ 0
+
+
+ Mg
+ SMARTS([#12])
+ 0
+
+
+ K
+ SMARTS([#19])
+ 0
+
+
+ Ca
+ SMARTS([#20])
+ 0
+
+
+ Cu
+ SMARTS([#29])
+ 0
+
+
+ Zn
+ SMARTS([#30])
+ 0
+
+
+ Fe
+ SMARTS([#26])
+ 0
+
+
+ Cl
+ SMARTS([#17-])
+ 0
+
+
+ Cl
+ SMARTS([#17])
+ 64
+ 0
+ 64
+ 128
+ 128
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/bond_lengths/BondOrderGAFF.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrderGAFF.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,306 @@
+
+
+
+
+ H
+ SMARTS([#1])
+ 64
+ 0
+ 64
+
+
+ F
+ SMARTS(F)
+ 64
+ 0
+ 64
+
+
+ Cl
+ SMARTS(Cl)
+ 64
+ 0
+ 64
+
+
+ Br
+ SMARTS(Br)
+ 64
+ 0
+ 64
+
+
+ I
+ SMARTS(I)
+ 64
+ 0
+ 64
+
+
+ C
+ SMARTS([$([#6D1](~[#7D2]))])
+
+ 0
+ 1
+ 32
+
+
+ C
+ SMARTS([#6D1])
+ 1
+ 0
+ 32
+
+
+ C
+ SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])
+ 32
+ 0
+ 32
+
+
+ C
+ SMARTS([#6])
+ 64
+ 32
+ 0
+ 32
+ 64
+
+
+ Si
+ SMARTS([#14])
+ 0
+
+
+ N
+ SMARTS([$([#7D1](~[#7D2]))])
+ 0
+ 0
+
+
+ N
+ SMARTS([#7D1])
+ 3
+ 0
+ 32
+
+
+ N
+ SMARTS([$([#7D2](~[#7D1]))])
+ 1
+ 0
+
+
+ N
+ SMARTS([#7D2])
+ 4
+ 0
+ 2
+
+
+ N
+ SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])
+ 64
+ 32
+ 0
+ 32
+
+
+ N
+
+ SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])
+ 1
+ 0
+
+
+ N
+ SMARTS([#7D3])
+ 32
+ 0
+ 1
+ 2
+
+
+ N
+ SMARTS([#7D4])
+ 64
+ 0
+ 64
+
+
+ O
+ SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(O)
+ 0
+ 1
+
+
+ O
+ SMARTS([#8D1])
+ 1
+ 0
+ 64
+
+
+ O
+ SMARTS([#8D2])
+ 32
+ 0
+ 64
+
+
+ P
+ SMARTS(#15D1)
+ 2
+ 0
+ 32
+
+
+ P
+ SMARTS(#15D2)
+ 4
+ 0
+ 2
+
+
+ P
+ SMARTS(#15D3)
+ 32
+ 0
+ 1
+ 2
+
+
+ P
+
+ SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])
+ 32
+ 0
+ 32
+
+
+ P
+ SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])
+ 32
+ 0
+
+
+ P
+
+ SMARTS(#15D4)
+ 64
+ 1
+ 0
+ 32
+
+
+ S
+ SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)
+ 0
+ 1
+
+
+ S
+ SMARTS([#16D1])
+ 2
+ 0
+ 64
+
+
+ S
+ SMARTS([#16D2])
+
+ 2
+ 0
+ 64
+
+
+ S
+ SMARTS([#16D3])
+ 1
+ 0
+ 2
+ 2
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])
+ 0
+ 32
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])
+ 32
+ 0
+
+
+ S
+ SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])
+ 32
+ 0
+
+
+ S
+ SMARTS([#16D4])
+ 4
+ 2
+ 0
+
+
+
+ Li
+ SMARTS([#3])
+ 0
+
+
+ Na
+ SMARTS([#11])
+ 0
+
+
+ Mg
+ SMARTS([#12])
+ 0
+
+
+ K
+ SMARTS([#19])
+ 0
+
+
+ Ca
+ SMARTS([#20])
+ 0
+
+
+ Cu
+ SMARTS([#29])
+ 0
+
+
+ Zn
+ SMARTS([#30])
+ 0
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/bond_lengths/bond_lengths.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,257 @@
+BondLengthsDB
+ 1
+ Names
+ Hydrogen
+ H
+
+ Partners
+ 6
+ BondLengths
+ max1.15
+ single1.09
+ min0.95
+
+
+ 7
+ BondLengths
+ max1.10
+ single1.03
+ min0.9
+
+
+ 8
+ BondLengths
+ max1.1
+ single0.96
+ min0.9
+
+
+ 15
+ BondLengths
+ max1.5
+ single1.0
+ min0.9
+
+
+ 16
+ BondLengths
+ max1.5
+ single1.34
+ min1.1
+
+
+
+
+ 6
+ Names
+ Carbon
+ C
+
+ Partners
+ 6
+ BondLengths
+ max1.75
+ single1.47
+ aromatic1.39
+ double1.34
+ triple1.18
+ min1.15
+
+
+ 7
+ BondLengths
+ max1.65
+ single1.38
+ aromatic1.33
+ double1.29
+ triple1.15
+ min1.1
+
+
+ 8
+ BondLengths
+ max1.55
+ single1.42
+ double1.20
+ min1.10
+
+
+ 9
+ BondLengths
+ max1.45
+ single1.38
+ min1.0
+
+
+ 15
+ BondLengths
+ max1.95
+ single1.8
+ min1.7
+
+
+ 16
+ BondLengths
+ max1.95
+ single1.70
+ double1.63
+ min1.5
+
+
+ 17
+ BondLengths
+ max1.9
+ single1.8
+ min1.0
+
+
+ 35
+ BondLengths
+ max2.05
+ single1.96
+ min1.0
+
+
+ 53
+ BondLengths
+ max2.3
+ single2.1
+ min1.0
+
+
+
+
+ 7
+ Names
+ Nitrogen
+ N
+
+ Partners
+ 7
+ BondLengths
+ max1.55
+ single1.40
+ aromatic1.32
+ double1.22
+ min1.0
+
+
+ 8
+ BondLengths
+ max1.5
+ single1.4
+ double1.21
+ min1.15
+
+
+ 9
+ BondLengths
+ max1.5
+ single1.35
+ min1.25
+
+
+ 15
+ BondLengths
+ max1.8
+ single1.68
+ aromatic1.60
+ double1.58
+ min1.5
+
+
+ 16
+ BondLengths
+ max1.80
+ single1.65
+ aromatic1.56
+ double1.54
+ min1.50
+
+
+ 17
+ BondLengths
+ max1.85
+ single1.74
+ min1.65
+
+
+ 35
+ BondLengths
+ max2.0
+ single1.84
+ min1.7
+
+
+
+
+ 8
+ Names
+ Oxygen
+ O
+
+ Partners
+ 8
+ BondLengths
+ max1.55
+ single1.47
+ min1.40
+
+
+ 15
+ BondLengths
+ max1.75
+ single1.59
+ double1.49
+ min1.40
+
+
+ 16
+ BondLengths
+ max1.75
+ single1.56
+ double1.43
+ min1.38
+
+
+
+
+ 15
+ Names
+ Phosphorus
+ P
+
+ Partners
+ 15
+ BondLengths
+ max2.3
+ single2.2
+ double2.0
+ min1.9
+
+
+ 16
+ BondLengths
+ max2.2
+ double1.95
+ min1.85
+
+
+
+
+ 16
+ Names
+ Sulfur
+ S
+
+ Partners
+ 16
+ BondLengths
+ max2.2
+ single2.07
+ min1.9
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,1505 @@
+[BondLengths]
+key:I key:deg_I key:J key:deg_J key:order value:r0
+@unit_r0=Angstrom
+;
+;
+; I deg_I J deg_J order r0
+ --- ------- --- ------- ------- ---------
+ C 1 C 1 1 1.508
+ C 1 C 2 1 1.508
+ C 1 C 3 1 1.508
+ C 1 C 4 1 1.5086
+ C 2 C 1 1 1.508
+ C 2 C 2 1 1.5086
+ C 2 C 3 1 1.5072
+ C 2 C 4 1 1.5093
+ C 3 C 1 1 1.508
+ C 3 C 2 1 1.5072
+ C 3 C 3 1 1.5066
+ C 3 C 4 1 1.51
+ C 4 C 1 1 1.5086
+ C 4 C 2 1 1.5093
+ C 4 C 3 1 1.51
+ C 4 C 4 1 1.5121
+ C 1 C 1 2 1.333
+ C 1 C 2 2 1.333
+ C 1 C 3 2 1.3333
+ C 1 C 4 2 1.344
+ C 2 C 1 2 1.333
+ C 2 C 2 2 1.3333
+ C 2 C 3 2 1.3341
+ C 2 C 4 2 1.3453
+ C 3 C 1 2 1.3333
+ C 3 C 2 2 1.3341
+ C 3 C 3 2 1.3358
+ C 3 C 4 2 1.3477
+ C 4 C 1 2 1.344
+ C 4 C 2 2 1.3453
+ C 4 C 3 2 1.3477
+ C 4 C 4 2 1.3624
+ C 1 C 1 3 1.192
+ C 1 C 2 3 1.4529
+ C 1 C 3 3 1.192
+ C 1 C 4 3 1.1917
+ C 2 C 1 3 1.452
+ C 2 C 2 3 1.211
+ C 2 C 3 3 1.3034
+ C 2 C 4 3 1.4768
+ C 3 C 1 3 1.192
+ C 3 C 2 3 1.299
+ C 3 C 3 3 1.3358
+ C 3 C 4 3 1.4835
+ C 4 C 1 3 1.1917
+ C 4 C 2 3 1.468
+ C 4 C 3 3 1.4833
+ C 4 C 4 3 1.5121
+ C 1 N 1 1 1.4556
+ C 1 N 2 1 1.4556
+ C 1 N 3 1 1.451
+ C 1 N 4 1 1.4801
+ C 1 N 5 1 1.5343
+ C 2 N 1 1 1.4556
+ C 2 N 3 1 1.4508
+ C 2 N 4 1 1.4808
+ C 3 N 1 1 1.4556
+ C 3 N 3 1 1.4507
+ C 3 N 4 1 1.4814
+ C 4 N 1 1 1.4545
+ C 4 N 3 1 1.452
+ C 4 N 4 1 1.4757
+ C 1 N 1 2 1.29
+ C 1 N 2 2 1.29
+ C 1 N 3 2 1.28
+ C 1 N 4 2 1.2913
+ C 1 N 5 2 1.2904
+ C 2 N 1 2 1.29
+ C 2 N 2 2 1.289
+ C 2 N 3 2 1.2811
+ C 2 N 4 2 1.2904
+ C 2 N 5 2 1.2901
+ C 3 N 1 2 1.2866
+ C 3 N 2 2 1.2868
+ C 3 N 3 2 1.2798
+ C 3 N 4 2 1.2881
+ C 3 N 5 2 1.2904
+ C 4 N 1 2 1.3265
+ C 4 N 2 2 1.3277
+ C 4 N 3 2 1.29
+ C 4 N 4 2 1.3347
+ C 4 N 5 2 1.3364
+ C 1 N 1 3 1.3756
+ C 1 N 2 3 1.2075
+ C 1 N 3 3 1.3756
+ C 1 N 4 3 1.4018
+ C 1 N 5 3 1.4163
+ C 2 N 1 3 1.1897
+ C 3 N 1 3 1.1154
+ C 4 N 1 3 1.3758
+ C 1 O 1 1 1.402
+ C 1 O 2 1 1.418
+ C 1 O 3 1 1.402
+ C 2 O 1 1 1.402
+ C 2 O 2 1 1.4184
+ C 2 O 3 1 1.4023
+ C 3 O 1 1 1.402
+ C 3 O 2 1 1.4176
+ C 3 O 3 1 1.4025
+ C 4 O 1 1 1.3246
+ C 4 O 2 1 1.4157
+ C 4 O 3 1 1.4014
+ C 1 O 1 2 1.222
+ C 1 O 2 2 1.29
+ C 1 O 3 2 1.222
+ C 2 O 1 2 1.222
+ C 2 O 2 2 1.2905
+ C 3 O 1 2 1.2246
+ C 3 O 2 2 1.2928
+ C 4 O 1 2 1.2649
+ C 4 O 2 2 1.3136
+ C 1 O 1 3 1.062
+ C 1 O 2 3 1.062
+ C 1 O 3 3 1.062
+ C 2 O 1 3 1.3947
+ C 2 O 3 3 1.4092
+ C 3 O 1 3 1.0599
+ C 3 O 3 3 1.3525
+ C 4 O 1 3 1.0617
+ C 4 O 3 3 1.4161
+ C 1 P 1 1 1.8346
+ C 1 P 2 1 1.8347
+ C 1 P 3 1 1.83
+ C 1 P 4 1 1.7992
+ C 1 P 5 1 2.0222
+ C 1 P 6 1 2.2431
+ C 2 P 1 1 1.8347
+ C 2 P 3 1 1.8304
+ C 2 P 4 1 1.7982
+ C 3 P 1 1 1.8347
+ C 3 P 3 1 1.8299
+ C 3 P 4 1 1.7971
+ C 4 P 1 1 1.8321
+ C 4 P 3 1 1.8344
+ C 4 P 4 1 1.7955
+ C 1 P 1 2 1.6347
+ C 1 P 2 2 1.71
+ C 1 P 3 2 1.6346
+ C 1 P 4 2 1.6475
+ C 1 P 5 2 1.6547
+ C 1 P 6 2 1.6704
+ C 2 P 1 2 1.6347
+ C 2 P 2 2 1.7099
+ C 3 P 1 2 1.6347
+ C 3 P 2 2 1.7011
+ C 4 P 1 2 1.6743
+ C 4 P 2 2 1.7554
+ C 1 P 1 3 1.4947
+ C 1 P 2 3 1.4947
+ C 1 P 3 3 1.4947
+ C 1 P 4 3 1.5018
+ C 1 P 5 3 1.5058
+ C 1 P 6 3 1.5137
+ C 2 P 1 3 1.7624
+ C 3 P 1 3 1.4947
+ C 4 P 1 3 1.494
+ C 1 S 1 1 1.801
+ C 1 S 2 1 1.805
+ C 1 S 3 1 1.805
+ C 1 S 4 1 1.7882
+ C 1 S 5 1 1.779
+ C 1 S 6 1 1.7789
+ C 2 S 1 1 1.801
+ C 2 S 2 1 1.8055
+ C 2 S 3 1 1.805
+ C 2 S 4 1 1.7875
+ C 2 S 5 1 1.778
+ C 2 S 6 1 1.7802
+ C 3 S 1 1 1.801
+ C 3 S 2 1 1.8052
+ C 3 S 3 1 1.8051
+ C 3 S 4 1 1.7868
+ C 3 S 5 1 1.777
+ C 3 S 6 1 1.777
+ C 4 S 1 1 1.8265
+ C 4 S 2 1 1.804
+ C 4 S 3 1 1.8042
+ C 4 S 4 1 1.786
+ C 4 S 5 1 1.7765
+ C 4 S 6 1 1.7805
+ C 1 S 1 2 1.665
+ C 1 S 2 2 1.665
+ C 1 S 3 2 1.665
+ C 1 S 4 2 1.6803
+ C 1 S 5 2 1.6889
+ C 1 S 6 2 1.7087
+ C 2 S 1 2 1.665
+ C 3 S 1 2 1.6701
+ C 4 S 1 2 1.7243
+ C 1 S 1 3 1.4584
+ C 1 S 2 3 1.4584
+ C 1 S 3 3 1.4584
+ C 1 S 4 3 1.4502
+ C 1 S 5 3 1.4442
+ C 1 S 6 3 1.4468
+ C 2 S 1 3 1.7357
+ C 2 S 2 3 1.7594
+ C 2 S 3 3 1.7704
+ C 2 S 4 3 1.741
+ C 2 S 5 3 1.7226
+ C 2 S 6 3 1.7233
+ C 3 S 1 3 1.7187
+ C 3 S 2 3 1.7203
+ C 3 S 3 3 1.7213
+ C 3 S 4 3 1.6958
+ C 3 S 5 3 1.6865
+ C 3 S 6 3 1.6844
+ C 4 S 1 3 1.8039
+ C 4 S 2 3 1.804
+ C 4 S 3 3 1.8042
+ C 4 S 4 3 1.786
+ C 4 S 5 3 1.7765
+ C 4 S 6 3 1.7805
+ C 1 H 1 1 1.093
+ C 2 H 1 1 1.093
+ C 3 H 1 1 1.093
+ C 4 H 1 1 1.0922
+ C 1 H 1 2 1.083
+ C 2 H 1 2 1.083
+ C 3 H 1 2 1.0826
+ C 4 H 1 2 1.0922
+ C 1 H 1 3 1.0907
+ C 2 H 1 3 1.0701
+ C 3 H 1 3 1.0826
+ C 4 H 1 3 1.0922
+ C 1 Cl 1 1 1.773
+ C 1 Cl 2 1 1.773
+ C 1 Cl 3 1 1.773
+ C 1 Cl 4 1 1.7993
+ C 2 Cl 1 1 1.773
+ C 3 Cl 1 1 1.773
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+ S 2 C 1 1 1.805
+ S 2 C 2 1 1.8055
+ S 2 C 3 1 1.8052
+ S 2 C 4 1 1.804
+ S 3 C 1 1 1.805
+ S 3 C 2 1 1.8053
+ S 3 C 3 1 1.8052
+ S 3 C 4 1 1.8042
+ S 4 C 1 1 1.7882
+ S 4 C 2 1 1.7875
+ S 4 C 3 1 1.7868
+ S 4 C 4 1 1.786
+ S 5 C 1 1 1.779
+ S 5 C 2 1 1.7781
+ S 5 C 3 1 1.777
+ S 5 C 4 1 1.7765
+ S 6 C 1 1 1.7815
+ S 6 C 2 1 1.78
+ S 6 C 3 1 1.7812
+ S 6 C 4 1 1.7808
+ S 1 C 1 2 1.665
+ S 1 C 2 2 1.665
+ S 1 C 3 2 1.6701
+ S 1 C 4 2 1.7243
+ S 2 C 1 2 1.665
+ S 3 C 1 2 1.665
+ S 4 C 1 2 1.6803
+ S 5 C 1 2 1.6889
+ S 6 C 1 2 1.7086
+ S 1 C 1 3 1.4584
+ S 1 C 2 3 1.7389
+ S 1 C 3 3 1.7187
+ S 1 C 4 3 1.8039
+ S 2 C 1 3 1.4584
+ S 2 C 2 3 1.7594
+ S 2 C 3 3 1.7203
+ S 2 C 4 3 1.804
+ S 3 C 1 3 1.4584
+ S 3 C 2 3 1.7586
+ S 3 C 3 3 1.7213
+ S 3 C 4 3 1.8042
+ S 4 C 1 3 1.4502
+ S 4 C 2 3 1.737
+ S 4 C 3 3 1.6958
+ S 4 C 4 3 1.786
+ S 5 C 1 3 1.4442
+ S 5 C 2 3 1.7251
+ S 5 C 3 3 1.6865
+ S 5 C 4 3 1.7765
+ S 6 C 1 3 1.4468
+ S 6 C 2 3 1.7195
+ S 6 C 3 3 1.6847
+ S 6 C 4 3 1.7808
+ S 1 N 1 1 1.7181
+ S 1 N 2 1 1.7181
+ S 1 N 3 1 1.652
+ S 1 N 4 1 1.7132
+ S 1 N 5 1 1.8397
+ S 2 N 1 1 1.7181
+ S 2 N 3 1 1.6536
+ S 2 N 4 1 1.7215
+ S 3 N 1 1 1.7181
+ S 3 N 3 1 1.6568
+ S 3 N 4 1 1.7302
+ S 4 N 1 1 1.6908
+ S 4 N 3 1 1.6347
+ S 4 N 4 1 1.7048
+ S 5 N 1 1 1.6742
+ S 5 N 3 1 1.626
+ S 5 N 4 1 1.7001
+ S 6 N 1 1 1.6812
+ S 6 N 3 1 1.6271
+ S 6 N 4 1 1.7058
+ S 1 N 1 2 1.5181
+ S 1 N 2 2 1.5181
+ S 1 N 3 2 1.5181
+ S 1 N 4 2 1.5442
+ S 1 N 5 2 1.5591
+ S 2 N 1 2 1.5181
+ S 2 N 3 2 1.5188
+ S 3 N 1 2 1.5181
+ S 3 N 3 2 1.5191
+ S 4 N 1 2 1.5063
+ S 4 N 3 2 1.5102
+ S 5 N 1 2 1.4972
+ S 5 N 3 2 1.5058
+ S 6 N 1 2 1.5003
+ S 6 N 3 2 1.5046
+ S 1 N 1 3 1.6381
+ S 1 N 2 3 1.7093
+ S 1 N 3 3 1.6381
+ S 1 N 4 3 1.6849
+ S 1 N 5 3 1.7141
+ S 2 N 1 3 1.6381
+ S 3 N 1 3 1.6381
+ S 4 N 1 3 1.6171
+ S 5 N 1 3 1.607
+ S 6 N 1 3 1.6054
+ S 1 O 1 1 1.6632
+ S 1 O 2 1 1.661
+ S 1 O 3 1 1.6632
+ S 2 O 1 1 1.6632
+ S 2 O 2 1 1.6636
+ S 2 O 3 1 1.6606
+ S 3 O 1 1 1.661
+ S 3 O 2 1 1.6638
+ S 3 O 3 1 1.6738
+ S 4 O 1 1 1.6179
+ S 4 O 2 1 1.6478
+ S 4 O 3 1 1.6549
+ S 5 O 1 1 1.6344
+ S 5 O 2 1 1.6399
+ S 5 O 3 1 1.6498
+ S 6 O 1 1 1.6331
+ S 6 O 2 1 1.6397
+ S 6 O 3 1 1.6488
+ S 1 O 1 2 1.5
+ S 1 O 2 2 1.4632
+ S 1 O 3 2 1.5
+ S 2 O 1 2 1.5
+ S 3 O 1 2 1.5
+ S 4 O 1 2 1.5008
+ S 5 O 1 2 1.503
+ S 6 O 1 2 1.5062
+ S 1 O 1 3 1.3232
+ S 1 O 2 3 1.3232
+ S 1 O 3 3 1.661
+ S 2 O 1 3 1.3232
+ S 2 O 3 3 1.6592
+ S 3 O 1 3 1.3232
+ S 3 O 2 3 1.6638
+ S 3 O 3 3 1.6685
+ S 4 O 1 3 1.3194
+ S 4 O 2 3 1.6478
+ S 4 O 3 3 1.65
+ S 5 O 1 3 1.3167
+ S 5 O 2 3 1.6399
+ S 5 O 3 3 1.6437
+ S 6 O 1 3 1.3163
+ S 6 O 2 3 1.6397
+ S 6 O 3 3 1.6422
+ S 1 P 1 1 2.0694
+ S 1 P 2 1 2.0694
+ S 1 P 3 1 2.0694
+ S 1 P 4 1 1.94
+ S 1 P 5 1 2.1158
+ S 1 P 6 1 2.1603
+ S 2 P 1 1 2.0994
+ S 2 P 3 1 2.107
+ S 2 P 4 1 2.0942
+ S 3 P 1 1 2.0994
+ S 3 P 3 1 2.1076
+ S 3 P 4 1 2.0932
+ S 4 P 1 1 2.0924
+ S 4 P 3 1 2.0602
+ S 4 P 4 1 2.0484
+ S 5 P 1 1 2.0582
+ S 5 P 3 1 2.0471
+ S 5 P 4 1 2.0344
+ S 6 P 1 1 2.0526
+ S 6 P 3 1 2.0396
+ S 6 P 4 1 2.0263
+ S 1 P 1 2 1.8994
+ S 1 P 2 2 1.8994
+ S 1 P 3 2 1.8994
+ S 1 P 4 2 1.9151
+ S 1 P 5 2 1.9244
+ S 1 P 6 2 1.9437
+ S 2 P 1 2 1.8994
+ S 3 P 1 2 1.8994
+ S 4 P 1 2 1.8737
+ S 5 P 1 2 1.8624
+ S 6 P 1 2 1.8723
+ S 1 P 1 3 1.7594
+ S 1 P 2 3 1.7594
+ S 1 P 3 3 1.7595
+ S 1 P 4 3 1.7688
+ S 1 P 5 3 1.7743
+ S 1 P 6 3 1.7843
+ S 2 P 1 3 1.7594
+ S 3 P 1 3 1.7594
+ S 4 P 1 3 1.7438
+ S 5 P 1 3 1.7359
+ S 6 P 1 3 1.7418
+ S 1 S 1 1 2.05
+ S 1 S 2 1 2.05
+ S 1 S 3 1 2.05
+ S 1 S 4 1 2.007
+ S 1 S 5 1 1.9923
+ S 1 S 6 1 1.9875
+ S 2 S 1 1 2.05
+ S 2 S 2 1 2.0515
+ S 2 S 3 1 2.0496
+ S 2 S 4 1 2.0082
+ S 2 S 5 1 1.9947
+ S 2 S 6 1 1.9865
+ S 3 S 1 1 2.05
+ S 3 S 2 1 2.0496
+ S 3 S 3 1 2.0528
+ S 3 S 4 1 2.0097
+ S 3 S 5 1 1.9973
+ S 3 S 6 1 1.9924
+ S 4 S 1 1 2.007
+ S 4 S 2 1 2.0082
+ S 4 S 3 1 2.0097
+ S 4 S 4 1 1.9769
+ S 4 S 5 1 1.9671
+ S 4 S 6 1 1.9605
+ S 5 S 1 1 1.9923
+ S 5 S 2 1 1.9947
+ S 5 S 3 1 1.9972
+ S 5 S 4 1 1.9671
+ S 5 S 5 1 1.9587
+ S 5 S 6 1 1.9559
+ S 6 S 1 1 1.9875
+ S 6 S 2 1 1.9866
+ S 6 S 3 1 1.9924
+ S 6 S 4 1 1.9606
+ S 6 S 5 1 1.9566
+ S 6 S 6 1 1.9493
+ S 1 S 1 2 2.05
+ S 1 S 2 2 2.05
+ S 1 S 3 2 2.05
+ S 1 S 4 2 2.007
+ S 1 S 5 2 1.9923
+ S 1 S 6 2 1.9875
+ S 2 S 1 2 2.05
+ S 2 S 2 2 2.0515
+ S 2 S 3 2 2.0496
+ S 2 S 4 2 2.0082
+ S 2 S 5 2 1.9947
+ S 2 S 6 2 1.9865
+ S 3 S 1 2 2.05
+ S 3 S 2 2 2.0496
+ S 3 S 3 2 2.0528
+ S 3 S 4 2 2.0097
+ S 3 S 5 2 1.9973
+ S 3 S 6 2 1.9924
+ S 4 S 1 2 2.007
+ S 4 S 2 2 2.0082
+ S 4 S 3 2 2.0097
+ S 4 S 4 2 1.9769
+ S 4 S 5 2 1.9671
+ S 4 S 6 2 1.9605
+ S 5 S 1 2 1.9923
+ S 5 S 2 2 1.9947
+ S 5 S 3 2 1.9972
+ S 5 S 4 2 1.9671
+ S 5 S 5 2 1.9587
+ S 5 S 6 2 1.9559
+ S 6 S 1 2 1.9875
+ S 6 S 2 2 1.9866
+ S 6 S 3 2 1.9924
+ S 6 S 4 2 1.9606
+ S 6 S 5 2 1.9566
+ S 6 S 6 2 1.9493
+ S 1 S 1 3 2.05
+ S 1 S 2 3 2.05
+ S 1 S 3 3 2.05
+ S 1 S 4 3 2.007
+ S 1 S 5 3 1.9923
+ S 1 S 6 3 1.9875
+ S 2 S 1 3 2.05
+ S 2 S 2 3 2.0515
+ S 2 S 3 3 2.0496
+ S 2 S 4 3 2.0082
+ S 2 S 5 3 1.9947
+ S 2 S 6 3 1.9865
+ S 3 S 1 3 2.05
+ S 3 S 2 3 2.0496
+ S 3 S 3 3 2.0528
+ S 3 S 4 3 2.0097
+ S 3 S 5 3 1.9973
+ S 3 S 6 3 1.9924
+ S 4 S 1 3 2.007
+ S 4 S 2 3 2.0082
+ S 4 S 3 3 2.0097
+ S 4 S 4 3 1.9769
+ S 4 S 5 3 1.9671
+ S 4 S 6 3 1.9605
+ S 5 S 1 3 1.9923
+ S 5 S 2 3 1.9947
+ S 5 S 3 3 1.9972
+ S 5 S 4 3 1.9671
+ S 5 S 5 3 1.9587
+ S 5 S 6 3 1.9559
+ S 6 S 1 3 1.9875
+ S 6 S 2 3 1.9866
+ S 6 S 3 3 1.9924
+ S 6 S 4 3 1.9606
+ S 6 S 5 3 1.9566
+ S 6 S 6 3 1.9493
+ S 1 H 1 1 1.341
+ S 2 H 1 1 1.341
+ S 3 H 1 1 1.341
+ S 4 H 1 1 1.3318
+ S 5 H 1 1 1.3272
+ S 6 H 1 1 1.3317
+ S 1 H 1 2 1.341
+ S 2 H 1 2 1.341
+ S 3 H 1 2 1.341
+ S 4 H 1 2 1.3318
+ S 5 H 1 2 1.3272
+ S 6 H 1 2 1.3317
+ S 1 H 1 3 1.341
+ S 2 H 1 3 1.341
+ S 3 H 1 3 1.341
+ S 4 H 1 3 1.3318
+ S 5 H 1 3 1.3272
+ S 6 H 1 3 1.3317
+ S 1 Cl 1 1 2.031
+ S 1 Cl 2 1 2.031
+ S 1 Cl 3 1 2.031
+ S 1 Cl 4 1 2.0566
+ S 2 Cl 1 1 2.031
+ S 3 Cl 1 1 2.031
+ S 4 Cl 1 1 1.9985
+ S 5 Cl 1 1 1.9855
+ S 6 Cl 1 1 1.9827
+ S 1 Cl 1 2 2.031
+ S 1 Cl 2 2 2.031
+ S 1 Cl 3 2 2.031
+ S 1 Cl 4 2 2.0566
+ S 2 Cl 1 2 2.031
+ S 3 Cl 1 2 2.031
+ S 4 Cl 1 2 1.9985
+ S 5 Cl 1 2 1.9855
+ S 6 Cl 1 2 1.9827
+ S 1 Cl 1 3 2.031
+ S 1 Cl 2 3 2.031
+ S 1 Cl 3 3 2.031
+ S 1 Cl 4 3 2.0566
+ S 2 Cl 1 3 2.031
+ S 3 Cl 1 3 2.031
+ S 4 Cl 1 3 1.9985
+ S 5 Cl 1 3 1.9855
+ S 6 Cl 1 3 1.9827
+ H 1 C 1 1 1.093
+ H 1 C 2 1 1.093
+ H 1 C 3 1 1.093
+ H 1 C 4 1 1.0922
+ H 1 C 1 2 1.083
+ H 1 C 2 2 1.083
+ H 1 C 3 2 1.0826
+ H 1 C 4 2 1.0922
+ H 1 C 1 3 1.0907
+ H 1 C 2 3 1.0701
+ H 1 C 3 3 1.0826
+ H 1 C 4 3 1.0922
+ H 1 N 1 1 1.0189
+ H 1 N 2 1 1.0189
+ H 1 N 3 1 1.019
+ H 1 N 4 1 1.0268
+ H 1 N 5 1 1.0449
+ H 1 N 1 2 1.0189
+ H 1 N 2 2 1.0189
+ H 1 N 3 2 1.028
+ H 1 N 4 2 1.0319
+ H 1 N 5 2 1.0449
+ H 1 N 1 3 1.0189
+ H 1 N 2 3 1.0268
+ H 1 N 3 3 1.0189
+ H 1 N 4 3 1.0319
+ H 1 N 5 3 1.0449
+ H 1 O 1 1 0.97781
+ H 1 O 2 1 0.969
+ H 1 O 3 1 0.991
+ H 1 O 1 2 0.97781
+ H 1 O 2 2 0.987
+ H 1 O 3 2 0.97784
+ H 1 O 1 3 0.991
+ H 1 O 2 3 0.97781
+ H 1 O 3 3 0.97784
+ H 1 P 1 1 1.4168
+ H 1 P 2 1 1.4168
+ H 1 P 3 1 1.415
+ H 1 P 4 1 1.411
+ H 1 P 5 1 1.4168
+ H 1 P 6 1 1.4168
+ H 1 P 1 2 1.4168
+ H 1 P 2 2 1.4168
+ H 1 P 3 2 1.4168
+ H 1 P 4 2 1.4168
+ H 1 P 5 2 1.4168
+ H 1 P 6 2 1.4168
+ H 1 P 1 3 1.4168
+ H 1 P 2 3 1.4168
+ H 1 P 3 3 1.4168
+ H 1 P 4 3 1.4168
+ H 1 P 5 3 1.4168
+ H 1 P 6 3 1.4168
+ H 1 S 1 1 1.341
+ H 1 S 2 1 1.341
+ H 1 S 3 1 1.341
+ H 1 S 4 1 1.3318
+ H 1 S 5 1 1.3335
+ H 1 S 6 1 1.3317
+ H 1 S 1 2 1.341
+ H 1 S 2 2 1.341
+ H 1 S 3 2 1.341
+ H 1 S 4 2 1.3318
+ H 1 S 5 2 1.3335
+ H 1 S 6 2 1.3317
+ H 1 S 1 3 1.341
+ H 1 S 2 3 1.341
+ H 1 S 3 3 1.341
+ H 1 S 4 3 1.3318
+ H 1 S 5 3 1.3335
+ H 1 S 6 3 1.3317
+ H 1 H 1 1 0.66
+ H 1 H 1 2 0.66
+ H 1 H 1 3 0.66
+ H 1 Cl 1 1 1.3138
+ H 1 Cl 2 1 1.3138
+ H 1 Cl 3 1 1.3138
+ H 1 Cl 4 1 1.3138
+ H 1 Cl 1 2 1.3138
+ H 1 Cl 2 2 1.3138
+ H 1 Cl 3 2 1.3138
+ H 1 Cl 4 2 1.3138
+ H 1 Cl 1 3 1.3138
+ H 1 Cl 2 3 1.3138
+ H 1 Cl 3 3 1.3138
+ H 1 Cl 4 3 1.3138
+ Cl 1 C 1 1 1.773
+ Cl 1 C 2 1 1.773
+ Cl 1 C 3 1 1.773
+ Cl 1 C 4 1 1.767
+ Cl 2 C 1 1 1.773
+ Cl 3 C 1 1 1.773
+ Cl 4 C 1 1 1.7993
+ Cl 1 C 1 2 1.72
+ Cl 1 C 2 2 1.72
+ Cl 1 C 3 2 1.7018
+ Cl 1 C 4 2 1.767
+ Cl 2 C 1 2 1.72
+ Cl 3 C 1 2 1.72
+ Cl 4 C 1 2 1.7425
+ Cl 1 C 1 3 1.4231
+ Cl 1 C 2 3 1.7739
+ Cl 1 C 3 3 1.7018
+ Cl 1 C 4 3 1.767
+ Cl 2 C 1 3 1.4231
+ Cl 3 C 1 3 1.423
+ Cl 4 C 1 3 1.4294
+ Cl 1 N 1 1 1.7292
+ Cl 1 N 2 1 1.7292
+ Cl 1 N 3 1 1.761
+ Cl 1 N 4 1 1.725
+ Cl 1 N 5 1 1.8244
+ Cl 2 N 1 1 1.7291
+ Cl 3 N 1 1 1.7292
+ Cl 4 N 1 1 1.7485
+ Cl 1 N 1 2 1.5292
+ Cl 1 N 2 2 1.5292
+ Cl 1 N 3 2 1.5292
+ Cl 1 N 4 2 1.5515
+ Cl 1 N 5 2 1.5638
+ Cl 2 N 1 2 1.5292
+ Cl 3 N 1 2 1.5292
+ Cl 4 N 1 2 1.5376
+ Cl 1 N 1 3 1.6492
+ Cl 1 N 2 3 1.6956
+ Cl 1 N 3 3 1.6492
+ Cl 1 N 4 3 1.6884
+ Cl 1 N 5 3 1.7114
+ Cl 2 N 1 3 1.6492
+ Cl 3 N 1 3 1.6492
+ Cl 4 N 1 3 1.6631
+ Cl 1 O 1 1 1.6843
+ Cl 1 O 2 1 1.6843
+ Cl 1 O 3 1 1.6843
+ Cl 2 O 1 1 1.6843
+ Cl 3 O 1 1 1.6843
+ Cl 4 O 1 1 1.6998
+ Cl 1 O 1 2 1.4843
+ Cl 1 O 2 2 1.4843
+ Cl 1 O 3 2 1.4843
+ Cl 2 O 1 2 1.4843
+ Cl 3 O 1 2 1.4844
+ Cl 4 O 1 2 1.491
+ Cl 1 O 1 3 1.3443
+ Cl 1 O 2 3 1.3443
+ Cl 1 O 3 3 1.3443
+ Cl 2 O 1 3 1.3443
+ Cl 3 O 1 3 1.3444
+ Cl 4 O 1 3 1.3479
+ Cl 1 P 1 1 2.0445
+ Cl 1 P 2 1 2.0445
+ Cl 1 P 3 1 2.1
+ Cl 1 P 4 1 2.0103
+ Cl 1 P 5 1 2.0863
+ Cl 1 P 6 1 2.1254
+ Cl 2 P 1 1 2.0445
+ Cl 3 P 1 1 2.0447
+ Cl 4 P 1 1 2.0745
+ Cl 1 P 1 2 1.8445
+ Cl 1 P 2 2 1.8445
+ Cl 1 P 3 2 1.8446
+ Cl 1 P 4 2 1.8573
+ Cl 1 P 5 2 1.8648
+ Cl 1 P 6 2 1.8799
+ Cl 2 P 1 2 1.8445
+ Cl 3 P 1 2 1.8445
+ Cl 4 P 1 2 1.8591
+ Cl 1 P 1 3 1.7045
+ Cl 1 P 2 3 1.7045
+ Cl 1 P 3 3 1.7045
+ Cl 1 P 4 3 1.7121
+ Cl 1 P 5 3 1.7165
+ Cl 1 P 6 3 1.7244
+ Cl 2 P 1 3 1.7045
+ Cl 3 P 1 3 1.7045
+ Cl 4 P 1 3 1.7132
+ Cl 1 S 1 1 2.031
+ Cl 1 S 2 1 2.031
+ Cl 1 S 3 1 2.031
+ Cl 1 S 4 1 1.9985
+ Cl 1 S 5 1 1.9855
+ Cl 1 S 6 1 1.9827
+ Cl 2 S 1 1 2.031
+ Cl 3 S 1 1 2.031
+ Cl 4 S 1 1 2.0566
+ Cl 1 S 1 2 2.031
+ Cl 1 S 2 2 2.031
+ Cl 1 S 3 2 2.031
+ Cl 1 S 4 2 1.9985
+ Cl 1 S 5 2 1.9855
+ Cl 1 S 6 2 1.9827
+ Cl 2 S 1 2 2.031
+ Cl 3 S 1 2 2.031
+ Cl 4 S 1 2 2.0566
+ Cl 1 S 1 3 2.031
+ Cl 1 S 2 3 2.031
+ Cl 1 S 3 3 2.031
+ Cl 1 S 4 3 1.9985
+ Cl 1 S 5 3 1.9855
+ Cl 1 S 6 3 1.9827
+ Cl 2 S 1 3 2.031
+ Cl 3 S 1 3 2.031
+ Cl 4 S 1 3 2.0566
+ Cl 1 H 1 1 1.3138
+ Cl 2 H 1 1 1.3138
+ Cl 3 H 1 1 1.3138
+ Cl 4 H 1 1 1.3138
+ Cl 1 H 1 2 1.3138
+ Cl 2 H 1 2 1.3138
+ Cl 3 H 1 2 1.3138
+ Cl 4 H 1 2 1.3138
+ Cl 1 H 1 3 1.3138
+ Cl 2 H 1 3 1.3138
+ Cl 3 H 1 3 1.3138
+ Cl 4 H 1 3 1.3138
+ Cl 1 Cl 1 1 2.02
+ Cl 1 Cl 2 1 2.02
+ Cl 1 Cl 3 1 2.02
+ Cl 1 Cl 4 1 2.0439
+ Cl 2 Cl 1 1 2.02
+ Cl 3 Cl 1 1 2.02
+ Cl 4 Cl 1 1 2.0439
+ Cl 1 Cl 1 2 1.82
+ Cl 1 Cl 2 2 1.82
+ Cl 1 Cl 3 2 1.82
+ Cl 1 Cl 4 2 1.8317
+ Cl 2 Cl 1 2 1.82
+ Cl 3 Cl 1 2 1.8201
+ Cl 4 Cl 1 2 1.8317
+ Cl 1 Cl 1 3 1.68
+ Cl 1 Cl 2 3 1.68
+ Cl 1 Cl 3 3 1.68
+ Cl 1 Cl 4 3 1.6869
+ Cl 2 Cl 1 3 1.68
+ Cl 3 Cl 1 3 1.68
+ Cl 4 Cl 1 3 1.6869
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/A.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/A.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,107 @@
+A
+ Names
+ Adenine
+ Adenin
+ A
+
+ Atoms
+ PP 23.872 39.165 31.119
+ O1PO 25.231 39.217 30.523
+ O2PO 22.847 40.110 30.636
+ O5*O 24.015 39.407 32.681
+ C5*C 23.898 38.444 33.717
+ 1H5*H 23.427 37.536 33.341
+ 2H5*H 23.266 38.889 34.485
+ C4*C 25.259 38.091 34.326
+ H4*H 25.156 37.622 35.304
+ O4*O 25.979 37.144 33.552
+ C3*C 26.180 39.302 34.326
+ H3*H 26.158 39.977 33.470
+ O3*O 25.805 40.074 35.470
+ C2*C 27.544 38.641 34.414
+ 1H2*H 28.301 39.314 34.011
+ 2H2*H 27.774 38.419 35.456
+ C1*C 27.277 37.165 34.164
+ H1*H 27.382 36.562 35.066
+ N9N 28.236 36.536 33.230
+ C8C 28.440 36.783 31.901
+ H8H 27.912 37.594 31.421
+ N7N 29.329 36.020 31.347
+ C5C 29.751 35.206 32.384
+ C6C 30.698 34.181 32.452
+ N6N 31.417 33.777 31.410
+ 1H6H 32.088 33.030 31.518
+ 2H6H 31.292 34.217 30.509
+ N1N 30.867 33.595 33.636
+ C2C 30.158 33.991 34.674
+ 2HH 30.296 33.518 35.635
+ N3N 29.245 34.933 34.744
+ C4C 29.090 35.512 33.538
+
+ Bonds
+ 1P O1P s
+ 2P O2P d
+ 3P O5* s
+ 4O5* C5* s
+ 5C5* C4* s
+ 6C4* O4* s
+ 7C4* C3* s
+ 8C3* O3* s
+ 9C3* C2* s
+ 10C2* C1* s
+ 11C1* O4* s
+ 12C1* N9 s
+ 13N9 C8 s
+ 14C8 N7 d
+ 15N7 C5 s
+ 16C5 C6 s
+ 17C5 C4 d
+ 18C4 N9 s
+ 19C6 N6 s
+ 20C6 N1 d
+ 21N1 C2 s
+ 22C2 N3 d
+ 23N3 C4 s
+ 24C5* 1H5* s
+ 25C5* 2H5* s
+ 26C4* H4* s
+ 27C1* H1* s
+ 28C3* H3* s
+ 29C2* 1H2* s
+ 30C2* 2H2* s
+ 31C8 H8 s
+ 32N6 1H6 s
+ 33N6 2H6 s
+ 34C2 2H s
+
+ Connections
+ 5-termP 3-term s 1.62 0.5
+ 3-termO3* 5-term s 1.62 0.5
+
+ Properties
+ NUCLEOTIDE
+
+ Variants
+ A-M
+ Properties
+ 5_PRIME
+ 3_PRIME
+
+
+ Default
+ Properties
+
+
+ A-3
+ Properties
+ 3_PRIME
+
+
+ A-5
+ Properties
+ 5_PRIME
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ACE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ACE.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,47 @@
+ACE
+ Names
+ ACE
+ acetic acid
+
+ Atoms
+ CC -0.710977 -1.12008 0.000774821
+ CH3C 0.0997794 -2.40762 0.00202052
+ OO -1.92224 -1.17518 0.00112378
+ 1HH3H -0.167239 -2.98461 0.880642
+ 2HH3H 1.1711 -2.24422 -0.00400307
+ 3HH3H -0.176322 -2.99236 -0.868617
+ OXTO -0.0809243 0.0851695 -0.000720861
+
+ Bonds
+ 1C CH3 s
+ 2C O d
+ 3C OXT s
+ 4CH3 1HH3 s
+ 5CH3 2HH3 s
+ 6CH3 3HH3 s
+
+ Connections
+ C-term
+ C N-term s 1.33 0.5
+
+
+
+ Properties
+
+ Variants
+ ACE-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+ ACE-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ALA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ALA.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,82 @@
+ALA
+ Names
+ Alanine
+ Alanin
+ Ala
+ A
+
+ Atoms
+ NN 0.09952427 1.425946 -0.01392276
+ 3HH 0.9122966 2.021833 0.09543685
+ CAC -0.6343572 1.904422 -1.199327
+ HAH -0.06613517 1.608824 -2.082189
+ CC -0.7061328 3.434369 -1.195026
+ OO 0.2770563 4.020259 -0.6877273
+ CBC -2.018631 1.250585 -1.273356
+ 1HBH -2.525042 1.535779 -2.196084
+ 2HBH -1.909473 0.1656088 -1.256012
+ 3HBH -2.621985 1.560564 -0.4192078
+ OXTO -1.554726 3.968913 -1.942107
+ 1HH -0.4859746 1.514033 0.8043322
+ 2HH 0.3756785 0.4622824 -0.137128
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 213HB CB s
+ 22OXT C s
+ 231H N s
+ 242H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ ALA-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ ALA-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ ALA-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ARG.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ARG.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,110 @@
+ARG
+ Names
+ Arginine
+ Arginin
+ Arg
+ R
+
+ Atoms
+ NN 0.04658213 1.228698 -0.008203848
+ 3HH 1.029144 1.468065 -0.01885969
+ CAC -0.651675 1.900984 -1.120636
+ HAH -0.1560273 1.589999 -2.041618
+ CC -0.5384113 3.425156 -1.007164
+ OO -0.4560871 4.056512 -2.083366
+ CBC -2.115081 1.438444 -1.186192
+ 1HBH -2.126043 0.3475202 -1.20068
+ 2HBH -2.643967 1.778842 -0.2945162
+ CGC -2.829752 1.953359 -2.443151
+ 1HGH -2.889884 3.042607 -2.412891
+ 2HGH -2.25911 1.654155 -3.324525
+ CDC -4.246704 1.376451 -2.533151
+ 1HDH -4.174877 0.2870844 -2.574071
+ 2HDH -4.797596 1.672022 -1.637285
+ NEN -4.940577 1.875193 -3.731703
+ HEH -4.414851 2.512341 -4.314554
+ CZC -6.193176 1.546153 -4.088384
+ NH1N -6.900425 0.7030471 -3.327994
+ 1HH1H -6.480561 0.3232263 -2.492691
+ 2HH1H -7.843661 0.4323652 -3.563007
+ NH2N -6.730267 2.060851 -5.200565
+ 1HH2H -6.201764 2.698435 -5.778988
+ 2HH2H -7.669785 1.826959 -5.486362
+ OXTO -0.796168 3.930999 0.1074273
+ 1HH -0.3621705 1.521632 0.867786
+ 2HH -0.05222332 0.2284002 -0.1067282
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 251HG CG s
+ 262HG CG s
+ 27CD CG s
+ 311HD CD s
+ 322HD CD s
+ 33NE CD s
+ 36HE NE s
+ 37CZ NE s
+ 40NH1 CZ a
+ 431HH1 NH1 s
+ 442HH1 NH1 s
+ 45NH2 CZ a
+ 481HH2 NH2 s
+ 492HH2 NH2 s
+ 50OXT C s
+ 511H N s
+ 522H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ ARG-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ ARG-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ ARG-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ASN.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASN.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,90 @@
+ASN
+ Names
+ Asparagine
+ Asparagin
+ Asn
+ N
+
+ Atoms
+ NN -0.01239826 1.297873 -0.0455736
+ 3HH 0.8807231 1.768826 0.03701005
+ CAC -0.7474616 1.91653 -1.164926
+ HAH -0.1937652 1.691628 -2.077897
+ CC -0.757567 3.441771 -1.010304
+ OO 0.3769885 3.962902 -0.9276295
+ CBC -2.149851 1.302218 -1.30196
+ 1HBH -2.042859 0.2235991 -1.423685
+ 2HBH -2.723301 1.490943 -0.3934487
+ CGC -2.91901 1.84635 -2.50453
+ OD1O -2.442698 2.721974 -3.218464
+ ND2N -4.125435 1.339006 -2.736042
+ 1HD2H -4.50376 0.6180301 -2.140929
+ 2HD2H -4.647904 1.686222 -3.525954
+ 1HH -0.5352049 1.417775 0.8102037
+ 2HH 0.1272759 0.3139404 -0.2256562
+ OXTO -1.806735 3.963976 -0.572751
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 24OD1 CG d
+ 25ND2 CG s
+ 281HD2 ND2 s
+ 292HD2 ND2 s
+ 301H N s
+ 312H N s
+ 32OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ ASN-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ ASN-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ ASN-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ASP.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASP.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,86 @@
+ASP
+ Names
+ Aspartate
+ Aspartat
+ Asp
+ D
+
+ Atoms
+ NN 0.1006113 1.231053 -0.1065504
+ 3HH 0.7826706 1.919109 0.1901606
+ CAC -0.6776782 1.854581 -1.196471
+ HAH -0.140641 1.67647 -2.129506
+ CC -0.7684437 3.377808 -1.00658
+ OO -0.1755398 3.814352 0.008837678
+ CBC -2.059715 1.201639 -1.304611
+ 1HBH -1.947421 0.1437317 -1.541582
+ 2HBH -2.583309 1.296861 -0.3531539
+ CGC -2.895658 1.868856 -2.384729
+ OD1O -2.861295 1.365629 -3.526181
+ OD2O -3.508188 2.905267 -2.052321
+ OXTO -0.9198192 4.048685 -2.051676
+ 1HH -0.5109496 1.02733 0.6709606
+ 2HH 0.5472904 0.3836241 -0.4264945
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 24OD1 CG a
+ 25OD2 CG a
+ 26OXT C s
+ 271H N s
+ 282H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ ASP-M
+ Properties
+ N_TERMINAL
+ C_TERMINAL
+
+
+ ASP-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+ ASP-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Benzene-Skeleton.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Benzene-Skeleton.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,23 @@
+Benzene-Skeleton
+ Names
+ Benzene-Skeleton
+
+ Atoms
+ C1C 0.066248 -1.287634 0.144514
+ C2C 0.057081 -0.613884 1.337852
+ C3C 0.045766 0.796088 1.307799
+ C4C 0.054862 1.462219 0.071058
+ C5C 0.073086 0.728404 -1.129738
+ C6C 0.091744 -0.671622 -1.107443
+
+ Bonds
+ 1C1 C2 s
+ 2C2 C3 d
+ 3C3 C4 s
+ 4C4 C5 d
+ 5C5 C6 s
+ 6C6 C1 d
+
+ Properties
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/C.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/C.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,102 @@
+C
+ Names
+ Cytosine
+ Cytosin
+ C
+
+ Atoms
+ PP 15.644 29.327 35.222
+ O1PO 15.393 28.440 36.382
+ O2PO 14.638 30.335 34.831
+ O5*O 15.947 28.383 33.968
+ C5*C 16.069 28.915 32.657
+ 1H5*H 16.821 29.704 32.690
+ 2H5*H 15.119 29.333 32.322
+ C4*C 16.513 27.844 31.682
+ H4*H 16.609 28.228 30.666
+ O4*O 17.830 27.370 32.014
+ C3*C 15.542 26.637 31.746
+ H3*H 14.654 26.736 32.370
+ O3*O 15.186 26.233 30.429
+ C2*C 16.448 25.569 32.322
+ 1H2*H 16.102 25.297 33.319
+ 2H2*H 16.428 24.689 31.678
+ C1*C 17.781 25.967 31.722
+ H1*H 17.935 25.853 30.649
+ N1N 18.940 25.252 32.322
+ C6C 18.970 24.882 33.637
+ H6H 18.141 25.127 34.285
+ C5C 20.022 24.211 34.147
+ H5H 20.029 23.926 35.199
+ C4C 21.100 23.907 33.243
+ N4N 22.167 23.241 33.694
+ 1H4H 22.908 23.042 33.037
+ 2H4H 22.216 22.954 34.661
+ N3N 21.059 24.280 31.953
+ C2C 19.992 24.955 31.461
+ O2O 19.963 25.291 30.279
+
+ Bonds
+ 1P O1P s
+ 2P O2P d
+ 3P O5* s
+ 4O5* C5* s
+ 5C5* C4* s
+ 6C4* O4* s
+ 7C4* C3* s
+ 8C3* O3* s
+ 9C3* C2* s
+ 10C2* C1* s
+ 11C1* O4* s
+ 12C1* N1 s
+ 13N1 C6 s
+ 14C6 C5 d
+ 15C5 C4 s
+ 16C4 N4 s
+ 17C4 N3 d
+ 18N3 C2 s
+ 19C2 O2 d
+ 20C2 N1 s
+ 21C5* 1H5* s
+ 22C5* 2H5* s
+ 23C4* H4* s
+ 24C1* H1* s
+ 25C3* H3* s
+ 26C2* 1H2* s
+ 27C2* 2H2* s
+ 28C6 H6 s
+ 29C5 H5 s
+ 30N4 1H4 s
+ 31N4 2H4 s
+
+ Connections
+ 5-termP 3-term s 1.62 0.5
+ 3-termO3* 5-term s 1.62 0.5
+
+ Properties
+ NUCLEOTIDE
+
+ Variants
+ C-M
+ Properties
+ 5_PRIME
+ 3_PRIME
+
+
+ Default
+ Properties
+
+
+ C-3
+ Properties
+ 3_PRIME
+
+
+ C-5
+ Properties
+ 5_PRIME
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/CA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CA.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,18 @@
+CA
+ Names
+ Calcium ion
+ Ca2+
+
+ Atoms
+ CACa 0.0 0.0 0.0
+
+ Bonds
+
+ Connections
+
+ Properties
+
+ Variants
+ Default
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/CYS.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CYS.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,123 @@
+CYS
+ Names
+ Cysteine
+ Cystein
+ Cys
+ C
+
+ Atoms
+ NN 0.02405081 1.288152 -0.04523527
+ 3HH 0.9139157 1.764642 0.02587458
+ CAC -0.7231978 1.84877 -1.18869
+ HAH -0.1383485 1.663318 -2.090963
+ CC -0.8891953 3.364114 -1.049031
+ OO 0.1143772 4.039036 -1.368143
+ CBC -2.074845 1.154028 -1.367605
+ 1HBH -1.930864 0.09969049 -1.603445
+ 2HBH -2.672614 1.244251 -0.4604313
+ SGS -2.936402 1.968095 -2.733035
+ HGH -4.084388 1.292503 -2.621688
+ 1HH -0.5030248 1.428972 0.8047693
+ 2HH 0.1769028 0.3003187 -0.1898637
+ OXTO -1.790595 3.760744 -0.2774832
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21SG CB s
+ 25HG SG s
+ 281H N s
+ 292H N s
+ 30OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+ S-termSG S-term s 2.05 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ CYS-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ CYS-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+ CYS-S
+ Delete
+ OXT
+ 1H
+ 2H
+ HG
+
+ Rename
+ 3HH
+
+ Properties
+ HAS_SSBOND
+
+
+ CYS-CS
+ Delete
+ 1H
+ 2H
+ HG
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+ HAS_SSBOND
+
+
+ CYS-NS
+ Delete
+ OXT
+ HG
+
+ Properties
+ N_TERMINAL
+ HAS_SSBOND
+
+
+ CYS-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Editing-Fragments.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Editing-Fragments.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,47 @@
+Fragments
+ #include:ALAfragments/ALA.db:/ALA
+ #include:ARGfragments/ARG.db:/ARG
+ #include:ASPfragments/ASP.db:/ASP
+ #include:ASNfragments/ASN.db:/ASN
+ #include:CYSfragments/CYS.db:/CYS
+ #include:GLNfragments/GLN.db:/GLN
+ #include:GLUfragments/GLU.db:/GLU
+ #include:GLYfragments/GLY.db:/GLY
+ #include:HISfragments/HIS.db:/HIS
+ #include:ILEfragments/ILE.db:/ILE
+ #include:LEUfragments/LEU.db:/LEU
+ #include:LYSfragments/LYS.db:/LYS
+ #include:METfragments/MET.db:/MET
+ #include:PHEfragments/PHE.db:/PHE
+ #include:PROfragments/PRO.db:/PRO
+ #include:SERfragments/SER.db:/SER
+ #include:THRfragments/THR.db:/THR
+ #include:TRPfragments/TRP.db:/TRP
+ #include:TYRfragments/TYR.db:/TYR
+ #include:VALfragments/VAL.db:/VAL
+ #include:PCAfragments/PCA.db:/PCA
+ #include:ACEfragments/ACE.db:/ACE
+ #include:NMEfragments/NME.db:/NME
+ #include:CAfragments/CA.db:/CA
+ #include:MGfragments/MG.db:/MG
+ #include:ZNfragments/ZN.db:/ZN
+ #include:HOHfragments/HOH.db:/HOH
+ #include:Afragments/A.db:/A
+ #include:Cfragments/C.db:/C
+ #include:Gfragments/G.db:/G
+ #include:Tfragments/T.db:/T
+ #include:Ufragments/U.db:/U
+ #include:Pyrrole-Skeletonfragments/Pyrrole-Skeleton.db:/Pyrrole-Skeleton
+ #include:Benzene-Skeletonfragments/Benzene-Skeleton.db:/Benzene-Skeleton
+ #include:Indole-Skeletonfragments/Indole-Skeleton.db:/Indole-Skeleton
+
+Names
+ #include:Discoverfragments/Names.Discover.db:/Discover
+ #include:Amberfragments/Names.Amber.db:/Amber
+ #include:CHARMMfragments/Names.CHARMM.db:/CHARMM
+ #include:XPLORfragments/Names.XPLOR.db:/XPLOR
+ #include:Starfragments/Names.Star.db:/Star
+
+Defaults
+ NamingPDB
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Fragments.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Fragments.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,46 @@
+Fragments
+ #include:ALAfragments/ALA.db:/ALA
+ #include:ARGfragments/ARG.db:/ARG
+ #include:ASPfragments/ASP.db:/ASP
+ #include:ASNfragments/ASN.db:/ASN
+ #include:CYSfragments/CYS.db:/CYS
+ #include:GLNfragments/GLN.db:/GLN
+ #include:GLUfragments/GLU.db:/GLU
+ #include:GLYfragments/GLY.db:/GLY
+ #include:HISfragments/HIS.db:/HIS
+ #include:ILEfragments/ILE.db:/ILE
+ #include:LEUfragments/LEU.db:/LEU
+ #include:LYSfragments/LYS.db:/LYS
+ #include:METfragments/MET.db:/MET
+ #include:MSEfragments/MSE.db:/MSE
+ #include:PHEfragments/PHE.db:/PHE
+ #include:PROfragments/PRO.db:/PRO
+ #include:SERfragments/SER.db:/SER
+ #include:THRfragments/THR.db:/THR
+ #include:TRPfragments/TRP.db:/TRP
+ #include:TYRfragments/TYR.db:/TYR
+ #include:VALfragments/VAL.db:/VAL
+ #include:PCAfragments/PCA.db:/PCA
+ #include:ACEfragments/ACE.db:/ACE
+ #include:NMEfragments/NME.db:/NME
+ #include:CAfragments/CA.db:/CA
+ #include:MGfragments/MG.db:/MG
+ #include:ZNfragments/ZN.db:/ZN
+ #include:HOHfragments/HOH.db:/HOH
+ #include:Afragments/A.db:/A
+ #include:Cfragments/C.db:/C
+ #include:Gfragments/G.db:/G
+ #include:Tfragments/T.db:/T
+ #include:Ufragments/U.db:/U
+
+Names
+ #include:Discoverfragments/Names.Discover.db:/Discover
+ #include:Amberfragments/Names.Amber.db:/Amber
+ #include:CHARMMfragments/Names.CHARMM.db:/CHARMM
+ #include:XPLORfragments/Names.XPLOR.db:/XPLOR
+ #include:Starfragments/Names.Star.db:/Star
+ #include:DNAfragments/Names.DNA.db:/DNA
+
+Defaults
+ NamingPDB
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/G.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/G.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,107 @@
+G
+ Names
+ Guanine
+ Guanin
+ G
+
+ Atoms
+ PP 32.612 26.662 40.051
+ O1PO 33.579 26.377 41.135
+ O2PO 32.257 25.612 39.055
+ O5*O 31.233 27.248 40.656
+ C5*C 31.159 28.416 41.468
+ 1H5*H 32.062 29.003 41.301
+ 2H5*H 31.095 28.140 42.520
+ C4*C 29.940 29.254 41.095
+ H4*H 29.785 30.090 41.777
+ O4*O 30.102 29.870 39.801
+ C3*C 28.712 28.348 41.021
+ O3*O 27.645 28.918 41.772
+ H3*H 28.886 27.326 41.358
+ C2*C 28.364 28.341 39.559
+ 1H2*H 28.348 27.314 39.193
+ 2H2*H 27.382 28.792 39.416
+ C1*C 28.928 29.637 39.018
+ H1*H 28.284 30.517 39.013
+ N9N 29.311 29.477 37.601
+ C8C 30.238 28.616 37.067
+ H8H 30.771 27.925 37.703
+ N7N 30.381 28.736 35.780
+ C5C 29.485 29.746 35.436
+ C6C 29.204 30.305 34.166
+ O6O 29.745 30.037 33.101
+ N1N 28.225 31.296 34.247
+ 1HH 27.948 31.750 33.400
+ C2C 27.605 31.699 35.418
+ N2N 26.693 32.662 35.319
+ 1H2H 26.407 33.145 34.479
+ 2H2H 26.252 32.956 36.179
+ N3N 27.881 31.170 36.610
+ C4C 28.823 30.204 36.543
+
+ Bonds
+ 1P O1P s
+ 2P O2P d
+ 3P O5* s
+ 4O5* C5* s
+ 5C5* C4* s
+ 6C4* O4* s
+ 7C4* C3* s
+ 8C3* O3* s
+ 9C3* C2* s
+ 10C2* C1* s
+ 11C1* O4* s
+ 12C1* N9 s
+ 13N9 C8 s
+ 14C8 N7 d
+ 15N7 C5 s
+ 16C5 C4 d
+ 17C4 N9 s
+ 18C5 C6 s
+ 19C6 O6 d
+ 20C6 N1 s
+ 21N1 C2 s
+ 22C2 N2 s
+ 23C2 N3 d
+ 24N3 C4 s
+ 25C5* 1H5* s
+ 26C5* 2H5* s
+ 27C4* H4* s
+ 28C1* H1* s
+ 29C3* H3* s
+ 30C2* 1H2* s
+ 31C2* 2H2* s
+ 32C8 H8 s
+ 33N1 1H s
+ 34N2 1H2 s
+ 35N2 2H2 s
+
+ Connections
+ 5-termP 3-term s 1.62 0.5
+ 3-termO3* 5-term s 1.62 0.5
+
+ Properties
+ NUCLEOTIDE
+
+ Variants
+ G-M
+ Properties
+ 5_PRIME
+ 3_PRIME
+
+
+ Default
+ Properties
+
+
+ G-5
+ Properties
+ 5_PRIME
+
+ G-3
+ Properties
+ 3_PRIME
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/GLN.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLN.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,96 @@
+GLN
+ Names
+ Glutamine
+ Glutamin
+ Gln
+ Q
+
+ Atoms
+ NN -1.694353 -0.2940789 3.487573
+ 3HH -1.993324 -0.7771879 2.60663
+ CAC -1.339968 1.106833 3.061471
+ HAH -2.035373 1.840381 3.535663
+ CC -1.613526 1.110178 1.459362
+ OO -1.452083 2.138383 0.8146671
+ CBC 0.1053884 1.466314 3.38408
+ 2HBH 0.4078564 1.068117 4.376333
+ 1HBH 0.7844938 0.9955081 2.644168
+ CGC 0.2953307 2.976142 3.377398
+ 2HGH -0.08479181 3.405704 2.425381
+ 1HGH -0.3113416 3.443596 4.179154
+ CDC 1.757013 3.318817 3.588054
+ OE1O 2.263759 3.493683 4.689262
+ NE2N 2.607646 3.349533 2.459146
+ 2HE2H 3.553186 3.659591 2.602335
+ 1HE2H 2.182977 3.3032491 1.543895
+ OXTO -2.00241 -0.02523248 1.056456
+ 2HH -2.440811 -0.2844597 4.149324
+ 1HH -0.9086809 -0.7656706 3.887856
+
+ Bonds
+ 13H N s
+ 2CA N s
+ 3HA CA s
+ 4C CA s
+ 5O C d
+ 6CB CA s
+ 72HB CB s
+ 81HB CB s
+ 9CG CB s
+ 102HG CG s
+ 111HG CG s
+ 12CD CG s
+ 13OE1 CD d
+ 14NE2 CD s
+ 152HE2 NE2 s
+ 161HE2 NE2 s
+ 17OXT C s
+ 182H N s
+ 191H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ GLN-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ GLN-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ GLN-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/GLU.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLU.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,92 @@
+GLU
+ Names
+ Glutamate
+ Glutamat
+ Glu
+ Q
+
+ Atoms
+ NN 0.09036078 1.20944 -0.09877955
+ 3HH 0.992178 1.663159 -0.02552702
+ CAC -0.6644503 1.887128 -1.167784
+ HAH -0.1401839 1.690991 -2.10393
+ CC -0.6415405 3.403009 -0.9416856
+ OO 0.5018099 3.910433 -0.8834405
+ CBC -2.078524 1.299661 -1.288965
+ 1HBH -2.006071 0.2127525 -1.352877
+ 2HBH -2.670931 1.54428 -0.4052964
+ CGC -2.807634 1.790975 -2.546677
+ 1HGH -2.881274 2.877187 -2.559357
+ 2HGH -2.268831 1.463546 -3.436255
+ CDC -4.223983 1.236637 -2.597517
+ OE1O -5.044554 1.733033 -1.797006
+ OE2O -4.450723 0.3260741 -3.421581
+ 1HH -0.4043283 1.301303 0.7769806
+ 2HH 0.2085563 0.2320959 -0.3244812
+ OXTO -1.674247 3.928742 -0.470977
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 251HG CG s
+ 262HG CG s
+ 27CD CG s
+ 30OE1 CD a
+ 31OE2 CD a
+ 321H N s
+ 332H N s
+ 34OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ GLU-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ GLU-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ GLU-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/GLY.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLY.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,76 @@
+GLY
+ Names
+ Glycine
+ Glycin
+ Gly
+ G
+
+ Atoms
+ NN 0.09000722 1.216287 -0.1108443
+ 3HH 0.8807056 1.803007 0.1270226
+ CAC -0.6332095 1.869306 -1.215941
+ 1HAH -0.02850649 1.801736 -2.120623
+ 2HAH -1.579168 1.352425 -1.380715
+ CC -0.8818576 3.344497 -0.910938
+ OO 0.06351577 3.962237 -0.3713815
+ 1HH -0.5183882 1.138782 0.691625
+ 2HH 0.4027565 0.2984461 -0.3934918
+ OXTO -1.901015 3.866009 -1.413833
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 101HA CA s
+ 112HA CA s
+ 12C CA s
+ 15O C d
+ 161H N s
+ 172H N s
+ 18OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ GLY-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ GLY-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ GLY-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/HIS.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HIS.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,99 @@
+HIS
+ Names
+ Histidine
+ Histidin
+ His
+ H
+
+ Atoms
+ NN 0.2528806 1.616447 -0.2212145
+ 3HH 0.7991534 2.328624 0.245802
+ CAC -0.9251888 2.215651 -0.8776516
+ HAH -0.5465931 2.966134 -1.573552
+ CC -1.833067 2.919479 0.1419996
+ OO -2.654072 3.735267 -0.3389743
+ CBC -1.677425 1.144471 -1.688265
+ 1HBH -0.9314069 0.53022 -2.195623
+ 2HBH -2.228334 0.4977131 -1.00345
+ CGC -2.625881 1.668474 -2.74672
+ ND1N -3.385668 2.821612 -2.671887
+ HD1H -3.38348 3.467654 -1.88095
+ CD2C -2.893428 1.068907 -3.947961
+ HD2H -2.46763 0.1453506 -4.317409
+ CE1C -4.09971 2.924621 -3.807559
+ HE1H -4.788648 3.724259 -4.045286
+ NE2N -3.815619 1.869323 -4.597533
+ HE2H -4.210977 1.69118 -5.511979
+ 1HH -0.05550323 0.9331897 0.4557269
+ 2HH 0.827899 1.162407 -0.9164186
+ OXTO -1.921441 2.400639 1.276749
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 24ND1 CG a
+ 27HD1 ND1 s
+ 28CD2 CG a
+ 31HD2 CD2 s
+ 32CE1 ND1 a
+ 35HE1 CE1 s
+ 36NE2 CE1 a
+ 37NE2 CD2 a
+ 39HE2 NE2 s
+ 401H N s
+ 412H N s
+ 42OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ HIS-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ HIS-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ HIS-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/HOH.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HOH.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,21 @@
+HOH
+ Names
+ Water
+
+ Atoms
+ O O 15.118 9.944 8.582
+ 1HH 15.211 9.386 7.809
+ 2HH 14.173 9.992 8.730
+
+ Bonds
+ 11H O s
+ 22H O s
+
+ Connections
+
+ Properties
+
+ Variants
+ Default
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ILE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ILE.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,100 @@
+ILE
+ Names
+ Isoleucine
+ Isoleucin
+ Ile
+ I
+
+ Atoms
+ NN 0.1219419 1.159209 -0.1919851
+ 3HH 0.9740559 1.689959 -0.04711162
+ CAC -0.7030041 1.935257 -1.138673
+ HAH -0.2842833 1.745549 -2.127681
+ CC -0.5392811 3.43721 -0.8683466
+ OO 0.4636989 3.750649 -0.1867381
+ CBC -2.165631 1.439687 -1.121375
+ HBH -2.124804 0.349284 -1.14618
+ CG1C -2.945574 1.890833 -2.370761
+ 1HG1H -3.189406 2.951118 -2.312008
+ 2HG1H -2.330654 1.72068 -3.255403
+ CG2C -2.890608 1.852801 0.1693949
+ 1HG2H -3.851115 1.343782 0.2388784
+ 2HG2H -2.299751 1.573039 1.041283
+ 3HG2H -3.060911 2.929328 0.1868919
+ CD1C -4.249351 1.108805 -2.558935
+ 1HD1H -4.709754 1.403511 -3.502415
+ 2HD1H -4.043807 0.03831363 -2.586494
+ 3HD1H -4.947758 1.324118 -1.751006
+ 1HH -0.3580201 1.071109 0.6916124
+ 2HH 0.3236403 0.2433889 -0.5670705
+ OXTO -1.135264 4.21782 -1.641576
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 19HB CB s
+ 20CG1 CB s
+ 241HG1 CG1 s
+ 252HG1 CG1 s
+ 26CG2 CB s
+ 301HG2 CG2 s
+ 312HG2 CG2 s
+ 323HG2 CG2 s
+ 33CD1 CG1 s
+ 371HD1 CD1 s
+ 382HD1 CD1 s
+ 393HD1 CD1 s
+ 401H N s
+ 412H N s
+ 42OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ ILE-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ ILE-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ ILE-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Indole-Skeleton.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Indole-Skeleton.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,30 @@
+Indole-Skeleton
+ Names
+ Indole-Skeleton
+
+ Atoms
+ C1C 0.098272 0.968184 -2.108448
+ N2N 0.106846 2.054217 -1.259124
+ C3C 0.08464 1.665738 0.063892
+ C4C 0.060104 0.240281 0.014949
+ C5C 0.062069 -0.174574 -1.386187
+ C6C 0.084854 2.377612 1.27264
+ C7C 0.060305 1.667968 2.483589
+ C8C 0.039354 0.262233 2.470668
+ C9C 0.039595 -0.441663 1.251419
+
+ Bonds
+ 1C1 N2 s
+ 2N2 C3 s
+ 3C3 C4 d
+ 4C4 C5 s
+ 5C5 C1 d
+ 6C3 C6 s
+ 7C6 C7 d
+ 8C7 C8 s
+ 9C8 C9 d
+ 10C9 C4 s
+
+ Properties
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/LEU.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LEU.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,100 @@
+LEU
+ Names
+ Leucine
+ Leucin
+ Leu
+ L
+
+ Atoms
+ NN -0.003476313 1.235853 0.02699674
+ 3HH 0.7720473 1.82942 0.3005252
+ CAC -0.6514053 1.883178 -1.129898
+ HAH -0.07017973 1.598957 -2.006831
+ CC -0.5708863 3.410168 -0.9936234
+ OO 0.1419036 3.827524 -0.05211589
+ CBC -2.091007 1.359104 -1.274005
+ 1HBH -2.046227 0.2694775 -1.310338
+ 2HBH -2.646399 1.642544 -0.3785246
+ CGC -2.872831 1.847369 -2.507179
+ HGH -3.019899 2.926006 -2.455012
+ CD1C -2.162796 1.498542 -3.821336
+ 1HD1H -2.800384 1.766798 -4.664294
+ 2HD1H -1.228827 2.051352 -3.913459
+ 3HD1H -1.954294 0.4288859 -3.861405
+ CD2C -4.261661 1.198464 -2.502073
+ 1HD2H -4.845348 1.564912 -3.347144
+ 2HD2H -4.171115 0.1141629 -2.575422
+ 3HD2H -4.785489 1.451318 -1.579679
+ OXTO -0.8228753 4.072413 -2.02374
+ 1HH -0.6580312 1.186075 0.7945588
+ 2HH 0.3136166 0.3082535 -0.2161924
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 25HG CG s
+ 26CD1 CG s
+ 301HD1 CD1 s
+ 312HD1 CD1 s
+ 323HD1 CD1 s
+ 33CD2 CG s
+ 371HD2 CD2 s
+ 382HD2 CD2 s
+ 393HD2 CD2 s
+ 40OXT C s
+ 411H N s
+ 422H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ LEU-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ LEU-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ LEU-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/LYS.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LYS.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,106 @@
+LYS
+ Names
+ Lysine
+ Lysin
+ Lys
+ K
+
+ Atoms
+ NN 0.03796386 1.172592 -0.009692425
+ 3HH 1.016744 1.426445 0.004398665
+ CAC -0.6562778 1.887361 -1.097957
+ HAH -0.1455905 1.623495 -2.025311
+ CC -0.5601511 3.406333 -0.9147748
+ OO -0.5440148 4.087965 -1.963232
+ CBC -2.114089 1.411355 -1.200695
+ 1HBH -2.113627 0.3206328 -1.233166
+ 2HBH -2.662723 1.730462 -0.3130743
+ CGC -2.816849 1.934443 -2.461919
+ 1HGH -2.878444 3.023734 -2.425601
+ 2HGH -2.232982 1.645706 -3.338356
+ CDC -4.230651 1.346997 -2.563318
+ 1HDH -4.153291 0.2577495 -2.598617
+ 2HDH -4.790445 1.632903 -1.669734
+ CEC -4.93697 1.869824 -3.82334
+ 1HEH -4.991973 2.959915 -3.77821
+ 2HEH -4.353527 1.590667 -4.70365
+ NZN -6.304516 1.325968 -3.962642
+ 1HZH -6.733165 1.692468 -4.802127
+ 2HZH -6.276195 0.31765 -4.027733
+ 3HZH -6.870414 1.591293 -3.16824
+ 1HH -0.3857403 1.416816 0.8740513
+ 2HH -0.04427324 0.17682 -0.1571643
+ OXTO -0.7869474 3.85405 0.2308864
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 251HG CG s
+ 262HG CG s
+ 27CD CG s
+ 311HD CD s
+ 322HD CD s
+ 33CE CD s
+ 371HE CE s
+ 382HE CE s
+ 39NZ CE s
+ 431HZ NZ s
+ 442HZ NZ s
+ 453HZ NZ s
+ 461H N s
+ 472H N s
+ 48OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ LYS-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ LYS-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ LYS-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/MET.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MET.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,96 @@
+MET
+ Names
+ Methionine
+ Methionin
+ Met
+ M
+
+ Atoms
+ NN 0.0654056 1.215812 -0.06949145
+ 3HH 0.9974914 1.608735 -0.04203663
+ CAC -0.6988745 1.893029 -1.131979
+ HAH -0.1911148 1.68141 -2.074138
+ CC -0.6694928 3.410054 -0.9194202
+ OO 0.4107355 3.973423 -1.201833
+ CBC -2.121216 1.317703 -1.225039
+ 1HBH -2.050125 0.2325057 -1.312704
+ 2HBH -2.682049 1.549083 -0.318349
+ CGC -2.887041 1.8377 -2.448318
+ 1HGH -2.99595 2.919347 -2.383954
+ 2HGH -2.322049 1.593525 -3.347709
+ SDS -4.546617 1.137771 -2.634913
+ CEC -5.081393 1.965263 -4.148402
+ 1HEH -6.08969 1.634787 -4.393987
+ 2HEH -5.078839 3.043304 -3.993342
+ 3HEH -4.404794 1.706412 -4.961773
+ OXTO -1.565656 3.902471 -0.1992161
+ 1HH -0.3889995 1.363342 0.8203897
+ 2HH 0.1172404 0.226119 -0.264187
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 251HG CG s
+ 262HG CG s
+ 27SD CG s
+ 33CE SD s
+ 371HE CE s
+ 382HE CE s
+ 393HE CE s
+ 40OXT C s
+ 411H N s
+ 422H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ MET-M
+ Properties
+ N_TERMINAL
+ C_TERMINAL
+
+
+ MET-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ MET-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/MG.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MG.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,18 @@
+MG
+ Names
+ Magnesium ion
+ Mg2+
+
+ Atoms
+ MGMg 0.0 0.0 0.0
+
+ Bonds
+
+ Connections
+
+ Properties
+
+ Variants
+ Default
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/MSE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MSE.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,95 @@
+MSE
+ Names
+ Selenomethionine
+ Selenomethionin
+ Mse
+
+ Atoms
+ NN 0.0654056 1.215812 -0.06949145
+ 3HH 0.9974914 1.608735 -0.04203663
+ CAC -0.6988745 1.893029 -1.131979
+ HAH -0.1911148 1.68141 -2.074138
+ CC -0.6694928 3.410054 -0.9194202
+ OO 0.4107355 3.973423 -1.201833
+ CBC -2.121216 1.317703 -1.225039
+ 1HBH -2.050125 0.2325057 -1.312704
+ 2HBH -2.682049 1.549083 -0.318349
+ CGC -2.887041 1.8377 -2.448318
+ 1HGH -2.99595 2.919347 -2.383954
+ 2HGH -2.322049 1.593525 -3.347709
+ SESe -4.546617 1.137771 -2.634913
+ CEC -5.081393 1.965263 -4.148402
+ 1HEH -6.08969 1.634787 -4.393987
+ 2HEH -5.078839 3.043304 -3.993342
+ 3HEH -4.404794 1.706412 -4.961773
+ OXTO -1.565656 3.902471 -0.1992161
+ 1HH -0.3889995 1.363342 0.8203897
+ 2HH 0.1172404 0.226119 -0.264187
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 251HG CG s
+ 262HG CG s
+ 27SE CG s
+ 33CE SE s
+ 371HE CE s
+ 382HE CE s
+ 393HE CE s
+ 40OXT C s
+ 411H N s
+ 422H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ MET-M
+ Properties
+ N_TERMINAL
+ C_TERMINAL
+
+
+ MET-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ MET-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/NME.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/NME.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,46 @@
+NME
+ Names
+ Methylamine
+
+ Atoms
+ NN 0.724 0.000 -0.079
+ CH3C -0.742 0.000 0.011
+ 1HH 1.046 0.810 0.431
+ 2HH 1.046 -0.810 0.431
+ 1HH3H -1.139 -0.861 -0.527
+ 2HH3H -1.042 -0.056 1.057
+ 3HH3H -1.133 0.917 -0.431
+
+ Bonds
+ 1N CH3 s
+ 2N 1H s
+ 3N 2H s
+ 4CH3 1HH3 s
+ 5CH3 2HH3 s
+ 6CH3 3HH3 s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+
+ Properties
+
+ Variants
+ NME-C
+ Delete
+ 2H
+
+ Rename
+ 1HH
+
+ Properties
+ C_TERMINAL
+
+
+ NME-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Names.Amber.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Amber.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,486 @@
+AmberPDB
+ *:H1*:1H
+ *:H2*:2H
+ *:H3*:3H
+ *:N*:N
+ *:C*:C
+ *:O*:O
+ *:H*:H
+ ALA:CAALA:CA
+ ALA:HAALA:HA
+ ALA:CBALA:CB
+ ALA:HB1ALA:1HB
+ ALA:HB2ALA:2HB
+ ALA:HB3ALA:3HB
+ ARG:CAARG:CA
+ ARG:HAARG:HA
+ ARG:CBARG:CB
+ ARG:HB2ARG:1HB
+ ARG:HB3ARG:2HB
+ ARG:CGARG:CG
+ ARG:HG2ARG:1HG
+ ARG:HG3ARG:2HG
+ ARG:CDARG:CD
+ ARG:HD2ARG:1HD
+ ARG:HD3ARG:2HD
+ ARG:NEARG:NE
+ ARG:HEARG:HE
+ ARG:CZARG:CZ
+ ARG:NH1ARG:NH1
+ ARG:HH11ARG:1HH1
+ ARG:HH12ARG:2HH1
+ ARG:NH2ARG:NH2
+ ARG:HH21ARG:1HH2
+ ARG:HH22ARG:2HH2
+ ASN:CAASN:CA
+ ASN:HAASN:HA
+ ASN:CBASN:CB
+ ASN:HB2ASN:1HB
+ ASN:HB3ASN:2HB
+ ASN:CGASN:CG
+ ASN:OD1ASN:OD1
+ ASN:ND2ASN:ND2
+ ASN:HD21ASN:1HD2
+ ASN:HD22ASN:2HD2
+ ASP:CAASP:CA
+ ASP:HAASP:HA
+ ASP:CBASP:CB
+ ASP:HB2ASP:1HB
+ ASP:HB3ASP:2HB
+ ASP:CGASP:CG
+ ASP:OD1ASP:OD1
+ ASP:OD2ASP:OD2
+ CYS:CACYS:CA
+ CYS:HACYS:HA
+ CYS:CBCYS:CB
+ CYS:HB2CYS:1HB
+ CYS:HB3CYS:2HB
+ CYS:SGCYS:SG
+ CYS:HGCYS:HG
+ CYS:HSGCYS:HG
+ GLU:CAGLU:CA
+ GLU:HAGLU:HA
+ GLU:CBGLU:CB
+ GLU:HB2GLU:1HB
+ GLU:HB3GLU:2HB
+ GLU:CGGLU:CG
+ GLU:HG2GLU:1HG
+ GLU:HG3GLU:2HG
+ GLU:CDGLU:CD
+ GLU:OE1GLU:OE1
+ GLU:OE2GLU:OE2
+ GLN:CAGLN:CA
+ GLN:HAGLN:HA
+ GLN:CBGLN:CB
+ GLN:HB2GLN:1HB
+ GLN:HB3GLN:2HB
+ GLN:CGGLN:CG
+ GLN:HG2GLN:1HG
+ GLN:HG3GLN:2HG
+ GLN:CDGLN:CD
+ GLN:OE1GLN:OE1
+ GLN:NE2GLN:NE2
+ GLN:HE21GLN:1HE2
+ GLN:HE22GLN:2HE2
+ GLY:CAGLY:CA
+ GLY:HA2GLY:1HA
+ GLY:HA3GLY:2HA
+ HIS:CAHIS:CA
+ HIS:HAHIS:HA
+ HIS:CBHIS:CB
+ HIS:HB2HIS:1HB
+ HIS:HB3HIS:2HB
+ HIS:CGHIS:CG
+ HIS:ND1HIS:ND1
+ HIS:HD1HIS:HD1
+ HIS:CE1HIS:CE1
+ HIS:HE1HIS:HE1
+ HIS:NE2HIS:NE2
+ HIS:HE2HIS:HE2
+ HIS:CD2HIS:CD2
+ HIS:HD2HIS:HD2
+ ILE:CAILE:CA
+ ILE:HAILE:HA
+ ILE:CBILE:CB
+ ILE:HBILE:HB
+ ILE:CG2ILE:CG2
+ ILE:HG21ILE:1HG2
+ ILE:HG22ILE:2HG2
+ ILE:HG23ILE:3HG2
+ ILE:CG1ILE:CG1
+ ILE:HG12ILE:1HG1
+ ILE:HG13ILE:2HG1
+ ILE:CD1ILE:CD1
+ ILE:HD11ILE:1HD1
+ ILE:HD12ILE:2HD1
+ ILE:HD13ILE:3HD1
+ LEU:CALEU:CA
+ LEU:HALEU:HA
+ LEU:CBLEU:CB
+ LEU:HB2LEU:1HB
+ LEU:HB3LEU:2HB
+ LEU:CGLEU:CG
+ LEU:HGLEU:HG
+ LEU:CD1LEU:CD1
+ LEU:HD11LEU:1HD1
+ LEU:HD12LEU:2HD1
+ LEU:HD13LEU:3HD1
+ LEU:CD2LEU:CD2
+ LEU:HD21LEU:1HD2
+ LEU:HD22LEU:2HD2
+ LEU:HD23LEU:3HD2
+ LYS:CALYS:CA
+ LYS:HALYS:HA
+ LYS:CBLYS:CB
+ LYS:HB2LYS:1HB
+ LYS:HB3LYS:2HB
+ LYS:CGLYS:CG
+ LYS:HG2LYS:1HG
+ LYS:HG3LYS:2HG
+ LYS:CDLYS:CD
+ LYS:HD2LYS:1HD
+ LYS:HD3LYS:2HD
+ LYS:CELYS:CE
+ LYS:HE2LYS:1HE
+ LYS:HE3LYS:2HE
+ LYS:NZLYS:NZ
+ LYS:HZ1LYS:1HZ
+ LYS:HZ2LYS:2HZ
+ LYS:HZ3LYS:3HZ
+ MET:CAMET:CA
+ MET:HAMET:HA
+ MET:CBMET:CB
+ MET:HB2MET:1HB
+ MET:HB3MET:2HB
+ MET:CGMET:CG
+ MET:HG2MET:1HG
+ MET:HG3MET:2HG
+ MET:SDMET:SD
+ MET:CEMET:CE
+ MET:HE1MET:1HE
+ MET:HE2MET:2HE
+ MET:HE3MET:3HE
+ PHE:CAPHE:CA
+ PHE:HAPHE:HA
+ PHE:CBPHE:CB
+ PHE:HB2PHE:1HB
+ PHE:HB3PHE:2HB
+ PHE:CGPHE:CG
+ PHE:CD1PHE:CD1
+ PHE:HD1PHE:HD1
+ PHE:CE1PHE:CE1
+ PHE:HE1PHE:HE1
+ PHE:CZPHE:CZ
+ PHE:HZPHE:HZ
+ PHE:CE2PHE:CE2
+ PHE:HE2PHE:HE2
+ PHE:CD2PHE:CD2
+ PHE:HD2PHE:HD2
+ PRO:CAPRO:CA
+ PRO:HAPRO:HA
+ PRO:CDPRO:CD
+ PRO:HD2PRO:1HD
+ PRO:HD3PRO:2HD
+ PRO:CGPRO:CG
+ PRO:HG2PRO:1HG
+ PRO:HG3PRO:2HG
+ PRO:CBPRO:CB
+ PRO:HB2PRO:1HB
+ PRO:HB3PRO:2HB
+ SER:CASER:CA
+ SER:HASER:HA
+ SER:CBSER:CB
+ SER:HB2SER:1HB
+ SER:HB3SER:2HB
+ SER:OGSER:OG
+ SER:HGSER:HG
+ THR:CATHR:CA
+ THR:HATHR:HA
+ THR:CBTHR:CB
+ THR:HBTHR:HB
+ THR:CG2THR:CG2
+ THR:HG21THR:1HG2
+ THR:HG22THR:2HG2
+ THR:HG23THR:3HG2
+ THR:OG1THR:OG1
+ THR:HG1THR:HG1
+ TRP:CATRP:CA
+ TRP:HATRP:HA
+ TRP:CBTRP:CB
+ TRP:HB2TRP:1HB
+ TRP:HB3TRP:2HB
+ TRP:CGTRP:CG
+ TRP:CD1TRP:CD1
+ TRP:HD1TRP:HD1
+ TRP:NE1TRP:NE1
+ TRP:HE1TRP:HE1
+ TRP:CE2TRP:CE2
+ TRP:CZ2TRP:CZ2
+ TRP:HZ2TRP:HZ2
+ TRP:CH2TRP:CH2
+ TRP:HH2TRP:HH2
+ TRP:CZ3TRP:CZ3
+ TRP:HZ3TRP:HZ3
+ TRP:CE3TRP:CE3
+ TRP:HE3TRP:HE3
+ TRP:CD2TRP:CD2
+ TYR:CATYR:CA
+ TYR:HATYR:HA
+ TYR:CBTYR:CB
+ TYR:HB2TYR:1HB
+ TYR:HB3TYR:2HB
+ TYR:CGTYR:CG
+ TYR:CD1TYR:CD1
+ TYR:HD1TYR:HD1
+ TYR:CE1TYR:CE1
+ TYR:HE1TYR:HE1
+ TYR:CZTYR:CZ
+ TYR:OHTYR:OH
+ TYR:HHTYR:HH
+ TYR:CE2TYR:CE2
+ TYR:HE2TYR:HE2
+ TYR:CD2TYR:CD2
+ TYR:HD2TYR:HD2
+ VAL:CAVAL:CA
+ VAL:HAVAL:HA
+ VAL:CBVAL:CB
+ VAL:HBVAL:HB
+ VAL:CG1VAL:CG1
+ VAL:HG11VAL:1HG1
+ VAL:HG12VAL:2HG1
+ VAL:HG13VAL:3HG1
+ VAL:CG2VAL:CG2
+ VAL:HG21VAL:1HG2
+ VAL:HG22VAL:2HG2
+ VAL:HG23VAL:3HG2
+ DC:PC:P
+ DC:O1PC:O1P
+ DC:O2PC:O2P
+ DC:O5'C:O5*
+ DC:C5'C:C5*
+ DC:H5'1C:1H5*
+ DC:H5'2C:2H5*
+ DC:C4'C:C4*
+ DC:H4'C:H4*
+ DC:O4'C:O4*
+ DC:C1'C:C1*
+ DC:H1'C:H1*
+ DC:N1C:N1
+ DC:C6C:C6
+ DC:H6C:H6
+ DC:C5C:C5
+ DC:H5C:H5
+ DC:C4C:C4
+ DC:N4C:N4
+ DC:H41C:1H4
+ DC:H42C:2H4
+ DC:N3C:N3
+ DC:C2C:C2
+ DC:O2C:O2
+ DC:C3'C:C3*
+ DC:H3'C:H3*
+ DC:C2'C:C2*
+ DC:H2'1C:1H2*
+ DC:H2'2C:2H2*
+ DC:O3'C:O3*
+ DA:PA:P
+ DA:O1PA:O1P
+ DA:O2PA:O2P
+ DA:O5'A:O5*
+ DA:C5'A:C5*
+ DA:H5'1A:1H5*
+ DA:H5'2A:2H5*
+ DA:C4'A:C4*
+ DA:H4'A:H4*
+ DA:O4'A:O4*
+ DA:C1'A:C1*
+ DA:H1'A:H1*
+ DA:N9A:N9
+ DA:C8A:C8
+ DA:H8A:H8
+ DA:N7A:N7
+ DA:C5A:C5
+ DA:C6A:C6
+ DA:N6A:N6
+ DA:H61A:1H6
+ DA:H62A:2H6
+ DA:N1A:N1
+ DA:C2A:C2
+ DA:H2A:2H
+ DA:N3A:N3
+ DA:C4A:C4
+ DA:C3'A:C3*
+ DA:H3'A:H3*
+ DA:C2'A:C2*
+ DA:H2'1A:1H2*
+ DA:H2'2A:2H2*
+ DA:O3'A:O3*
+ DT:PT:P
+ DT:O1PT:O1P
+ DT:O2PT:O2P
+ DT:O5'T:O5*
+ DT:C5'T:C5*
+ DT:H5'1T:1H5*
+ DT:H5'2T:2H5*
+ DT:C4'T:C4*
+ DT:H4'T:H4*
+ DT:O4'T:O4*
+ DT:C1'T:C1*
+ DT:H1'T:H1*
+ DT:N1T:N1
+ DT:C6T:C6
+ DT:H6T:H6
+ DT:C5T:C5
+ DT:C7T:C5M
+ DT:H71T:1H5M
+ DT:H72T:2H5M
+ DT:H73T:3H5M
+ DT:C4T:C4
+ DT:O4T:O4
+ DT:N3T:N3
+ DT:H3T:3H
+ DT:C2T:C2
+ DT:O2T:O2
+ DT:C3'T:C3*
+ DT:H3'T:H3*
+ DT:C2'T:C2*
+ DT:H2'1T:1H2*
+ DT:H2'2T:2H2*
+ DT:O3'T:O3*
+ DG:PG:P
+ DG:O1PG:O1P
+ DG:O2PG:O2P
+ DG:O5'G:O5*
+ DG:C5'G:C5*
+ DG:H5'1G:1H5*
+ DG:H5'2G:2H5*
+ DG:C4'G:C4*
+ DG:H4'G:H4*
+ DG:O4'G:O4*
+ DG:C1'G:C1*
+ DG:H1'G:H1*
+ DG:N9G:N9
+ DG:C8G:C8
+ DG:H8G:H8
+ DG:N7G:N7
+ DG:C5G:C5
+ DG:C6G:C6
+ DG:O6G:O6
+ DG:N1G:N1
+ DG:H1G:1H
+ DG:C2G:C2
+ DG:N2G:N2
+ DG:H21G:1H2
+ DG:H22G:2H2
+ DG:N3G:N3
+ DG:C4G:C4
+ DG:C3'G:C3*
+ DG:H3'G:H3*
+ DG:C2'G:C2*
+ DG:H2'1G:1H2*
+ DG:H2'2G:2H2*
+ DG:O3'G:O3*
+
+ *:OXT*:OXT
+
+ GLH:CAGLH:CA
+ GLH:HAGLH:HA
+ GLH:CBGLH:CB
+ GLH:HB2GLH:1HB
+ GLH:HB3GLH:2HB
+ GLH:CGGLH:CG
+ GLH:HG2GLH:1HG
+ GLH:HG3GLH:2HG
+ GLH:CDGLH:CD
+ GLH:OE1GLH:OE1
+ GLH:OE2GLH:OE2
+ GLH:HE2GLH:2HE
+
+ HID:CAHID:CA
+ HID:HAHID:HA
+ HID:CBHID:CB
+ HID:HB2HID:1HB
+ HID:HB3HID:2HB
+ HID:CGHID:CG
+ HID:ND1HID:ND1
+ HID:HD1HID:HD1
+ HID:CE1HID:CE1
+ HID:HE1HID:HE1
+ HID:NE2HID:NE2
+ HID:HE2HID:HE2
+ HID:CD2HID:CD2
+ HID:HD2HID:HD2
+
+ HIE:CAHIE:CA
+ HIE:HAHIE:HA
+ HIE:CBHIE:CB
+ HIE:HB2HIE:1HB
+ HIE:HB3HIE:2HB
+ HIE:CGHIE:CG
+ HIE:ND1HIE:ND1
+ HIE:HD1HIE:HD1
+ HIE:CE1HIE:CE1
+ HIE:HE1HIE:HE1
+ HIE:NE2HIE:NE2
+ HIE:HE2HIE:HE2
+ HIE:CD2HIE:CD2
+ HIE:HD2HIE:HD2
+
+ HIP:CAHIP:CA
+ HIP:HAHIP:HA
+ HIP:CBHIP:CB
+ HIP:HB2HIP:1HB
+ HIP:HB3HIP:2HB
+ HIP:CGHIP:CG
+ HIP:ND1HIP:ND1
+ HIP:HD1HIP:HD1
+ HIP:CE1HIP:CE1
+ HIP:HE1HIP:HE1
+ HIP:NE2HIP:NE2
+ HIP:HE2HIP:HE2
+ HIP:CD2HIP:CD2
+ HIP:HD2HIP:HD2
+
+ CYM:CACYM:CA
+ CYM:CBCYM:CB
+ CYM:HACYM:HA
+ CYM:HB2CYM:1HB
+ CYM:HB3CYM:2HB
+ CYM:SGCYM:SG
+ CYM:HNCYM:HN
+
+ CYX:CACYX:CA
+ CYX:CBCYX:CB
+ CYX:HACYX:HA
+ CYX:HB2CYX:1HB
+ CYX:HB3CYX:2HB
+ CYX:SGCYX:SG
+
+ ACE:CH3ACE:CH3
+ ACE:HH31ACE:1HH3
+ ACE:HH32ACE:2HH3
+ ACE:HH33ACE:3HH3
+ NME:CH3NME:CH3
+ NME:HH31NME:1HH3
+ NME:HH32NME:2HH3
+ NME:HH33NME:3HH3
+
+ LYN:NZLYN:NZ
+ LYN:CALYN:CA
+ LYN:CBLYN:CB
+ LYN:CGLYN:CG
+ LYN:CDLYN:CD
+ LYN:CELYN:CE
+ LYN:HALYN:HA
+ LYN:HB2LYN:1HB
+ LYN:HB3LYN:2HB
+ LYN:HD2LYN:1HD
+ LYN:HD3LYN:2HD
+ LYN:HE2LYN:1HE
+ LYN:HE3LYN:2HE
+ LYN:HG2LYN:1HG
+ LYN:HG3LYN:2HG
+ LYN:HZ2LYN:2HZ
+ LYN:HZ3LYN:3HZ
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Names.CHARMM.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.CHARMM.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,279 @@
+CHARMMPDB
+ *:H1*:1H
+ *:H2*:2H
+ *:H3*:3H
+ *:N*:N
+ *:C*:C
+ *:CA*:CA
+ *:O*:O
+ *:H*:H
+ *:OT1*:O
+ *:OT2*:OXT
+ *:OCT1*:O
+ *:OCT2*:OXT
+ *:HT1*:1H
+ *:HT2*:2H
+ *:HT3*:3H
+ ALA:HB1ALA:1HB
+ ALA:HB2ALA:2HB
+ ALA:HB3ALA:3HB
+ ARG:HB2ARG:1HB
+ ARG:HB3ARG:2HB
+ ARG:HG2ARG:1HG
+ ARG:HG3ARG:2HG
+ ARG:HD2ARG:1HD
+ ARG:HD3ARG:2HD
+ ARG:HH1ARG:1HH1
+ ARG:HH2ARG:1HH2
+ ARG:HH11ARG:1HH1
+ ARG:HH12ARG:2HH1
+ ARG:HH21ARG:1HH2
+ ARG:HH22ARG:2HH2
+ ASN:HB2ASN:1HB
+ ASN:HB3ASN:2HB
+ ASN:HD1ASN:1HD1
+ ASN:HD2ASN:1HD2
+ ASN:HD21ASN:1HD2
+ ASN:HD22ASN:2HD2
+ ASP:HB2ASP:1HB
+ ASP:HB3ASP:2HB
+ CYS:HB2CYS:1HB
+ CYS:HB3CYS:2HB
+ GLU:HB2GLU:1HB
+ GLU:HB3GLU:2HB
+ GLU:HG2GLU:1HG
+ GLU:HG3GLU:2HG
+ GLN:HB2GLN:1HB
+ GLN:HB3GLN:2HB
+ GLN:HG2GLN:1HG
+ GLN:HG3GLN:2HG
+ GLN:HE21GLN:1HE2
+ GLN:HE22GLN:2HE2
+ GLN:HE1GLN:1HE1
+ GLN:HE2GLN:1HE2
+ GLY:HA2GLY:1HA
+ GLY:HA3GLY:2HA
+ HIS:HB2HIS:1HB
+ HIS:HB3HIS:2HB
+ HIE:*HIS:*
+ HID:*HIS:*
+ HIP:*HIS:*
+ ILE:HG21ILE:1HG2
+ ILE:HG22ILE:2HG2
+ ILE:HG23ILE:3HG2
+ ILE:HG12ILE:1HG1
+ ILE:HG13ILE:2HG1
+ ILE:HD11ILE:1HD1
+ ILE:HD12ILE:2HD1
+ ILE:HD13ILE:3HD1
+ ILE:CDILE:CD1
+ LEU:HB2LEU:1HB
+ LEU:HB3LEU:2HB
+ LEU:HD11LEU:1HD1
+ LEU:HD12LEU:2HD1
+ LEU:HD13LEU:3HD1
+ LEU:HD21LEU:1HD2
+ LEU:HD22LEU:2HD2
+ LEU:HD23LEU:3HD2
+ LYS:HB2LYS:1HB
+ LYS:HB3LYS:2HB
+ LYS:HG2LYS:1HG
+ LYS:HG3LYS:2HG
+ LYS:HD2LYS:1HD
+ LYS:HD3LYS:2HD
+ LYS:HE2LYS:1HE
+ LYS:HE3LYS:2HE
+ LYS:HZ1LYS:1HZ
+ LYS:HZ2LYS:2HZ
+ LYS:HZ3LYS:3HZ
+ MET:HB2MET:1HB
+ MET:HB3MET:2HB
+ MET:HG2MET:1HG
+ MET:HG3MET:2HG
+ MET:HE1MET:1HE
+ MET:HE2MET:2HE
+ MET:HE3MET:3HE
+ PHE:HB2PHE:1HB
+ PHE:HB3PHE:2HB
+ PRO:HD2PRO:1HD
+ PRO:HD3PRO:2HD
+ PRO:HG2PRO:1HG
+ PRO:HG3PRO:2HG
+ PRO:HB2PRO:1HB
+ PRO:HB3PRO:2HB
+ SER:HB2SER:1HB
+ SER:HB3SER:2HB
+ THR:HG21THR:1HG2
+ THR:HG22THR:2HG2
+ THR:HG23THR:3HG2
+ TRP:HB2TRP:1HB
+ TRP:HB3TRP:2HB
+ TYR:HB2TYR:1HB
+ TYR:HB3TYR:2HB
+ VAL:HG11VAL:1HG1
+ VAL:HG12VAL:2HG1
+ VAL:HG13VAL:3HG1
+ VAL:HG21VAL:1HG2
+ VAL:HG22VAL:2HG2
+ VAL:HG23VAL:3HG2
+ ACE:HH31ACE:1HH3
+ ACE:HH32ACE:2HH3
+ ACE:HH33ACE:3HH3
+ NME:HH31NME:1HH3
+ NME:HH32NME:2HH3
+ NME:HH33NME:3HH3
+ ALA:CAALA:CA
+ ALA:HAALA:HA
+ ALA:CBALA:CB
+ ARG:CAARG:CA
+ ARG:HAARG:HA
+ ARG:CBARG:CB
+ ARG:CGARG:CG
+ ARG:CDARG:CD
+ ARG:NEARG:NE
+ ARG:HEARG:HE
+ ARG:CZARG:CZ
+ ARG:NH1ARG:NH1
+ ARG:NH2ARG:NH2
+ ASN:CAASN:CA
+ ASN:HAASN:HA
+ ASN:CBASN:CB
+ ASN:CGASN:CG
+ ASN:OD1ASN:OD1
+ ASN:ND2ASN:ND2
+ ASP:CAASP:CA
+ ASP:HAASP:HA
+ ASP:CBASP:CB
+ ASP:CGASP:CG
+ ASP:OD1ASP:OD1
+ ASP:OD2ASP:OD2
+ CYS:CACYS:CA
+ CYS:HACYS:HA
+ CYS:CBCYS:CB
+ CYS:SGCYS:SG
+ CYS:HGCYS:HG
+ GLU:CAGLU:CA
+ GLU:HAGLU:HA
+ GLU:CBGLU:CB
+ GLU:CGGLU:CG
+ GLU:CDGLU:CD
+ GLU:OE1GLU:OE1
+ GLU:OE2GLU:OE2
+ GLN:CAGLN:CA
+ GLN:HAGLN:HA
+ GLN:CBGLN:CB
+ GLN:CGGLN:CG
+ GLN:CDGLN:CD
+ GLN:OE1GLN:OE1
+ GLN:NE2GLN:NE2
+ GLY:CAGLY:CA
+ HIS:CAHIS:CA
+ HIS:HAHIS:HA
+ HIS:CBHIS:CB
+ HIS:CGHIS:CG
+ HIS:ND1HIS:ND1
+ HIS:HD1HIS:HD1
+ HIS:CE1HIS:CE1
+ HIS:HE1HIS:HE1
+ HIS:NE2HIS:NE2
+ HIS:HE2HIS:HE2
+ HIS:CD2HIS:CD2
+ HIS:HD2HIS:HD2
+ ILE:CAILE:CA
+ ILE:HAILE:HA
+ ILE:CBILE:CB
+ ILE:HBILE:HB
+ ILE:CG2ILE:CG2
+ ILE:CG1ILE:CG1
+ ILE:CD1ILE:CD1
+ LEU:CALEU:CA
+ LEU:HALEU:HA
+ LEU:CBLEU:CB
+ LEU:CGLEU:CG
+ LEU:HGLEU:HG
+ LEU:CD1LEU:CD1
+ LEU:CD2LEU:CD2
+ LYS:CALYS:CA
+ LYS:HALYS:HA
+ LYS:CBLYS:CB
+ LYS:CGLYS:CG
+ LYS:CDLYS:CD
+ LYS:CELYS:CE
+ LYS:NZLYS:NZ
+ MET:CAMET:CA
+ MET:HAMET:HA
+ MET:CBMET:CB
+ MET:CGMET:CG
+ MET:SDMET:SD
+ MET:CEMET:CE
+ PHE:CAPHE:CA
+ PHE:HAPHE:HA
+ PHE:CBPHE:CB
+ PHE:CGPHE:CG
+ PHE:CD1PHE:CD1
+ PHE:HD1PHE:HD1
+ PHE:CE1PHE:CE1
+ PHE:HE1PHE:HE1
+ PHE:CZPHE:CZ
+ PHE:HZPHE:HZ
+ PHE:CE2PHE:CE2
+ PHE:HE2PHE:HE2
+ PHE:CD2PHE:CD2
+ PHE:HD2PHE:HD2
+ PRO:CAPRO:CA
+ PRO:HAPRO:HA
+ PRO:CDPRO:CD
+ PRO:CGPRO:CG
+ PRO:CBPRO:CB
+ SER:CASER:CA
+ SER:HASER:HA
+ SER:CBSER:CB
+ SER:OGSER:OG
+ SER:HGSER:HG
+ THR:CATHR:CA
+ THR:HATHR:HA
+ THR:CBTHR:CB
+ THR:HBTHR:HB
+ THR:CG2THR:CG2
+ THR:OG1THR:OG1
+ THR:HG1THR:HG1
+ TRP:CATRP:CA
+ TRP:HATRP:HA
+ TRP:CBTRP:CB
+ TRP:CGTRP:CG
+ TRP:CD1TRP:CD1
+ TRP:HD1TRP:HD1
+ TRP:NE1TRP:NE1
+ TRP:HE1TRP:HE1
+ TRP:CE2TRP:CE2
+ TRP:CZ2TRP:CZ2
+ TRP:HZ2TRP:HZ2
+ TRP:CH2TRP:CH2
+ TRP:HH2TRP:HH2
+ TRP:CZ3TRP:CZ3
+ TRP:HZ3TRP:HZ3
+ TRP:CE3TRP:CE3
+ TRP:HE3TRP:HE3
+ TRP:CD2TRP:CD2
+ TYR:CATYR:CA
+ TYR:HATYR:HA
+ TYR:CBTYR:CB
+ TYR:CGTYR:CG
+ TYR:CD1TYR:CD1
+ TYR:HD1TYR:HD1
+ TYR:CE1TYR:CE1
+ TYR:HE1TYR:HE1
+ TYR:CZTYR:CZ
+ TYR:OHTYR:OH
+ TYR:HHTYR:HH
+ TYR:CE2TYR:CE2
+ TYR:HE2TYR:HE2
+ TYR:CD2TYR:CD2
+ TYR:HD2TYR:HD2
+ VAL:CAVAL:CA
+ VAL:HAVAL:HA
+ VAL:CBVAL:CB
+ VAL:HBVAL:HB
+ VAL:CG1VAL:CG1
+ VAL:CG2VAL:CG2
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Names.DNA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.DNA.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,174 @@
+DNAPDB
+ C:PC:P
+ DC:OP1C:O1P
+ DC:OP2C:O2P
+ DC:*C:*
+ C:OP1C:O1P
+ C:OP2C:O2P
+ C:O5'C:O5*
+ C:C5'C:C5*
+ C:H5'C:1H5*
+ C:H5''C:2H5*
+ C:C4'C:C4*
+ C:H4'C:H4*
+ C:O4'C:O4*
+ C:C1'C:C1*
+ C:H1'C:H1*
+ C:N1C:N1
+ C:C6C:C6
+ C:H6C:H6
+ C:C5C:C5
+ C:H5C:H5
+ C:C4C:C4
+ C:N4C:N4
+ C:H41C:1H4
+ C:H42C:2H4
+ C:N3C:N3
+ C:C2C:C2
+ C:O2C:O2
+ C:O2'C:O2*
+ C:HO2'C:HO3*
+ C:C3'C:C3*
+ C:H3'C:H3*
+ C:C2'C:C2*
+ C:H2'C:1H2*
+ C:H2''C:2H2*
+ C:O3'C:O3*
+ A:PA:P
+ DA:OP1A:O1P
+ DA:OP2A:O2P
+ DA:*A:*
+ A:OP1A:O1P
+ A:OP2A:O2P
+ A:O5'A:O5*
+ A:C5'A:C5*
+ A:H5'A:1H5*
+ A:H5''A:2H5*
+ A:C4'A:C4*
+ A:H4'A:H4*
+ A:O4'A:O4*
+ A:C1'A:C1*
+ A:H1'A:H1*
+ A:N9A:N9
+ A:C8A:C8
+ A:H8A:H8
+ A:N7A:N7
+ A:C5A:C5
+ A:C6A:C6
+ A:N6A:N6
+ A:H61A:1H6
+ A:H62A:2H6
+ A:N1A:N1
+ A:C2A:C2
+ A:H2A:2H
+ A:N3A:N3
+ A:C4A:C4
+ A:C3'A:C3*
+ A:H3'A:H3*
+ A:C2'A:C2*
+ A:H2'A:1H2*
+ A:H2''A:2H2*
+ A:O3'A:O3*
+ U:PU:P
+ U:OP1U:O1P
+ U:OP2U:O2P
+ U:O5'U:O5*
+ U:C5'U:C5*
+ U:H5'U:1H5*
+ U:H5''U:2H5*
+ U:C4'U:C4*
+ U:H4'U:H4*
+ U:O4'U:O4*
+ U:C1'U:C1*
+ U:H1'U:H1*
+ U:N1U:N1
+ U:C6U:C6
+ U:H6U:H6
+ U:C5U:C5
+ U:C4U:C4
+ U:O4U:O4
+ U:N3U:N3
+ U:H3U:H3
+ U:C2U:C2
+ U:O2U:O2
+ U:O2'U:O2*
+ U:HO2'U:HO2*
+ U:C3'U:C3*
+ U:H3'U:H3*
+ U:C2'U:C2*
+ U:H2'U:1H2*
+ U:H2''U:2H2*
+ U:O3'U:O3*
+
+ T:PT:P
+ DT:OP1T:O1P
+ DT:OP2T:O2P
+ DT:*T:*
+ T:OP1T:O1P
+ T:OP2T:O2P
+ T:O5'T:O5*
+ T:C5'T:C5*
+ T:H5'T:1H5*
+ T:H5''T:2H5*
+ T:C4'T:C4*
+ T:H4'T:H4*
+ T:O4'T:O4*
+ T:C1'T:C1*
+ T:H1'T:H1*
+ T:N1T:N1
+ T:C6T:C6
+ T:H6T:H6
+ T:C5T:C5
+ T:C7T:C5M
+ T:H71T:1H5M
+ T:H72T:2H5M
+ T:H73T:3H5M
+ T:C4T:C4
+ T:O4T:O4
+ T:N3T:N3
+ T:C2T:C2
+ T:O2T:O2
+ T:C3'T:C3*
+ T:H3'T:H3*
+ T:C2'T:C2*
+ T:H2'T:1H2*
+ T:H2''T:2H2*
+ T:O3'T:O3*
+ T:H3T:3H
+ G:PG:P
+ DG:OP1G:O1P
+ DG:OP2G:O2P
+ DG:*G:*
+ G:OP1G:O1P
+ G:OP2G:O2P
+ G:O5'G:O5*
+ G:C5'G:C5*
+ G:H5'G:1H5*
+ G:H5''G:2H5*
+ G:C4'G:C4*
+ G:H4'G:H4*
+ G:O4'G:O4*
+ G:C1'G:C1*
+ G:H1'G:H1*
+ G:N9G:N9
+ G:C8G:C8
+ G:H8G:H8
+ G:N7G:N7
+ G:C5G:C5
+ G:C6G:C6
+ G:O6G:O6
+ G:N1G:N1
+ G:H1G:1H
+ G:C2G:C2
+ G:N2G:N2
+ G:H21G:1H2
+ G:H22G:2H2
+ G:N3G:N3
+ G:C4G:C4
+ G:C3'G:C3*
+ G:H3'G:H3*
+ G:C2'G:C2*
+ G:H2'G:1H2*
+ G:H2''G:2H2*
+ G:O3'G:O3*
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Names.Discover.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Discover.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,255 @@
+DiscoverPDB
+ *:H1*:1H
+ *:H2*:2H
+ *:H3*:3H
+ *:N*:N
+ *:O*:O
+ *:C*:C
+ *:HN*:H
+ ALA:CAALA:CA
+ ALA:HAALA:HA
+ ALA:CBALA:CB
+ ALA:HB1ALA:1HB
+ ALA:HB2ALA:2HB
+ ALA:HB3ALA:3HB
+ ARG:CAARG:CA
+ ARG:HAARG:HA
+ ARG:CBARG:CB
+ ARG:HB1ARG:1HB
+ ARG:HB2ARG:2HB
+ ARG:CGARG:CG
+ ARG:HG1ARG:1HG
+ ARG:HG2ARG:2HG
+ ARG:CDARG:CD
+ ARG:HD1ARG:1HD
+ ARG:HD2ARG:2HD
+ ARG:NEARG:NE
+ ARG:HEARG:HE
+ ARG:CZARG:CZ
+ ARG:NH1ARG:NH1
+ ARG:HH11ARG:1HH1
+ ARG:HH12ARG:2HH1
+ ARG:NH2ARG:NH2
+ ARG:HH21ARG:1HH2
+ ARG:HH22ARG:2HH2
+ ASN:CAASN:CA
+ ASN:HAASN:HA
+ ASN:CBASN:CB
+ ASN:HB1ASN:1HB
+ ASN:HB2ASN:2HB
+ ASN:CGASN:CG
+ ASN:OD1ASN:OD1
+ ASN:ND2ASN:ND2
+ ASN:HD21ASN:1HD2
+ ASN:HD22ASN:2HD2
+ ASP:CAASP:CA
+ ASP:HAASP:HA
+ ASP:CBASP:CB
+ ASP:HB1ASP:1HB
+ ASP:HB2ASP:2HB
+ ASP:CGASP:CG
+ ASP:OD1ASP:OD1
+ ASP:OD2ASP:OD2
+ CYS:CACYS:CA
+ CYS:HACYS:HA
+ CYS:CBCYS:CB
+ CYS:HB1CYS:1HB
+ CYS:HB2CYS:2HB
+ CYS:SGCYS:SG
+ CYS:HGCYS:HG
+ GLU:CAGLU:CA
+ GLU:HAGLU:HA
+ GLU:CBGLU:CB
+ GLU:HB1GLU:1HB
+ GLU:HB2GLU:2HB
+ GLU:CGGLU:CG
+ GLU:HG1GLU:1HG
+ GLU:HG2GLU:2HG
+ GLU:CDGLU:CD
+ GLU:OE1GLU:OE1
+ GLU:OE2GLU:OE2
+ GLN:CAGLN:CA
+ GLN:HAGLN:HA
+ GLN:CBGLN:CB
+ GLN:HB1GLN:1HB
+ GLN:HB2GLN:2HB
+ GLN:CGGLN:CG
+ GLN:HG1GLN:1HG
+ GLN:HG2GLN:2HG
+ GLN:CDGLN:CD
+ GLN:OE1GLN:OE1
+ GLN:NE2GLN:NE2
+ GLN:HE21GLN:1HE2
+ GLN:HE22GLN:2HE2
+ GLY:CAGLY:CA
+ GLY:HA1GLY:1HA
+ GLY:HA2GLY:2HA
+ HIS:CAHIS:CA
+ HIS:HAHIS:HA
+ HIS:CBHIS:CB
+ HIS:HB1HIS:1HB
+ HIS:HB2HIS:2HB
+ HIS:CGHIS:CG
+ HIS:ND1HIS:ND1
+ HIS:HD1HIS:HD1
+ HIS:CE1HIS:CE1
+ HIS:HE1HIS:HE1
+ HIS:NE2HIS:NE2
+ HIS:HE2HIS:HE2
+ HIS:CD2HIS:CD2
+ HIS:HD2HIS:HD2
+ ILE:CAILE:CA
+ ILE:HAILE:HA
+ ILE:CBILE:CB
+ ILE:HBILE:HB
+ ILE:CG2ILE:CG2
+ ILE:HG21ILE:1HG2
+ ILE:HG22ILE:2HG2
+ ILE:HG23ILE:3HG2
+ ILE:CG1ILE:CG1
+ ILE:HG11ILE:1HG1
+ ILE:HG12ILE:2HG1
+ ILE:CD1ILE:CD1
+ ILE:HD11ILE:1HD1
+ ILE:HD12ILE:2HD1
+ ILE:HD13ILE:3HD1
+ LEU:CALEU:CA
+ LEU:HALEU:HA
+ LEU:CBLEU:CB
+ LEU:HB1LEU:1HB
+ LEU:HB2LEU:2HB
+ LEU:CGLEU:CG
+ LEU:HGLEU:HG
+ LEU:CD1LEU:CD1
+ LEU:HD11LEU:1HD1
+ LEU:HD12LEU:2HD1
+ LEU:HD13LEU:3HD1
+ LEU:CD2LEU:CD2
+ LEU:HD21LEU:1HD2
+ LEU:HD22LEU:2HD2
+ LEU:HD23LEU:3HD2
+ LYS:CALYS:CA
+ LYS:HALYS:HA
+ LYS:CBLYS:CB
+ LYS:HB1LYS:1HB
+ LYS:HB2LYS:2HB
+ LYS:CGLYS:CG
+ LYS:HG1LYS:1HG
+ LYS:HG2LYS:2HG
+ LYS:CDLYS:CD
+ LYS:HD1LYS:1HD
+ LYS:HD2LYS:2HD
+ LYS:CELYS:CE
+ LYS:HE1LYS:1HE
+ LYS:HE2LYS:2HE
+ LYS:NZLYS:NZ
+ LYS:HZ1LYS:1HZ
+ LYS:HZ2LYS:2HZ
+ LYS:HZ3LYS:3HZ
+ MET:CAMET:CA
+ MET:HAMET:HA
+ MET:CBMET:CB
+ MET:HB1MET:1HB
+ MET:HB2MET:2HB
+ MET:CGMET:CG
+ MET:HG1MET:1HG
+ MET:HG2MET:2HG
+ MET:SDMET:SD
+ MET:CEMET:CE
+ MET:HE1MET:1HE
+ MET:HE2MET:2HE
+ MET:HE3MET:3HE
+ PHE:CAPHE:CA
+ PHE:HAPHE:HA
+ PHE:CBPHE:CB
+ PHE:HB1PHE:1HB
+ PHE:HB2PHE:2HB
+ PHE:CGPHE:CG
+ PHE:CD1PHE:CD1
+ PHE:HD1PHE:HD1
+ PHE:CE1PHE:CE1
+ PHE:HE1PHE:HE1
+ PHE:CZPHE:CZ
+ PHE:HZPHE:HZ
+ PHE:CE2PHE:CE2
+ PHE:HE2PHE:HE2
+ PHE:CD2PHE:CD2
+ PHE:HD2PHE:HD2
+ PRO:CAPRO:CA
+ PRO:HAPRO:HA
+ PRO:CDPRO:CD
+ PRO:HD1PRO:1HD
+ PRO:HD2PRO:2HD
+ PRO:CGPRO:CG
+ PRO:HG1PRO:1HG
+ PRO:HG2PRO:2HG
+ PRO:CBPRO:CB
+ PRO:HB1PRO:1HB
+ PRO:HB2PRO:2HB
+ SER:CASER:CA
+ SER:HASER:HA
+ SER:CBSER:CB
+ SER:HB1SER:1HB
+ SER:HB2SER:2HB
+ SER:OGSER:OG
+ SER:HGSER:HG
+ THR:CATHR:CA
+ THR:HATHR:HA
+ THR:CBTHR:CB
+ THR:HBTHR:HB
+ THR:CG2THR:CG2
+ THR:HG21THR:1HG2
+ THR:HG22THR:2HG2
+ THR:HG23THR:3HG2
+ THR:OG1THR:OG1
+ THR:HG1THR:HG1
+ TRP:CATRP:CA
+ TRP:HATRP:HA
+ TRP:CBTRP:CB
+ TRP:HB1TRP:1HB
+ TRP:HB2TRP:2HB
+ TRP:CGTRP:CG
+ TRP:CD1TRP:CD1
+ TRP:HD1TRP:HD1
+ TRP:NE1TRP:NE1
+ TRP:HE1TRP:HE1
+ TRP:CE2TRP:CE2
+ TRP:CZ2TRP:CZ2
+ TRP:HZ2TRP:HZ2
+ TRP:CH2TRP:CH2
+ TRP:HH2TRP:HH2
+ TRP:CZ3TRP:CZ3
+ TRP:HZ3TRP:HZ3
+ TRP:CE3TRP:CE3
+ TRP:HE3TRP:HE3
+ TRP:CD2TRP:CD2
+ TYR:CATYR:CA
+ TYR:HATYR:HA
+ TYR:CBTYR:CB
+ TYR:HB1TYR:1HB
+ TYR:HB2TYR:2HB
+ TYR:CGTYR:CG
+ TYR:CD1TYR:CD1
+ TYR:HD1TYR:HD1
+ TYR:CE1TYR:CE1
+ TYR:HE1TYR:HE1
+ TYR:CZTYR:CZ
+ TYR:OHTYR:OH
+ TYR:HHTYR:HH
+ TYR:CE2TYR:CE2
+ TYR:HE2TYR:HE2
+ TYR:CD2TYR:CD2
+ TYR:HD2TYR:HD2
+ VAL:CAVAL:CA
+ VAL:HAVAL:HA
+ VAL:CBVAL:CB
+ VAL:HBVAL:HB
+ VAL:CG1VAL:CG1
+ VAL:HG11VAL:1HG1
+ VAL:HG12VAL:2HG1
+ VAL:HG13VAL:3HG1
+ VAL:CG2VAL:CG2
+ VAL:HG21VAL:1HG2
+ VAL:HG22VAL:2HG2
+ VAL:HG23VAL:3HG2
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Names.Star.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Star.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,261 @@
+StarPDB
+ *:H1*:1H
+ *:H2*:2H
+ *:H3*:3H
+ *:HT1*:1H
+ *:HT2*:2H
+ *:HT3*:3H
+ *:OT1*:O
+ *:OT2*:OXT
+ *:N*:N
+ *:O*:O
+ *:C*:C
+ *:HN*:H
+ *:H*:H
+ ALA:CAALA:CA
+ ALA:HAALA:HA
+ ALA:CBALA:CB
+ ALA:HB1ALA:1HB
+ ALA:HB2ALA:2HB
+ ALA:HB3ALA:3HB
+ ARG:CAARG:CA
+ ARG:HAARG:HA
+ ARG:CBARG:CB
+ ARG:HB2ARG:1HB
+ ARG:HB3ARG:2HB
+ ARG:CGARG:CG
+ ARG:HG2ARG:1HG
+ ARG:HG3ARG:2HG
+ ARG:CDARG:CD
+ ARG:HD2ARG:1HD
+ ARG:HD3ARG:2HD
+ ARG:NEARG:NE
+ ARG:HEARG:HE
+ ARG:CZARG:CZ
+ ARG:NH1ARG:NH1
+ ARG:HH11ARG:1HH1
+ ARG:HH12ARG:2HH1
+ ARG:NH2ARG:NH2
+ ARG:HH21ARG:1HH2
+ ARG:HH22ARG:2HH2
+ ASN:CAASN:CA
+ ASN:HAASN:HA
+ ASN:CBASN:CB
+ ASN:HB2ASN:1HB
+ ASN:HB3ASN:2HB
+ ASN:CGASN:CG
+ ASN:OD1ASN:OD1
+ ASN:ND2ASN:ND2
+ ASN:HD21ASN:1HD2
+ ASN:HD22ASN:2HD2
+ ASP:CAASP:CA
+ ASP:HAASP:HA
+ ASP:CBASP:CB
+ ASP:HB2ASP:1HB
+ ASP:HB3ASP:2HB
+ ASP:CGASP:CG
+ ASP:OD1ASP:OD1
+ ASP:OD2ASP:OD2
+ CYS:CACYS:CA
+ CYS:HACYS:HA
+ CYS:CBCYS:CB
+ CYS:HB2CYS:1HB
+ CYS:HB3CYS:2HB
+ CYS:SGCYS:SG
+ CYS:HGCYS:HG
+ GLU:CAGLU:CA
+ GLU:HAGLU:HA
+ GLU:CBGLU:CB
+ GLU:HB2GLU:1HB
+ GLU:HB3GLU:2HB
+ GLU:CGGLU:CG
+ GLU:HG2GLU:1HG
+ GLU:HG3GLU:2HG
+ GLU:CDGLU:CD
+ GLU:OE1GLU:OE1
+ GLU:OE2GLU:OE2
+ GLN:CAGLN:CA
+ GLN:HAGLN:HA
+ GLN:CBGLN:CB
+ GLN:HB2GLN:1HB
+ GLN:HB3GLN:2HB
+ GLN:CGGLN:CG
+ GLN:HG2GLN:1HG
+ GLN:HG3GLN:2HG
+ GLN:CDGLN:CD
+ GLN:OE1GLN:OE1
+ GLN:NE2GLN:NE2
+ GLN:HE21GLN:1HE2
+ GLN:HE22GLN:2HE2
+ GLY:CAGLY:CA
+ GLY:HA2GLY:1HA
+ GLY:HA3GLY:2HA
+ HIS:CAHIS:CA
+ HIS:HAHIS:HA
+ HIS:CBHIS:CB
+ HIS:HB2HIS:1HB
+ HIS:HB3HIS:2HB
+ HIS:CGHIS:CG
+ HIS:ND1HIS:ND1
+ HIS:HD1HIS:HD1
+ HIS:CE1HIS:CE1
+ HIS:HE1HIS:HE1
+ HIS:NE2HIS:NE2
+ HIS:HE2HIS:HE2
+ HIS:CD2HIS:CD2
+ HIS:HD2HIS:HD2
+ ILE:CAILE:CA
+ ILE:HAILE:HA
+ ILE:CBILE:CB
+ ILE:HBILE:HB
+ ILE:CG2ILE:CG2
+ ILE:HG21ILE:1HG2
+ ILE:HG22ILE:2HG2
+ ILE:HG23ILE:3HG2
+ ILE:CG1ILE:CG1
+ ILE:HG12ILE:1HG1
+ ILE:HG13ILE:2HG1
+ ILE:CD1ILE:CD1
+ ILE:HD11ILE:1HD1
+ ILE:HD12ILE:2HD1
+ ILE:HD13ILE:3HD1
+ LEU:CALEU:CA
+ LEU:HALEU:HA
+ LEU:CBLEU:CB
+ LEU:HB2LEU:1HB
+ LEU:HB3LEU:2HB
+ LEU:CGLEU:CG
+ LEU:HGLEU:HG
+ LEU:CD1LEU:CD1
+ LEU:HD11LEU:1HD1
+ LEU:HD12LEU:2HD1
+ LEU:HD13LEU:3HD1
+ LEU:CD2LEU:CD2
+ LEU:HD21LEU:1HD2
+ LEU:HD22LEU:2HD2
+ LEU:HD23LEU:3HD2
+ LYS:CALYS:CA
+ LYS:HALYS:HA
+ LYS:CBLYS:CB
+ LYS:HB2LYS:1HB
+ LYS:HB3LYS:2HB
+ LYS:CGLYS:CG
+ LYS:HG2LYS:1HG
+ LYS:HG3LYS:2HG
+ LYS:CDLYS:CD
+ LYS:HD2LYS:1HD
+ LYS:HD3LYS:2HD
+ LYS:CELYS:CE
+ LYS:HE2LYS:1HE
+ LYS:HE3LYS:2HE
+ LYS:NZLYS:NZ
+ LYS:HZ1LYS:1HZ
+ LYS:HZ2LYS:2HZ
+ LYS:HZ3LYS:3HZ
+ MET:CAMET:CA
+ MET:HAMET:HA
+ MET:CBMET:CB
+ MET:HB2MET:1HB
+ MET:HB3MET:2HB
+ MET:CGMET:CG
+ MET:HG2MET:1HG
+ MET:HG3MET:2HG
+ MET:SDMET:SD
+ MET:CEMET:CE
+ MET:HE1MET:1HE
+ MET:HE2MET:2HE
+ MET:HE3MET:3HE
+ PHE:CAPHE:CA
+ PHE:HAPHE:HA
+ PHE:CBPHE:CB
+ PHE:HB2PHE:1HB
+ PHE:HB3PHE:2HB
+ PHE:CGPHE:CG
+ PHE:CD1PHE:CD1
+ PHE:HD1PHE:HD1
+ PHE:CE1PHE:CE1
+ PHE:HE1PHE:HE1
+ PHE:CZPHE:CZ
+ PHE:HZPHE:HZ
+ PHE:CE2PHE:CE2
+ PHE:HE2PHE:HE2
+ PHE:CD2PHE:CD2
+ PHE:HD2PHE:HD2
+ PRO:CAPRO:CA
+ PRO:HAPRO:HA
+ PRO:CDPRO:CD
+ PRO:HD2PRO:1HD
+ PRO:HD3PRO:2HD
+ PRO:CGPRO:CG
+ PRO:HG2PRO:1HG
+ PRO:HG3PRO:2HG
+ PRO:CBPRO:CB
+ PRO:HB2PRO:1HB
+ PRO:HB3PRO:2HB
+ SER:CASER:CA
+ SER:HASER:HA
+ SER:CBSER:CB
+ SER:HB2SER:1HB
+ SER:HB3SER:2HB
+ SER:OGSER:OG
+ SER:HGSER:HG
+ THR:CATHR:CA
+ THR:HATHR:HA
+ THR:CBTHR:CB
+ THR:HBTHR:HB
+ THR:CG2THR:CG2
+ THR:HG21THR:1HG2
+ THR:HG22THR:2HG2
+ THR:HG23THR:3HG2
+ THR:OG1THR:OG1
+ THR:HG1THR:HG1
+ TRP:CATRP:CA
+ TRP:HATRP:HA
+ TRP:CBTRP:CB
+ TRP:HB2TRP:1HB
+ TRP:HB3TRP:2HB
+ TRP:CGTRP:CG
+ TRP:CD1TRP:CD1
+ TRP:HD1TRP:HD1
+ TRP:NE1TRP:NE1
+ TRP:HE1TRP:HE1
+ TRP:CE2TRP:CE2
+ TRP:CZ2TRP:CZ2
+ TRP:HZ2TRP:HZ2
+ TRP:CH2TRP:CH2
+ TRP:HH2TRP:HH2
+ TRP:CZ3TRP:CZ3
+ TRP:HZ3TRP:HZ3
+ TRP:CE3TRP:CE3
+ TRP:HE3TRP:HE3
+ TRP:CD2TRP:CD2
+ TYR:CATYR:CA
+ TYR:HATYR:HA
+ TYR:CBTYR:CB
+ TYR:HB2TYR:1HB
+ TYR:HB3TYR:2HB
+ TYR:CGTYR:CG
+ TYR:CD1TYR:CD1
+ TYR:HD1TYR:HD1
+ TYR:CE1TYR:CE1
+ TYR:HE1TYR:HE1
+ TYR:CZTYR:CZ
+ TYR:OHTYR:OH
+ TYR:HHTYR:HH
+ TYR:CE2TYR:CE2
+ TYR:HE2TYR:HE2
+ TYR:CD2TYR:CD2
+ TYR:HD2TYR:HD2
+ VAL:CAVAL:CA
+ VAL:HAVAL:HA
+ VAL:CBVAL:CB
+ VAL:HBVAL:HB
+ VAL:CG1VAL:CG1
+ VAL:HG11VAL:1HG1
+ VAL:HG12VAL:2HG1
+ VAL:HG13VAL:3HG1
+ VAL:CG2VAL:CG2
+ VAL:HG21VAL:1HG2
+ VAL:HG22VAL:2HG2
+ VAL:HG23VAL:3HG2
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Names.XPLOR.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.XPLOR.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,256 @@
+XPLORPDB
+ *:H1*:1H
+ *:H2*:2H
+ *:H3*:3H
+ *:N*:N
+ *:O*:O
+ *:C*:C
+ *:HN*:H
+ *:H*:H
+ ALA:CAALA:CA
+ ALA:HAALA:HA
+ ALA:CBALA:CB
+ ALA:HB1ALA:1HB
+ ALA:HB2ALA:2HB
+ ALA:HB3ALA:3HB
+ ARG:CAARG:CA
+ ARG:HAARG:HA
+ ARG:CBARG:CB
+ ARG:HB1ARG:1HB
+ ARG:HB2ARG:2HB
+ ARG:CGARG:CG
+ ARG:HG1ARG:1HG
+ ARG:HG2ARG:2HG
+ ARG:CDARG:CD
+ ARG:HD1ARG:1HD
+ ARG:HD2ARG:2HD
+ ARG:NEARG:NE
+ ARG:HEARG:HE
+ ARG:CZARG:CZ
+ ARG:NH1ARG:NH1
+ ARG:HH11ARG:1HH1
+ ARG:HH12ARG:2HH1
+ ARG:NH2ARG:NH2
+ ARG:HH21ARG:1HH2
+ ARG:HH22ARG:2HH2
+ ASN:CAASN:CA
+ ASN:HAASN:HA
+ ASN:CBASN:CB
+ ASN:HB1ASN:1HB
+ ASN:HB2ASN:2HB
+ ASN:CGASN:CG
+ ASN:OD1ASN:OD1
+ ASN:ND2ASN:ND2
+ ASN:HD21ASN:1HD2
+ ASN:HD22ASN:2HD2
+ ASP:CAASP:CA
+ ASP:HAASP:HA
+ ASP:CBASP:CB
+ ASP:HB1ASP:1HB
+ ASP:HB2ASP:2HB
+ ASP:CGASP:CG
+ ASP:OD1ASP:OD1
+ ASP:OD2ASP:OD2
+ CYS:CACYS:CA
+ CYS:HACYS:HA
+ CYS:CBCYS:CB
+ CYS:HB1CYS:1HB
+ CYS:HB2CYS:2HB
+ CYS:SGCYS:SG
+ CYS:HGCYS:HG
+ GLU:CAGLU:CA
+ GLU:HAGLU:HA
+ GLU:CBGLU:CB
+ GLU:HB1GLU:1HB
+ GLU:HB2GLU:2HB
+ GLU:CGGLU:CG
+ GLU:HG1GLU:1HG
+ GLU:HG2GLU:2HG
+ GLU:CDGLU:CD
+ GLU:OE1GLU:OE1
+ GLU:OE2GLU:OE2
+ GLN:CAGLN:CA
+ GLN:HAGLN:HA
+ GLN:CBGLN:CB
+ GLN:HB1GLN:1HB
+ GLN:HB2GLN:2HB
+ GLN:CGGLN:CG
+ GLN:HG1GLN:1HG
+ GLN:HG2GLN:2HG
+ GLN:CDGLN:CD
+ GLN:OE1GLN:OE1
+ GLN:NE2GLN:NE2
+ GLN:HE21GLN:1HE2
+ GLN:HE22GLN:2HE2
+ GLY:CAGLY:CA
+ GLY:HA1GLY:1HA
+ GLY:HA2GLY:2HA
+ HIS:CAHIS:CA
+ HIS:HAHIS:HA
+ HIS:CBHIS:CB
+ HIS:HB1HIS:1HB
+ HIS:HB2HIS:2HB
+ HIS:CGHIS:CG
+ HIS:ND1HIS:ND1
+ HIS:HD1HIS:HD1
+ HIS:CE1HIS:CE1
+ HIS:HE1HIS:HE1
+ HIS:NE2HIS:NE2
+ HIS:HE2HIS:HE2
+ HIS:CD2HIS:CD2
+ HIS:HD2HIS:HD2
+ ILE:CAILE:CA
+ ILE:HAILE:HA
+ ILE:CBILE:CB
+ ILE:HBILE:HB
+ ILE:CG2ILE:CG2
+ ILE:HG21ILE:1HG2
+ ILE:HG22ILE:2HG2
+ ILE:HG23ILE:3HG2
+ ILE:CG1ILE:CG1
+ ILE:HG11ILE:1HG1
+ ILE:HG12ILE:2HG1
+ ILE:CD1ILE:CD1
+ ILE:HD11ILE:1HD1
+ ILE:HD12ILE:2HD1
+ ILE:HD13ILE:3HD1
+ LEU:CALEU:CA
+ LEU:HALEU:HA
+ LEU:CBLEU:CB
+ LEU:HB1LEU:1HB
+ LEU:HB2LEU:2HB
+ LEU:CGLEU:CG
+ LEU:HGLEU:HG
+ LEU:CD1LEU:CD1
+ LEU:HD11LEU:1HD1
+ LEU:HD12LEU:2HD1
+ LEU:HD13LEU:3HD1
+ LEU:CD2LEU:CD2
+ LEU:HD21LEU:1HD2
+ LEU:HD22LEU:2HD2
+ LEU:HD23LEU:3HD2
+ LYS:CALYS:CA
+ LYS:HALYS:HA
+ LYS:CBLYS:CB
+ LYS:HB1LYS:1HB
+ LYS:HB2LYS:2HB
+ LYS:CGLYS:CG
+ LYS:HG1LYS:1HG
+ LYS:HG2LYS:2HG
+ LYS:CDLYS:CD
+ LYS:HD1LYS:1HD
+ LYS:HD2LYS:2HD
+ LYS:CELYS:CE
+ LYS:HE1LYS:1HE
+ LYS:HE2LYS:2HE
+ LYS:NZLYS:NZ
+ LYS:HZ1LYS:1HZ
+ LYS:HZ2LYS:2HZ
+ LYS:HZ3LYS:3HZ
+ MET:CAMET:CA
+ MET:HAMET:HA
+ MET:CBMET:CB
+ MET:HB1MET:1HB
+ MET:HB2MET:2HB
+ MET:CGMET:CG
+ MET:HG1MET:1HG
+ MET:HG2MET:2HG
+ MET:SDMET:SD
+ MET:CEMET:CE
+ MET:HE1MET:1HE
+ MET:HE2MET:2HE
+ MET:HE3MET:3HE
+ PHE:CAPHE:CA
+ PHE:HAPHE:HA
+ PHE:CBPHE:CB
+ PHE:HB1PHE:1HB
+ PHE:HB2PHE:2HB
+ PHE:CGPHE:CG
+ PHE:CD1PHE:CD1
+ PHE:HD1PHE:HD1
+ PHE:CE1PHE:CE1
+ PHE:HE1PHE:HE1
+ PHE:CZPHE:CZ
+ PHE:HZPHE:HZ
+ PHE:CE2PHE:CE2
+ PHE:HE2PHE:HE2
+ PHE:CD2PHE:CD2
+ PHE:HD2PHE:HD2
+ PRO:CAPRO:CA
+ PRO:HAPRO:HA
+ PRO:CDPRO:CD
+ PRO:HD1PRO:1HD
+ PRO:HD2PRO:2HD
+ PRO:CGPRO:CG
+ PRO:HG1PRO:1HG
+ PRO:HG2PRO:2HG
+ PRO:CBPRO:CB
+ PRO:HB1PRO:1HB
+ PRO:HB2PRO:2HB
+ SER:CASER:CA
+ SER:HASER:HA
+ SER:CBSER:CB
+ SER:HB1SER:1HB
+ SER:HB2SER:2HB
+ SER:OGSER:OG
+ SER:HGSER:HG
+ THR:CATHR:CA
+ THR:HATHR:HA
+ THR:CBTHR:CB
+ THR:HBTHR:HB
+ THR:CG2THR:CG2
+ THR:HG21THR:1HG2
+ THR:HG22THR:2HG2
+ THR:HG23THR:3HG2
+ THR:OG1THR:OG1
+ THR:HG1THR:HG1
+ TRP:CATRP:CA
+ TRP:HATRP:HA
+ TRP:CBTRP:CB
+ TRP:HB1TRP:1HB
+ TRP:HB2TRP:2HB
+ TRP:CGTRP:CG
+ TRP:CD1TRP:CD1
+ TRP:HD1TRP:HD1
+ TRP:NE1TRP:NE1
+ TRP:HE1TRP:HE1
+ TRP:CE2TRP:CE2
+ TRP:CZ2TRP:CZ2
+ TRP:HZ2TRP:HZ2
+ TRP:CH2TRP:CH2
+ TRP:HH2TRP:HH2
+ TRP:CZ3TRP:CZ3
+ TRP:HZ3TRP:HZ3
+ TRP:CE3TRP:CE3
+ TRP:HE3TRP:HE3
+ TRP:CD2TRP:CD2
+ TYR:CATYR:CA
+ TYR:HATYR:HA
+ TYR:CBTYR:CB
+ TYR:HB1TYR:1HB
+ TYR:HB2TYR:2HB
+ TYR:CGTYR:CG
+ TYR:CD1TYR:CD1
+ TYR:HD1TYR:HD1
+ TYR:CE1TYR:CE1
+ TYR:HE1TYR:HE1
+ TYR:CZTYR:CZ
+ TYR:OHTYR:OH
+ TYR:HHTYR:HH
+ TYR:CE2TYR:CE2
+ TYR:HE2TYR:HE2
+ TYR:CD2TYR:CD2
+ TYR:HD2TYR:HD2
+ VAL:CAVAL:CA
+ VAL:HAVAL:HA
+ VAL:CBVAL:CB
+ VAL:HBVAL:HB
+ VAL:CG1VAL:CG1
+ VAL:HG11VAL:1HG1
+ VAL:HG12VAL:2HG1
+ VAL:HG13VAL:3HG1
+ VAL:CG2VAL:CG2
+ VAL:HG21VAL:1HG2
+ VAL:HG22VAL:2HG2
+ VAL:HG23VAL:3HG2
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/PCA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PCA.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,58 @@
+PCA
+ Names
+ Pyroglutamate
+ Pyroglutamat
+ PCA
+
+ Atoms
+ NN 0.633233 -0.738520 0.753950
+ HH 0.354342 -1.687937 0.623119
+ CAC -0.480480 0.254947 0.696080
+ CC -1.757691 -0.270758 -0.060790
+ OO -1.739275 -1.432777 -0.530185
+ CBC 0.102054 1.514384 0.035819
+ CGC 1.511340 1.164025 -0.440294
+ CDC 1.725147 -0.277577 -0.025832
+ OEO 2.716615 -0.966582 -0.238284
+ HAH -0.765277 0.458788 1.753344
+ 1HBH -0.540287 1.847529 -0.801287
+ 2HBH 0.122684 2.361261 0.746090
+ 1HGH 1.616550 1.265144 -1.535904
+ 2HGH 2.282434 1.821242 0.000860
+ OXTO -2.740502 0.498543 -0.143251
+
+ Bonds
+ 4H N s
+ 5C CA s
+ 8O C d
+ 11CB CA s
+ 13CG CB s
+ 17CD CG s
+ 19CD N s
+ 20OE CD d
+ 21HA CA s
+ 221HB CB s
+ 232HB CB s
+ 241HG CG s
+ 252HG CG s
+ 26OXT C s
+ 27N CA s
+
+ Connections
+ C-termC N-term s 1.33 0.5
+
+ Properties
+
+ Variants
+ Default
+
+ PCA-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/PHE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PHE.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,103 @@
+PHE
+ Names
+ Phenylalanine
+ Phenylalanin
+ Phe
+ F
+
+ Atoms
+ NN 0.1341407 1.351202 -0.07911759
+ 3HH 0.803193 2.035005 0.2534044
+ CAC -0.7211604 2.001838 -1.087341
+ HAH -0.07892336 2.270821 -1.926756
+ CC -1.300131 3.307535 -0.5325462
+ OO -0.4477309 4.171679 -0.229457
+ CBC -1.791856 1.027805 -1.599674
+ 1HBH -1.28636 0.160502 -2.026756
+ 2HBH -2.380364 0.6727667 -0.7525354
+ CGC -2.70873 1.607533 -2.661208
+ CD1C -4.074711 1.815559 -2.387768
+ HD1H -4.496757 1.527902 -1.435336
+ CD2C -2.185439 1.971959 -3.916095
+ HD2H -1.142983 1.801105 -4.144545
+ CE1C -4.90709 2.399215 -3.358655
+ HE1H -5.955226 2.557371 -3.147432
+ CE2C -3.019025 2.554821 -4.88633
+ HE2H -2.61471 2.832835 -5.84938
+ CZC -4.379117 2.771946 -4.606688
+ HZH -5.020426 3.217529 -5.354036
+ 1HH -0.4341985 1.034029 0.6931909
+ 2HH 0.6169096 0.5661594 -0.4922875
+ OXTO -2.460581 3.26509 -0.06804343
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 24CD1 CG a
+ 27HD1 CD1 s
+ 28CD2 CG a
+ 31HD2 CD2 s
+ 32CE1 CD1 a
+ 35HE1 CE1 s
+ 36CE2 CD2 a
+ 39HE2 CE2 s
+ 40CZ CE1 a
+ 41CZ CE2 a
+ 43HZ CZ s
+ 441H N s
+ 452H N s
+ 46OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ PHE-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ PHE-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ PHE-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/PRO.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PRO.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,85 @@
+PRO
+ Names
+ Proline
+ Prolin
+ Pro
+ P
+
+ Atoms
+ NN 0.03190848 1.374047 -0.2465853
+ CAC 0.4437964 0.4522487 -1.313841
+ HAH -0.4329885 0.1122399 -1.866649
+ CC 1.153984 -0.7795747 -0.7384319
+ OO 2.396496 -0.7261156 -0.5988901
+ CBC 1.34565 1.283736 -2.23033
+ 1HBH 2.062533 0.6767905 -2.785621
+ 2HBH 0.7182986 1.840951 -2.927554
+ CGC 2.02933 2.275858 -1.278275
+ 1HGH 3.057449 1.966999 -1.081919
+ 2HGH 2.018846 3.280874 -1.702292
+ CDC 1.21179 2.210818 0.01815094
+ 1HDH 0.9135454 3.204023 0.3557259
+ 2HDH 1.815136 1.733186 0.791898
+ OXTO 0.4228693 -1.712297 -0.3395816
+ 1HH -0.2823305 0.8858488 0.5799416
+ 2HH -0.7056003 1.96474 -0.6034356
+
+ Bonds
+ 5CA N s
+ 9HA CA s
+ 10C CA s
+ 13O C d
+ 14CB CA s
+ 181HB CB s
+ 192HB CB s
+ 20CG CB s
+ 241HG CG s
+ 252HG CG s
+ 26CD N s
+ 27CD CG s
+ 301HD CD s
+ 312HD CD s
+ 32OXT C s
+ 331H N s
+ 342H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+
+ PRO-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ PRO-C
+ Delete
+ 1H
+ 2H
+
+ Properties
+ C_TERMINAL
+
+
+ PRO-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/Pyrrole-Skeleton.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Pyrrole-Skeleton.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,21 @@
+Pyrrole-Skeleton
+ Names
+ Pyrrole-Skeleton
+
+ Atoms
+ C1C -0.028662 -0.037639 1.451927
+ N2N -0.002221 -1.136686 0.619895
+ C3C 0.0447 -0.76844 -0.708243
+ C4C 0.046187 0.65781 -0.681334
+ C5C -0.008647 1.094253 0.712146
+
+ Bonds
+ 1C1 N2 s
+ 2N2 C3 d
+ 3C3 C4 s
+ 4C4 C5 d
+ 5C5 C1 s
+
+ Properties
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/SER.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/SER.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,84 @@
+SER
+ Names
+ Serine
+ Serin
+ Ser
+ S
+
+ Atoms
+ NN 0.1130663 1.226434 -0.1468897
+ 3HH 0.8968111 1.837972 0.05464922
+ CAC -0.7048293 1.905604 -1.168307
+ HAH -0.2017423 1.780946 -2.128185
+ CC -0.7701361 3.410257 -0.8778276
+ OO 0.1488766 3.858471 -0.1539113
+ CBC -2.088618 1.24965 -1.250489
+ 1HBH -1.956628 0.1725609 -1.368818
+ 2HBH -2.637483 1.435655 -0.3253672
+ OGO -2.817839 1.744102 -2.356831
+ HGH -3.648096 1.264079 -2.429246
+ OXTO -1.487331 4.10633 -1.629405
+ 1HH -0.4311985 1.10388 0.6950446
+ 2HH 0.4303224 0.3296314 -0.4862972
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21OG CB s
+ 23HG OG s
+ 24OXT C s
+ 251H N s
+ 262H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ SER-M
+ Properties
+ N_TERMINAL
+ C_TERMINAL
+
+
+ SER-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+ SER-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/T.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/T.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,106 @@
+T
+ Names
+ Thymine
+ Thymin
+ T
+
+ Atoms
+ PP 38.566 27.407 37.821
+ O1PO 38.595 26.254 36.889
+ O2PO 39.157 27.302 39.179
+ O5*O 37.072 27.912 37.957
+ C5*C 36.632 28.815 38.965
+ 1H5*H 37.233 29.724 38.959
+ 2H5*H 36.702 28.339 39.943
+ C4*C 35.191 29.171 38.689
+ H4*H 34.765 29.830 39.445
+ O4*O 35.114 29.926 37.469
+ C3*C 34.331 27.906 38.457
+ H3*H 34.825 26.944 38.594
+ O3*O 33.163 27.975 39.270
+ C2*C 33.920 28.064 36.992
+ 1H2*H 34.360 27.260 36.402
+ 2H2*H 32.834 28.020 36.912
+ C1*C 33.860 29.573 36.906
+ H1*H 33.070 30.098 37.443
+ N1N 33.730 30.096 35.526
+ C6C 34.405 29.543 34.472
+ H6H 35.056 28.699 34.642
+ C5C 34.237 29.984 33.219
+ C5MC 35.018 29.323 32.073
+ 1H5MH 34.762 28.265 32.021
+ 2H5MH 34.759 29.806 31.130
+ 3H5MH 36.088 29.429 32.253
+ C4C 33.326 31.071 32.932
+ O4O 33.094 31.529 31.816
+ N3N 32.681 31.586 34.053
+ 3HH 31.993 32.416 33.893
+ C2C 32.839 31.151 35.352
+ O2O 32.225 31.690 36.276
+
+ Bonds
+ 1P O1P s
+ 2P O2P d
+ 3P O5* s
+ 4O5* C5* s
+ 5C5* C4* s
+ 6C4* O4* s
+ 7C4* C3* s
+ 8C3* O3* s
+ 9C3* C2* s
+ 10C2* C1* s
+ 11C1* O4* s
+ 12C1* N1 s
+ 13N1 C6 s
+ 14C6 C5 d
+ 15C5 C5M s
+ 16C5 C4 s
+ 17C4 O4 d
+ 18C4 N3 s
+ 19N3 C2 s
+ 20C2 O2 d
+ 21C2 N1 s
+ 22C5* 1H5* s
+ 23C5* 2H5* s
+ 24C4* H4* s
+ 25C1* H1* s
+ 26C3* H3* s
+ 27C2* 1H2* s
+ 28C2* 2H2* s
+ 29C6 H6 s
+ 30C5M 1H5M s
+ 31C5M 2H5M s
+ 32C5M 3H5M s
+ 33N3 3H s
+
+ Connections
+ 5-termP 3-term s 1.62 0.5
+ 3-termO3* 5-term s 1.62 0.5
+
+ Properties
+ NUCLEOTIDE
+
+ Variants
+ T-M
+ Properties
+ 5_PRIME
+ 3_PRIME
+
+
+ Default
+ Properties
+
+
+ T-3
+ Properties
+ 3_PRIME
+
+
+ T-5
+ Properties
+ 5_PRIME
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/THR.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/THR.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,90 @@
+THR
+ Names
+ Threonine
+ Threonin
+ Thr
+ T
+
+ Atoms
+ NN 0.07944571 1.265783 -0.06982248
+ 3HH 0.9103429 1.833856 0.0462634
+ CAC -0.730729 1.899472 -1.127707
+ HAH -0.2399387 1.69489 -2.079941
+ CC -0.7224239 3.419906 -0.9435946
+ OO 0.3746189 3.909003 -0.5883108
+ CBC -2.153607 1.314487 -1.182294
+ HBH -2.679771 1.729994 -2.044027
+ OG1O -2.862524 1.651035 -0.00717756
+ HG1H -3.698466 1.178201 0.002366092
+ CG2C -2.126356 -0.2100642 -1.334626
+ 1HG2H -3.140605 -0.5875605 -1.466431
+ 2HG2H -1.532317 -0.4833375 -2.207111
+ 3HG2H -1.690858 -0.6725402 -0.448057
+ 1HH -0.4419178 1.260401 0.7952214
+ 2HH 0.324596 0.3214647 -0.3308986
+ OXTO -1.661421 4.065769 -1.458723
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 19HB CB s
+ 20OG1 CB s
+ 22HG1 OG1 s
+ 23CG2 CB s
+ 271HG2 CG2 s
+ 282HG2 CG2 s
+ 293HG2 CG2 s
+ 301H N s
+ 312H N s
+ 32OXT C s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ THR-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ THR-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ THR-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/TRP.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TRP.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,112 @@
+TRP
+ Names
+ Tryptophane
+ Tryptophan
+ Trp
+ W
+
+ Atoms
+ NN 0.06601259 1.26337 0.1174229
+ 3HH 0.6980239 1.889212 0.6011554
+ CAC -0.7641827 2.069947 -0.7944807
+ HAH -0.09635611 2.49911 -1.541994
+ CC -1.398304 3.240995 -0.03709874
+ OO -0.5874859 4.036549 0.4871631
+ CBC -1.786919 1.186925 -1.524096
+ 1HBH -1.239827 0.4012884 -2.046958
+ 2HBH -2.428179 0.7027346 -0.7858279
+ CGC -2.643165 1.884437 -2.539373
+ CD1C -3.982776 2.050424 -2.457166
+ HD1H -4.607287 1.697167 -1.648804
+ CD2C -2.239992 2.518021 -3.792893
+ NE1N -4.432695 2.747722 -3.558181
+ HE1H -5.40488 2.982779 -3.697329
+ CE2C -3.401079 3.062783 -4.417417
+ CE3C -1.011219 2.68937 -4.467488
+ HE3H -0.1073443 2.284464 -4.037195
+ CZ2C -3.347395 3.744152 -5.642442
+ HZ2H -4.246768 4.143939 -6.087246
+ CZ3C -0.945238 3.371593 -5.697227
+ HZ3H 0.006688994 3.489207 -6.194728
+ CH2C -2.108581 3.899702 -6.284111
+ HH2H -2.049103 4.422244 -7.228023
+ OXTO -2.601413 3.132993 0.2872543
+ 1HH 0.590273 0.5789365 -0.4086703
+ 2HH -0.5252197 0.7968075 0.7903904
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 24CD1 CG a
+ 27HD1 CD1 s
+ 28CD2 CG a
+ 31NE1 CD1 a
+ 34HE1 NE1 s
+ 35CE2 CD2 a
+ 36CE2 NE1 a
+ 39CE3 CD2 a
+ 41HE3 CE3 s
+ 42CZ2 CE2 a
+ 45HZ2 CZ2 s
+ 47CZ3 CE3 a
+ 49HZ3 CZ3 s
+ 50CH2 CZ2 a
+ 51CH2 CZ3 a
+ 53HH2 CH2 s
+ 54OXT C s
+ 551H N s
+ 562H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ TRP-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ TRP-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ TRP-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/TYR.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TYR.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,105 @@
+TYR
+ Names
+ Tyrosine
+ Tyrosin
+ Tyr
+ Y
+
+ Atoms
+ NN 0.0892698 1.397582 0.01951128
+ 3HH 0.7468582 2.066645 0.3997705
+ CAC -0.7022205 2.069859 -1.026261
+ HAH -0.008099081 2.359834 -1.816127
+ CC -1.325588 3.357111 -0.4775957
+ OO -0.5109698 4.260831 -0.1874116
+ CBC -1.734457 1.10693 -1.63201
+ 1HBH -1.201299 0.2395796 -2.0242
+ 2HBH -2.395853 0.7504926 -0.8408001
+ CGC -2.557806 1.696825 -2.76258
+ CD1C -3.932589 1.947373 -2.588092
+ HD1H -4.418424 1.704676 -1.654011
+ CD2C -1.942974 2.007092 -3.98996
+ HD2H -0.8916094 1.806731 -4.138027
+ CE1C -4.68326 2.520281 -3.629397
+ HE1H -5.736402 2.710342 -3.483602
+ CE2C -2.6951 2.579179 -5.030118
+ HE2H -2.222162 2.818849 -5.971263
+ CZC -4.063968 2.83503 -4.851168
+ OHO -4.785331 3.388967 -5.865766
+ HHH -5.709894 3.51796 -5.645833
+ OXTO -2.492483 3.282188 -0.03387626
+ 1HH -0.5246789 1.074702 0.7536617
+ 2HH 0.5865244 0.613409 -0.3778604
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 191HB CB s
+ 202HB CB s
+ 21CG CB s
+ 24CD1 CG a
+ 27HD1 CD1 s
+ 28CD2 CG a
+ 31HD2 CD2 s
+ 32CE1 CD1 a
+ 35HE1 CE1 s
+ 36CE2 CD2 a
+ 39HE2 CE2 s
+ 40CZ CE1 a
+ 41CZ CE2 a
+ 43OH CZ s
+ 45HH OH s
+ 46OXT C s
+ 471H N s
+ 482H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ TYR-M
+ Properties
+ C_TERMINAL
+ N_TERMINAL
+
+
+ TYR-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ TYR-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/U.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/U.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,99 @@
+U
+ Names
+ Uracil
+ U
+
+ Atoms
+ PP 38.566 27.407 37.821
+ O1PO 38.595 26.254 36.889
+ O2PO 39.157 27.302 39.179
+ O5*O 37.072 27.912 37.957
+ C5*C 36.632 28.815 38.965
+ 1H5*H 37.233 29.724 38.959
+ 2H5*H 36.702 28.339 39.943
+ C4*C 35.191 29.171 38.689
+ H4*H 34.765 29.830 39.445
+ O4*O 35.114 29.926 37.469
+ C3*C 34.331 27.906 38.457
+ H3*H 34.825 26.944 38.594
+ O3*O 33.163 27.975 39.270
+ C2*C 33.920 28.064 36.992
+ 1H2*H 34.360 27.260 36.402
+ 2H2*H 32.834 28.020 36.912
+ C1*C 33.860 29.573 36.906
+ H1*H 33.070 30.098 37.443
+ N1N 33.730 30.096 35.526
+ C6C 34.405 29.543 34.472
+ H6H 35.056 28.699 34.642
+ C5C 34.237 29.984 33.219
+ H5H 35.018 29.323 32.073
+ C4C 33.326 31.071 32.932
+ O4O 33.094 31.529 31.816
+ N3N 32.681 31.586 34.053
+ H3H 31.993 32.416 33.893
+ C2C 32.839 31.151 35.352
+ O2O 32.225 31.690 36.276
+
+ Bonds
+ 1P O1P s
+ 2P O2P d
+ 3P O5* s
+ 4O5* C5* s
+ 5C5* C4* s
+ 6C4* O4* s
+ 7C4* C3* s
+ 8C3* O3* s
+ 9C3* C2* s
+ 10C2* C1* s
+ 11C1* O4* s
+ 12C1* N1 s
+ 13N1 C6 s
+ 14C6 C5 d
+ 15C5 H5 s
+ 16C5 C4 s
+ 17C4 O4 d
+ 18C4 N3 s
+ 19N3 C2 s
+ 20C2 O2 d
+ 21C2 N1 s
+ 22C5* 1H5* s
+ 23C5* 2H5* s
+ 24C4* H4* s
+ 25C1* H1* s
+ 26C3* H3* s
+ 27C2* 1H2* s
+ 28C2* 2H2* s
+ 29C6 H6 s
+ 30N3 H3 s
+
+ Connections
+ 5-termP 3-term s 1.62 0.5
+ 3-termO3* 5-term s 1.62 0.5
+
+ Properties
+ NUCLEOTIDE
+
+ Variants
+ U-M
+ Properties
+ 5_PRIME
+ 3_PRIME
+
+
+ Default
+ Properties
+
+
+ U-3
+ Properties
+ 3_PRIME
+
+
+ U-5
+ Properties
+ 5_PRIME
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/VAL.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/VAL.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,94 @@
+VAL
+ Names
+ Valine
+ Valin
+ Val
+ V
+
+ Atoms
+ NN 0.08111785 1.2013 -0.133711
+ 3HH 0.9032491 1.762717 0.06032801
+ CAC -0.698245 1.931722 -1.152099
+ HAH -0.2125321 1.7346 -2.108571
+ CC -0.5967644 3.443358 -0.9052255
+ OO 0.3370198 3.799585 -0.1501447
+ CBC -2.141793 1.389981 -1.219405
+ HBH -2.073082 0.3006792 -1.23859
+ CG1C -2.976131 1.780723 0.008393872
+ 1HG1H -3.953726 1.301327 -0.05053521
+ 2HG1H -2.483032 1.448739 0.9220271
+ 3HG1H -3.118463 2.860577 0.05077193
+ CG2C -2.878923 1.800528 -2.501579
+ 1HG2H -3.809818 1.237256 -2.575363
+ 2HG2H -3.122159 2.862025 -2.496346
+ 3HG2H -2.266089 1.572718 -3.374182
+ OXTO -1.142181 4.189281 -1.746952
+ 1HH -0.4588342 1.115157 0.7148547
+ 2HH 0.3376986 0.2854735 -0.4735033
+
+ Bonds
+ 53H N s
+ 6CA N s
+ 10HA CA s
+ 11C CA s
+ 14O C d
+ 15CB CA s
+ 19HB CB s
+ 20CG1 CB s
+ 241HG1 CG1 s
+ 252HG1 CG1 s
+ 263HG1 CG1 s
+ 27CG2 CB s
+ 311HG2 CG2 s
+ 322HG2 CG2 s
+ 333HG2 CG2 s
+ 34OXT C s
+ 351H N s
+ 362H N s
+
+ Connections
+ N-termN C-term s 1.33 0.5
+ C-termC N-term s 1.33 0.5
+
+ Properties
+ AMINO_ACID
+
+ Variants
+ Default
+ Delete
+ OXT
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+
+ VAL-M
+ Properties
+ N_TERMINAL
+ C_TERMINAL
+
+
+ VAL-C
+ Delete
+ 1H
+ 2H
+
+ Rename
+ 3HH
+
+ Properties
+ C_TERMINAL
+
+
+ VAL-N
+ Delete
+ OXT
+
+ Properties
+ N_TERMINAL
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/ZN.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ZN.db Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,18 @@
+ZN
+ Names
+ Zinc ion
+ Zn2+
+
+ Atoms
+ ZNZn 0.0 0.0 0.0
+
+ Bonds
+
+ Connections
+
+ Properties
+
+ Variants
+ Default
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/fragments/functionalGroups.smarts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/functionalGroups.smarts Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,133 @@
+C[*X1](C)([*X1])[*X1] terminal primary C(sp3)
+[C,c]([C,c])([C,c])(*)* total secondary C(sp3)
+[C,c]([C,c])([C,c])([C,c])* total tertiary C(sp3)
+[C,c]([C,c])([C,c])([C,c])[C,c] total quaternary C(sp3)
+[$([Cr,cr]([Cr,cr])([Cr,cr])(*)*),$([Cr,cr]([Cr,cr])([C,c])([*r])*)] ring secondary C(sp3)
+[$([Cr,cr]([Cr,cr])([Cr,cr])([C,c])*),$([Cr,cr]([Cr,cr])([C,c])([C,c])[*r])] ring tertiary C(sp3)
+[Cr,cr]([Cr,cr])([Cr,cr])([C,c])[C,c] ring quaternary C(sp3)
+[cX3] aromatic C(sp2)
+[Ch1,ch1]1[C,c][C,c][C,c][C,c][C,c]1 unsubstituted benzene C(sp2)
+[Ch0,ch0]1[C,c][C,c][C,c][C,c][C,c]1 substituted benzene C(sp2)
+O=CC1=CCCC=C1 non-aromatic conjugated C(sp2)
+[C,c]=[C,c](*)(*) terminal primary C(sp2)
+C=C(C)(*) aliphatic secondary C(sp2)
+C=C(C)(C) aliphatic tertiary C(sp2)
+[C,c]=[C,c]=[C,c] allenes groups
+[*X1][C,c]#C terminal C(sp)
+**[C,c]#C non-terminal C(sp)
+OC#N cyanates
+O=C=N isocyanates
+SC#N thiocyanates
+N=C=S isothiocyanates
+[OH,Oh]C=O carboxylic acids
+[*;!H]OC=O esters
+[NH2,Nh2]C=O primary amides
+[*;!H][NH,Nh]C=O secondary amides
+[*;!H]N([*;!H])C=O tertiary amides
+*N(*)C([O,S]*)=[O,S] (thio-)carbamates
+[F,Cl,Br,I,At]C(*)=O acyl halogenides
+[$([OH,Oh]C(*)=S),$([SH,Sh]C(*)=O)] thioacids
+[SH,Sh]C(*)=S dithioacids
+[$([*;!H]OC(*)=S),$([*;!H]SC(*)=O)] thioesters
+[*;!H]SC(*)=S dithioesters
+[CH,Ch](*)=O aldehydes
+*C(*)=O ketones
+[NX3]C([NX3])=[O,S] urea (-thio) derivatives
+[OX2,SX2]C([OX2,SX2])=[O,S] carbonate (-thio) derivatives
+[NX2]C([C,H])[NX3] amidine derivatives
+[NX3]C(=[NX2])[NX3] guanidine derivatives
+*C(*)=N[N,C,H] imines
+*C(*)=NO* oximes
+[NH2X3,Nh2X3] primary amines
+[NH1X3,Nh1X3] secondary amines
+[NH0X3;Nh0X3] tertiary amines
+[C,H][NX3][NX3][C,H] N hydrazines
+[C,H][NX2]=[NX2][C,H] N azo-derivatives
+N#C* nitriles
+[N+n] positive charged N
+[NX4] quaternary N
+*N(*)O* hydroxylamines
+*N(*)N=O nitrosamine
+*N=O nitroso groups
+*N(O)=O nitro groups
+[CX3](=[O,S])[NX3]([H,C])[CX3]=[O,S] imides
+[C,H]C([C,H])=NN([C,H])[C,H] hydrazones
+A[OX2h1,OX2H1] hydroxyl groups
+a[OX2h1,OX2H1] aromatic hydroxyls
+C[CH2,Ch2][OH,Oh] primary alcohols
+C[CH,Ch](C)[OH,Oh] secondary alcohols
+CC(C)(C)[OH,Oh] tertiary alcohols
+*O* ethers
+*O[F,Cl,Br,I,At] hypohalogenides
+[CX3](=[O,S])O[CX3][O,S] anhydrides
+[OH2,Oh2] water
+C[SH,Sh] thiols
+S=C(C)C thioketones
+C[SX2]C sulfides
+C[SX2][SX2]C disulfides
+[$(CS(C)=O),$(C=S=O),$(S=S=O)] sulfoxides
+[$(O=[SX4]=O),$(O=S(=[C,S])=O)] sulfones
+[SX2][Oh1,OH1,Sh1,SH1] sulfenic acids
+[SX3](=[O,S])[Oh1,OH1,Sh1,SH1] sulfinic acids
+[SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1] sulfonic acids
+[OX2,SX2][SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1] sulfuric acids
+[SX3](=[O,S])[OX2,SX2] sulfites
+[SX4](=[O,S])(=[O,S])[OX2,SX2] sulfonates
+[OX2,SX2][SX4](=[O,S])(=[O,S])[OX2,SX2] sulfates
+[$(C[SX4](=O)(=O)[NX3]),$(C[SX4](=S)(=O)[NX3]),$(C[SX3](=O)[NX3]),$(C[SX3](=S)[NX3]),$(CS[NX3])] sulfonamides/sulfinamides/sulfenamides
+[O,S]P([O,S])[O,S] phosphites/thiophosphites
+[O,S]P(=[O,S])([O,S])[O,S] phosphates/thiophosphates
+[O,S]P([O,S])[O,S] phosphanes
+[H,S,F,Cl,Br,I,At][PX4](=[S,O])([SX2,OX2])[SX2,OX2] phosphonates/thiophosphonates
+[$([H,S,F,Cl,Br,I,At][PX4](=[S,O])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At]),$([H,S,F,Cl,Br,I,At][PX5]([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At])] phosphoranes/thiophosphoranes
+[F,Cl,Br,I,At][CX4h2,CX4H2,cx4h2,cx4H2][C,c] CH2RX
+[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[C,c] CHR2X
+[F,Cl,Br,I,At][C,c]([C,c])([C,c])[C,c] CR3X
+[C,c]=[CX3h1,cX3h1,CX3H1,cX3H1][F,Cl,Br,I,At] R=CHX
+[C,c]=[C,c]([C,c])[F,Cl,Br,I,At] R=CRX
+[F,Cl,Br,I,At]C#C R#CX
+[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[F,Cl,Br,I,At] CHRX2
+[F,Cl,Br,I,At][C,c]([C,c])([C,c])[F,Cl,Br,I,At] CR2X2
+[C,c]=[C,c]([F,Cl,Br,I,At])[F,Cl,Br,I,At] R=CX2
+[F,Cl,Br,I,At][C,c]([C,c])([F,Cl,Br,I,At])[F,Cl,Br,I,At] CRX3
+[F,Cl,Br,I,At][ar] halogene on aromatic ring
+[CrX4,crX4][F,Cl,Br,I,At] X on ring C(sp3)
+[CrX3,crX3][F,Cl,Br,I,At] X on ring C(sp2)
+[C,c]=[C,c]([F,Cl,Br,I,At])[C,c]=[C,c] halogene on exo-conjugated C
+[N,n]1@[C,c]@[C,c]1 Aziridines
+[O,o]1@[C,c]@[C,c]1 Oxiranes
+[S,s]1@[C,c]@[C,c]1 Thiranes
+[N,n]1@[C,c]@[C,c]@[C,c]1 Azetidines
+[O,o]1@[C,c]@[C,c]@[C,c]1 Oxetanes
+[S,s]1@[C,c]@[C,c]@[C,c]1 Thioethanes
+[N,n]12@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1(@[C,c]@C2(=O)) Beta-Lactams
+[N,n]1@[C,c]@[C,c]@[C,c]1 Pyrrolidines
+[O,o]1[C,c][C,c][C,c][C,c]1 Oxolanes
+[S,s]1[C,c][C,c][C,c][C,c]1 tetrahydro-Thiophenes
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]1 Pyrroles
+[N,n]1@[N,n]@[C,c]@[C,c]@[C,c]1 Pyrazoles
+[N,n]1@[C,c]@[N,n]@[C,c]@[C,c]1 Imidazoles
+[O,o]1[C,c]=[C,c][C,c]=[C,c]1 Furanes
+[S,s]1[C,c]=[C,c][C,c]=[C,c]1 Thiophenes
+[O,o]1@[C,c]@[N,n]@[C,c]@[C,c]1 Oxazoles
+[O,o]1@[N,n]@[C,c]@[C,c]@[C,c]1 Isoxazoles
+[S,s]1@[C,c]@[N,n]@[C,c]@[C,c]1 Thiazoles
+[S,s]1@[N,n]@[C,c]@[C,c]@[C,c]1 Isothiazoles
+[$([N,n]1@[N,n]@[C,c]@[N,n]@C1),$([N,n]1@[N,n]@[N,n]@[C,c]@[C,c]1)] Triazoles
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1 Pyridines
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[N,n]1 Pyridazines
+[N,n]1@[C,c]@[C,c]@[C,c]@[N,n]@[C,c]1 Pyrimidines
+[N,n]1@[C,c]@[C,c]@[N,n]@[C,c]@[C,c]1 Pyrazines
+[N,n]1@[C,c]@[N,n]@[C,c]@[N,n]@[C,c]1 135-Triazines
+[N,n]1@[C,c]@[N,n]@[N,n]@[C,c]@[C,c]1 124-Triazines
+[C,c]1([Oh1,OH1])[C,c][C,c][C,c][C,c][C,c]1 Phenoles
+[C,c]1([C])[C,c][C,c][C,c][C,c][C,c]1 Phenyles
+[C,c]1([CH3,ch3])[C,c][C,c][C,c][C,c][C,c]1 Toluenes
+OC[C,c]1@[C,c](O)@[C,c](O)@[C,c](O)@[C,c](O)@[O,o]1 Glucose
+OC[C,c]1(O)@[C,c](O)@[C,c](O)@[C,c](CO)[O,o]1 Fructose
+[CH3,Ch3] Methyl
+[F,Cl,Br,I,At] Halogenides
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2,Ch3,CH3] Propyl
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3] Butyl
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3] Pentyl
+CC=C([CH3,Ch3])([CH3,Ch3]) Prenyl
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/gnuplot/FreeSans.ttf
Binary file CADDSuite/data/gnuplot/FreeSans.ttf has changed
diff -r e343494f18fe -r bb26168c5715 CADDSuite/data/gnuplot/prologue.ps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/gnuplot/prologue.ps Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,373 @@
+%
+% Gnuplot Prolog Version 4.4 (August 2010)
+%
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+%
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+ hpt neg vpt 1.62 mul V closepath stroke} def
+/TriDE {stroke [] 0 setdash vpt 1.12 mul sub M
+ hpt neg vpt 1.62 mul V
+ hpt 2 mul 0 V
+ hpt neg vpt -1.62 mul V closepath stroke} def
+/PentE {stroke [] 0 setdash gsave
+ translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
+ closepath stroke grestore} def
+/CircE {stroke [] 0 setdash
+ hpt 0 360 arc stroke} def
+/Opaque {gsave closepath 1 setgray fill grestore 0 setgray closepath} def
+/DiaW {stroke [] 0 setdash vpt add M
+ hpt neg vpt neg V hpt vpt neg V
+ hpt vpt V hpt neg vpt V Opaque stroke} def
+/BoxW {stroke [] 0 setdash exch hpt sub exch vpt add M
+ 0 vpt2 neg V hpt2 0 V 0 vpt2 V
+ hpt2 neg 0 V Opaque stroke} def
+/TriUW {stroke [] 0 setdash vpt 1.12 mul add M
+ hpt neg vpt -1.62 mul V
+ hpt 2 mul 0 V
+ hpt neg vpt 1.62 mul V Opaque stroke} def
+/TriDW {stroke [] 0 setdash vpt 1.12 mul sub M
+ hpt neg vpt 1.62 mul V
+ hpt 2 mul 0 V
+ hpt neg vpt -1.62 mul V Opaque stroke} def
+/PentW {stroke [] 0 setdash gsave
+ translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
+ Opaque stroke grestore} def
+/CircW {stroke [] 0 setdash
+ hpt 0 360 arc Opaque stroke} def
+/BoxFill {gsave Rec 1 setgray fill grestore} def
+/Density {
+ /Fillden exch def
+ currentrgbcolor
+ /ColB exch def /ColG exch def /ColR exch def
+ /ColR ColR Fillden mul Fillden sub 1 add def
+ /ColG ColG Fillden mul Fillden sub 1 add def
+ /ColB ColB Fillden mul Fillden sub 1 add def
+ ColR ColG ColB setrgbcolor} def
+/BoxColFill {gsave Rec PolyFill} def
+/PolyFill {gsave Density fill grestore grestore} def
+/h {rlineto rlineto rlineto gsave closepath fill grestore} bind def
+%
+% PostScript Level 1 Pattern Fill routine for rectangles
+% Usage: x y w h s a XX PatternFill
+% x,y = lower left corner of box to be filled
+% w,h = width and height of box
+% a = angle in degrees between lines and x-axis
+% XX = 0/1 for no/yes cross-hatch
+%
+/PatternFill {gsave /PFa [ 9 2 roll ] def
+ PFa 0 get PFa 2 get 2 div add PFa 1 get PFa 3 get 2 div add translate
+ PFa 2 get -2 div PFa 3 get -2 div PFa 2 get PFa 3 get Rec
+ gsave 1 setgray fill grestore clip
+ currentlinewidth 0.5 mul setlinewidth
+ /PFs PFa 2 get dup mul PFa 3 get dup mul add sqrt def
+ 0 0 M PFa 5 get rotate PFs -2 div dup translate
+ 0 1 PFs PFa 4 get div 1 add floor cvi
+ {PFa 4 get mul 0 M 0 PFs V} for
+ 0 PFa 6 get ne {
+ 0 1 PFs PFa 4 get div 1 add floor cvi
+ {PFa 4 get mul 0 2 1 roll M PFs 0 V} for
+ } if
+ stroke grestore} def
+%
+/languagelevel where
+ {pop languagelevel} {1} ifelse
+ 2 lt
+ {/InterpretLevel1 true def}
+ {/InterpretLevel1 Level1 def}
+ ifelse
+%
+% PostScript level 2 pattern fill definitions
+%
+/Level2PatternFill {
+/Tile8x8 {/PaintType 2 /PatternType 1 /TilingType 1 /BBox [0 0 8 8] /XStep 8 /YStep 8}
+ bind def
+/KeepColor {currentrgbcolor [/Pattern /DeviceRGB] setcolorspace} bind def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke}
+>> matrix makepattern
+/Pat1 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke
+ 0 4 M 4 8 L 8 4 L 4 0 L 0 4 L stroke}
+>> matrix makepattern
+/Pat2 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 0 M 0 8 L
+ 8 8 L 8 0 L 0 0 L fill}
+>> matrix makepattern
+/Pat3 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -4 8 M 8 -4 L
+ 0 12 M 12 0 L stroke}
+>> matrix makepattern
+/Pat4 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -4 0 M 8 12 L
+ 0 -4 M 12 8 L stroke}
+>> matrix makepattern
+/Pat5 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -2 8 M 4 -4 L
+ 0 12 M 8 -4 L 4 12 M 10 0 L stroke}
+>> matrix makepattern
+/Pat6 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -2 0 M 4 12 L
+ 0 -4 M 8 12 L 4 -4 M 10 8 L stroke}
+>> matrix makepattern
+/Pat7 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 8 -2 M -4 4 L
+ 12 0 M -4 8 L 12 4 M 0 10 L stroke}
+>> matrix makepattern
+/Pat8 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 -2 M 12 4 L
+ -4 0 M 12 8 L -4 4 M 8 10 L stroke}
+>> matrix makepattern
+/Pat9 exch def
+/Pattern1 {PatternBgnd KeepColor Pat1 setpattern} bind def
+/Pattern2 {PatternBgnd KeepColor Pat2 setpattern} bind def
+/Pattern3 {PatternBgnd KeepColor Pat3 setpattern} bind def
+/Pattern4 {PatternBgnd KeepColor Landscape {Pat5} {Pat4} ifelse setpattern} bind def
+/Pattern5 {PatternBgnd KeepColor Landscape {Pat4} {Pat5} ifelse setpattern} bind def
+/Pattern6 {PatternBgnd KeepColor Landscape {Pat9} {Pat6} ifelse setpattern} bind def
+/Pattern7 {PatternBgnd KeepColor Landscape {Pat8} {Pat7} ifelse setpattern} bind def
+} def
+%
+%
+%End of PostScript Level 2 code
+%
+/PatternBgnd {
+ TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse
+} def
+%
+% Substitute for Level 2 pattern fill codes with
+% grayscale if Level 2 support is not selected.
+%
+/Level1PatternFill {
+/Pattern1 {0.250 Density} bind def
+/Pattern2 {0.500 Density} bind def
+/Pattern3 {0.750 Density} bind def
+/Pattern4 {0.125 Density} bind def
+/Pattern5 {0.375 Density} bind def
+/Pattern6 {0.625 Density} bind def
+/Pattern7 {0.875 Density} bind def
+} def
+%
+% Now test for support of Level 2 code
+%
+Level1 {Level1PatternFill} {Level2PatternFill} ifelse
+%
+/Symbol-Oblique /Symbol findfont [1 0 .167 1 0 0] makefont
+dup length dict begin {1 index /FID eq {pop pop} {def} ifelse} forall
+currentdict end definefont pop
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/confFiles.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/confFiles.py Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+"""
+XML format classes
+"""
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+
+class ini( data.Text ):
+ file_ext = "ini"
+ def sniff( self, filename ):
+ self.no_sections = commands.getstatusoutput("grep -c \"\[Docking-Settings\]\" "+filename)
+ if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+ return True
+ else:
+ self.no_sections = commands.getstatusoutput("grep -c \"\[ReferenceArea\" "+filename)
+ if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+ return True
+ else:
+ self.no_sections = commands.getstatusoutput("grep -c \"\[PharmacophoreConstraint\" "+filename)
+ if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+ return True
+ else:
+ return False
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/countResidues.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/countResidues.sh Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,64 @@
+#!/bin/bash
+
+IFS=$'\n';
+residue_list=""
+hetsys_list=""
+hoh_list=""
+
+for line in $(cat $1); do
+ if [ "${line:0:4}" = "ATOM" ];then
+ residue_list+="${line:23:6}\n"
+ else
+ if [ "${line:0:6}" = "HETATM" ];then
+ s2=`echo $line | grep HOH`
+ if [ "$s2" != "" ];then
+ hoh_list+="${line:21:8}\n"
+ else
+ s3=`echo $line | grep WAT`
+ if [ "$s3" != "" ];then
+ hoh_list+="${line:21:8}\n"
+ else
+ hetsys_list+="${line:21:8}\n"
+ fi
+ fi
+ fi
+ fi
+done
+
+IFS=$' ';
+let num_res=`echo -e "\n"$residue_list | uniq | wc -l`
+let num_hoh=`echo -e "\n"$hoh_list | uniq | wc -l`
+let num_hetsys=`echo -e "\n"$hetsys_list | uniq | wc -l`
+
+# empty line at begin and end of lists -> substract 2
+let num_res-=2
+let num_hoh-=2
+let num_hetsys-=2
+if [ $num_res -lt 0 ]; then
+ let num_res=0
+fi
+if [ $num_hoh -lt 0 ]; then
+ let num_hoh=0
+fi
+if [ $num_hetsys -lt 0 ]; then
+ let num_hetsys=0
+fi
+
+echo -n "$num_res "
+if [ $num_res -eq 1 ]; then
+ echo "residue"
+else
+ echo "residues"
+fi
+echo -n "$num_hoh water "
+if [ $num_hoh -eq 1 ]; then
+ echo "molecule"
+else
+ echo "molecules"
+fi
+echo -n "$num_hetsys "
+if [ $num_hetsys -eq 1 ]; then
+ echo "heterosystem"
+else
+ echo "heterosystems"
+fi
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/datatypes_conf.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,33 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/molFiles.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/molFiles.py Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+class GenericMolFile( data.Text ):
+ file_ext = "mol2/sdf/drf"
+ def check_filetype( self,filename ):
+ self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ self.file_ext="sdf"
+ return True
+ self.no_mols = commands.getstatusoutput("grep -c @\MOLECULE "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ self.file_ext="mol2"
+ return True
+ self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ self.file_ext="drf"
+ return True
+ self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ self.file_ext="pdb"
+ return True
+ return False
+
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ if(self.check_filetype(dataset.file_name)) :
+ if (self.no_mols[1] == '1'):
+ dataset.blurb = "1 molecule"
+ else:
+ dataset.blurb = "%s molecules"%self.no_mols[1]
+ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def get_mime(self):
+ return 'text/plain'
+
+
+class GenericMultiMolFile( GenericMolFile ):
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ self.sniff(dataset.file_name)
+ if (self.no_mols[1] == '1'):
+ dataset.blurb = "1 molecule"
+ else:
+ dataset.blurb = "%s molecules"%self.no_mols[1]
+ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+class SDF( GenericMultiMolFile ):
+ file_ext = "sdf"
+ def sniff( self, filename ):
+ self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ return True
+ else:
+ return False
+
+class MOL2( GenericMultiMolFile ):
+ file_ext = "mol2"
+ def sniff( self, filename ):
+ self.no_mols = commands.getstatusoutput("grep -c @\MOLECULE "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ return True
+ else:
+ return False
+
+class DRF( GenericMultiMolFile ):
+ file_ext = "drf"
+ def sniff( self, filename ):
+ self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ return True
+ else:
+ return False
+
+class PDB( GenericMolFile ):
+ file_ext = "pdb"
+ def sniff( self, filename ):
+ self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+ if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+ return True
+ else:
+ return False
+ def set_peek( self, dataset, is_multi_byte=False ):
+ #def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
+ dataset.peek = res[1]
+ self.sniff(dataset.file_name)
+ if (self.no_mols[1] == '1'):
+ dataset.blurb = "1 protein structure"
+ else:
+ dataset.blurb = "%s protein structures"%self.no_mols[1]
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+class grd ( data.Text ) :
+ file_ext = "grd"
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ #dataset.peek = ""
+ dataset.blurb = "score-grids for docking"
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+class grdtgz ( data.Text ) :
+ file_ext = "grd.tgz"
+ def set_peek( self, dataset, is_multi_byte=False ):
+ if not dataset.dataset.purged:
+ #dataset.peek = ""
+ dataset.blurb = "compressed score-grids for docking"
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tool_conf.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,71 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,32 @@
+
+
+
+ rescore w/ anti-target dock-results
+
+
+
+
+
+
+
+
+ This tool rescores docking output poses.
+AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.
+
+As input we need:
+ * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target).
+ * a file containing the same compounds docked into the antitarget.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/AutoModel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,27 @@
+
+
+
+ automatically find best QSAR model
+
+
+
+
+
+
+
+
+ This tool tries to automatically find the best QSAR model for a given data set.
+
+It therefore applies nested validation, including feature selection, for each available model-type. The model with the best nested prediction quality is saved to the specified output file. However, if the best obtained nested prediction quality is smaller than the value specified by '-min_quality', an error will be shown and no model will be saved.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,36 @@
+
+
+
+ fix bindingdb.org downloads
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org.
+
+For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'.
+
+All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,32 @@
+
+
+
+ generate combinatorial lib
+
+
+
+
+
+
+
+ This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties.
+
+As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need:
+
+<scaffold>
+ Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
+<moietyR1>
+ [R1]C(C)(C)C
+<moietyR2>
+ [R2]OC(C)(C)C
+
+Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,38 @@
+
+
+
+ find strongly interacting residues
+
+
+
+
+
+
+
+
+
+ This tool searches protein residues with which the reference ligand interacts strongly.
+Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
+
+As input we need:
+ * a file containing a protonated protein in pdb-format
+ * a file containing a reference ligand.
+ This reference ligand should be located in the binding pocket.
+ Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/Converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Converter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,50 @@
+
+
+
+ interconvert molecular file-formats
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool can be used to convert between different molecular file-formats.
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/DBExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,97 @@
+
+
+
+ export molecules from data base
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/DBImporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,57 @@
+
+
+
+ import molecules into data base
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool imports molecules into a database.
+As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/DockResultMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,49 @@
+
+
+
+ merge docking output files
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool merges and sorts molecule files as generated by docking or rescoring.
+
+You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
+
+ Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/EvenSplit.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,41 @@
+
+
+
+ generate splits w/ equal property range
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool splits a molecule file into two subsets in such a way that each of them convers an equal range of a property. The property with respect to which this is to be done should be specified with '-prop'.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/FeatureSelector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,41 @@
+
+
+
+ run feature-selection on a QSAR model
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ FeatureSelector runs a feature-selection for a given QSAR model.
+
+The type of feature-selection to be done is specified by '-type'. Input of this tool is a data file as generated by InputReader containing the training data for feature-selection and a QSAR model file as generated by ModelCreator (or this tool itself). Note that you can apply several feature-selection methods in succession by using the output of one call of this tool as input for the next call.
+Model- and kernel-parameters (if any) will be automatically optimized by cross-validation after applying the desired feature-selection.
+
+Output of this tool is a model-file that can be used by other QuEasy tools (e.g. Validator).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,30 @@
+
+
+
+ generate galaxy tool-config files
+
+
+
+
+
+
+
+
+
+ This tool can be used to create galaxy tool-configuration files.
+As input, please supply a parameter-file as written by '-write_par' by all of our tools.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/GridBuilder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,38 @@
+
+
+
+ create score-grids for docking
+
+
+
+
+
+
+
+
+
+ This tool precalculates a score-grid for a binding pocket of a given receptor.
+
+As input we need:
+ * a file containing a protonated protein in pdb-format
+ * a file containing a reference ligand.
+ This reference ligand should be located in the binding pocket,
+ so that a grid can be precalculated around it.
+ Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/IMGDock.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,47 @@
+
+
+
+ Iterative Multi-Greedy Docking
+
+
+
+
+
+
+
+
+
+
+
+ IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
+As input we need:
+
+ * a file containing a protonated protein in pdb-format
+ * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+ * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here.
+ * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck.
+
+Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound.
+
+Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/InputPartitioner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,28 @@
+
+
+
+ split QSAR data set
+
+
+
+
+
+
+
+
+ InputPartitioner partitions a given QSAR data set into n partitions with evenly distributed response values.
+Thus, this tool can be useful as part of a nested validation pipeline.
+Input is a data file as generated by InputReader.
+Output will be written to n files postfixed '_TRAIN<i>.dat' and '_TEST<i>.dat', where <i> is the ID of the resp. partition. For each of these partitions, the training set contains only those compounds that were not selected for the resp. test set.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/InputReader.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,68 @@
+
+
+
+ generate QSAR data set
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool reads input from sd-files and generate features for QSAR analysis.
+Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
+The following number of features will be automatically created for each molecule in your sd-file:
+
+ * 40 atom and bond count descriptors
+ * 2 connectivity indices (Balaban and Zagreb index)
+ * 4 partial charge descriptors
+ * 14 surface descriptors
+ * 133 topological descriptors (functional group counts)
+
+If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
+Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,37 @@
+
+
+
+ define interaction constraint
+
+
+
+
+
+
+
+
+
+
+ This tool allows to define interaction constraints for docking or scoring.
+
+The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: <chain-ID>:<residue-ID>, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
+
+Output of this tool is a ini-file that contains the desired interaction constraint.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/LigCheck.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,45 @@
+
+
+
+ check molecules for errors
+
+
+
+
+
+
+
+
+
+
+ This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+The following checks are done for each molecule:
+
+ * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
+ * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
+ * each atom must have a valid assigned element
+ * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
+ * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+ * partial charges may not contain completely senseless values (>5 or <-5).
+ * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
+
+If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,30 @@
+
+
+
+ generate 3D coordinates for small molecules
+
+
+
+
+
+
+
+
+ This tool generates 3D conformations for small molecules and adds hydrogens to them.
+As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.
+
+Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.
+
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,84 @@
+
+
+
+ split molecule files
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LigandFileSplitter splits a molecule file into a given number of subsets.
+Note that the molecules are not sorted in any way for this.
+
+Since Galaxy does not support a flexible number of output-files, we will create 15 output files when you use LigandFileSplitter in Galaxy.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/ModelCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,52 @@
+
+
+
+ create a QSAR model
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ModelCreator creates a QSAR model using an input data set as generated by InputReader.
+
+The type of QSAR model to be used can be specified by '-type', the type of kernel-function (if any) can be chosen by '-kernel'. Optimization of model- and kernel-parmeters will be done automatically using cross-validation.
+
+Output of this tool is a model-file that can be used by other QuEasy tools (e.g. FeatureSelector).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/MolCombine.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,45 @@
+
+
+
+ combine molecular files
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
+
+If you want to match molecules regardless of their protonation state, use option '-ignH'.
+
+Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/MolDepict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,28 @@
+
+
+
+ create structure diagrams
+
+
+
+
+
+
+
+
+ This tool create structure diagrams for small molecules.
+Supported input-formats are mol, mol2, sdf, drf.
+
+Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/MolFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,60 @@
+
+
+
+ filter molecule files
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
+
+Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/MolPredictor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,50 @@
+
+
+
+ predict molecule activities with QSAR model
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool predictes the response values of compounds in the given molecule file using the specified QSAR model.
+
+Input of this tool is a molecule file (sdf,mol2,drf) and a model-file as generated by ModelCreator or FeatureSelector.
+Features for all molecules in the input file are generated automatically. However, if you used an additional, externally generated feature-set to generate your QSAR model, make sure to generate features in the same manner (i.e. using the same external tool with the same settings) for the molecule file to be used here and specify the csv-file with the above options.
+
+Output of this tool (as specified by '-o') is a molecule file containing the predicted values as a property tag named 'predicted_activity'.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/PDBCutter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,46 @@
+
+
+
+ separate ligand and receptor
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
+
+The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
+Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
+
+Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/PDBDownload.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,25 @@
+
+
+
+ retrieve pdb-file from pdb.org
+
+
+
+
+
+
+
+
+ Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,26 @@
+
+
+
+ transfer part. charges between files
+
+
+
+
+
+
+
+
+ This tool copies partial charges from a given file to the conformations read from a different file.
+This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/PocketDetector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,38 @@
+
+
+
+ detect binding pocket
+
+
+
+
+
+
+
+
+
+ This tool tries to detect the binding pocket in which the reference ligand is located.
+Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket.
+
+As input we need:
+ * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder.
+ * a file containing a reference ligand.
+ This reference ligand should be located in the binding pocket.
+ Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/Predictor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,30 @@
+
+
+
+ predict activities with QSAR model
+
+
+
+
+
+
+
+
+ This tool predictes the response values of compounds in the given data-file using the specified QSAR model.
+
+Input of this tool is a model-file as generated by ModelCreator or FeatureSelector and a data-file generated by InputReader.
+
+Output of this tool (as specified by '-o') is a text file containing the predicted and, if any, the expected response values in one column each.
+If you would prefer to use molecule files (sdf,mol2,drf) for input and output, please use the tool MolPredictor instead of this one.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/PropertyModifier.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,43 @@
+
+
+
+ modify molecule property tags
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ With this tools you can add, rename or delete molecule property tags.
+These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule.
+The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,35 @@
+
+
+
+ plot molecule properties
+
+
+
+
+
+
+
+
+
+ PropertyPlotter can be used to generate distribution- or scatter-plots of data contained in molecule property-tags.
+
+In case you want to create a scatter-plot, specify the name of both property-tags to be used with '-p1' and '-p2'. If you want to generate a distribution plot, just specify '-p1'.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The output of this tool is a plot in form of an eps or png-file (as chosen).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/ProteinCheck.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,34 @@
+
+
+
+ quality check for proteins structures
+
+
+
+
+
+
+
+
+ Check a given protein structure for the following errors:
+ * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
+ * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
+ * each atom must have a valid assigned element
+ * the protein must be protonated (since this is necessary for docking/(re-)scoring).
+ * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+ * there may be no senseless temperature factors (<1 or >100)
+ * there may be no sterical clashes between atoms
+
+A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,29 @@
+
+
+
+ protonate protein structures
+
+
+
+
+
+
+
+
+ ProteinProtonator allows you add hydrogens to a protein structure.
+
+Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
+
+Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,31 @@
+
+
+
+ calculate RMSD between poses
+
+
+
+
+
+
+
+
+ This tool calculates the RMSD between different conformations of the same molecule.
+
+Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
+Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
+
+Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,55 @@
+
+
+
+ generate ROC or enrichment plots
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
+
+The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The output of this tool is a plot in form of an eps or png-file (as chosen).
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,35 @@
+
+
+
+ analyze similarity between molecule files
+
+
+
+
+
+
+
+
+
+ This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.
+
+Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,49 @@
+
+
+
+ rescore docking results
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool rescores docking output poses.
+A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).
+
+As input we need:
+ * a file containing a protonated protein in pdb-format
+ * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+ * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,45 @@
+
+
+
+ define spatial constraint
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool allows to define spatial constraints for docking or scoring.
+
+For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
+Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
+
+Output of this tool is a ini-file that contains the desired spatial constraint.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/TaGRes-train.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,61 @@
+
+
+
+ Target-specific Grid-Rescoring, training
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
+As input we need:
+
+ * a file containing a protonated protein in pdb-format
+ * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+ * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein.
+
+A scoring function is applied and an interaction-grid is thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
+
+The output of TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/TaGRes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,67 @@
+
+
+
+ Target-specific Grid-Rescoring
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool rescores docking output poses using Target-specific Grid-Rescoring.
+Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool.
+As input TaGRes needs:
+
+ * a file containing a protonated protein in pdb-format
+ * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+ * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
+ * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
+
+TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/Validator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Validator.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,36 @@
+
+
+
+ evaluate quality of a QSAR model
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Validator evaluates the quality of a QSAR model.
+
+The validation technique to be used for this can selected by '-type'. As input this tools need a model-file as generate by InputReader or FeatureSelector and a data-file generated by InputReader containing the prediction data set. Note that the latter must contain response values so that predictions done by the supplied model can be compared to those values by the validation method.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/VendorFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,49 @@
+
+
+
+ search vendors for compounds
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool can be used to fetch information about vendors for each compound in the given input file from a data base.
+
+Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database.
+
+Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/WaterFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,55 @@
+
+
+
+ find strongly bound waters
+
+
+
+
+
+
+
+
+
+
+
+ This tool searches for crystal waters that
+ * either interact very strongly with the receptor
+ * or that interact strongly with receptor and reference ligand,
+ thus functioning as a water bridge.
+
+Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
+
+As input we need:
+ * a file containing a protonated protein in pdb-format.
+ This file should contain water molecules that are to be evaluated by this tool.
+ However, you can also use a separate pdb-file as input for the water molecules (see below).
+ * a file containing a reference ligand.
+ This reference ligand should be located in the binding pocket.
+ Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+ * optionally a file in pdb-format containing water molecules.
+ If you specify such a file , all water molecules appearing in the
+ protein input-file (if any) will be ignored.
+
+Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.
+
\ No newline at end of file
diff -r e343494f18fe -r bb26168c5715 CADDSuite/galaxyconfigs/tools/upload.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/upload.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,46 @@
+
+
+
+
+ from your computer
+
+
+
+ ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
+ #set $outnum = 0
+ #while $varExists('output%i' % $outnum):
+ #set $output = $getVar('output%i' % $outnum)
+ #set $outnum += 1
+ ${output.dataset.dataset.id}:${output.files_path}:${output}
+ #end while
+
+
+
+
+
+
+
+
+
+
+
+
+
+ not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/install.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/install.sh Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,84 @@
+#!/bin/bash
+
+QT_DIR=""
+INSTALL_DIR=""
+#OPT="Linux_x86_64"
+
+
+checkDir()
+{
+ echo -n "checking for "$1" ... "
+ if [ -f $QT_DIR/$1 ]; then
+ echo $QT_DIR/$1
+ return 1
+ else
+ echo "not found!"
+ return 0
+ fi
+}
+
+echo
+cat license.txt
+echo
+echo -n "Do you agree to this license?! (y/n) "
+read license_accepted
+echo
+
+if [ "$license_accepted" != "y" ] && [ "$license_accepted" != "yes" ]; then
+ echo "License was not accepted, aborting."
+ exit 1
+fi
+
+echo -n "Please enter *absolute* path to install target-directory: "
+
+read INSTALL_DIR
+if [ ! -d $INSTALL_DIR ]; then
+ mkdir $INSTALL_DIR
+fi
+
+if [ ! -d $INSTALL_DIR ]; then
+ echo
+ echo "[Error:] The desired install-directory does not exist and could also not be created!"
+ echo "Perhaps there was a typo or you do not have permission to create this folder."
+ echo "Aborting install."
+ echo
+ exit 1
+fi
+
+# if [ -f /usr/lib/libQtCore.so.4 ] && [ -f /usr/lib/libQtGui.so.4 ]; then
+# QT_DIR=/usr/lib
+# else
+# echo "Please enter absolute path to the directory containing"
+# echo -n "your Qt4 libraries (version>=4.3.5): "
+# read QT_DIR
+# fi
+
+# checkDir libQtCore.so.4; ok=$?;
+# checkDir libQtGui.so.4; if [ $ok = 1 ]; then let ok $?; fi
+# #checkDir libQtOpenGL.so; if [ $ok = 1 ]; then ok=$?; fi
+#
+# if [ $ok != 1 ]; then
+# echo "Aborting installation due to missing Qt4!"
+# exit 1
+# fi
+
+cd bin
+programs=`ls *.bin`
+cd ..
+for i in $programs; do
+ chmod +x ${i:0:${#i}-4}
+done
+
+
+mv * $INSTALL_DIR/
+
+if [ -f $INSTALL_DIR/CADDSuite-description.txt ]; then
+ echo
+ echo
+ cat $INSTALL_DIR/CADDSuite-description.txt
+fi
+
+echo
+echo "Installation finished."
+echo "You can find all installed programs in $INSTALL_DIR."
+echo
diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/Accelerate
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/QtSql
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libBALL.1.4.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libBLAS.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libboost_iostreams.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libboost_regex.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libboost_system.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libboost_thread.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libgsl.0.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libgslcblas.0.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libmysqlclient.18.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/lib/libopenbabel.4.dylib
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diff -r e343494f18fe -r bb26168c5715 CADDSuite/license.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/license.txt Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,20 @@
+-------------------------------------------------------------------------------
+ CADDSuite - A flexible and open framework and workflow system
+ for computer-aided drug design
+-------------------------------------------------------------------------------
+
+Copyright (C) 2011 Marcel Schumann
+
+CADDSuite is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or (at
+your option) any later version.
+
+CADDSuite is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, see .
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/setPathes.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/setPathes.sh Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,11 @@
+#!/bin/bash
+export LD_LIBRARY_PATH="$BASE_DIR"/lib
+export DYLD_LIBRARY_PATH="$BASE_DIR"/lib
+export BALL_DATA_PATH="$BASE_DIR"/data
+export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/
+export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/
+export PATH="$BASE_DIR"/bin:$PATH
+export GDFONTPATH="$BASE_DIR"/data/gnuplot
+export GNUPLOT_DEFAULT_GDFONT=FreeSans
+export GNUPLOT_PS_DIR="$BASE_DIR"/data/gnuplot
+
diff -r e343494f18fe -r bb26168c5715 CADDSuite/suite_config.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/suite_config.xml Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,141 @@
+
+
+
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+
+
+ from your computer
+
+
+
+ rescore w/ anti-target dock-results
+
+
+ automatically find best QSAR model
+
+
+ fix bindingdb.org downloads
+
+
+ generate combinatorial lib
+
+
+ find strongly interacting residues
+
+
+ interconvert molecular file-formats
+
+
+ export molecules from data base
+
+
+ import molecules into data base
+
+
+ merge docking output files
+
+
+ generate splits w/ equal property range
+
+
+ run feature-selection on a QSAR model
+
+
+ generate galaxy tool-config files
+
+
+ create score-grids for docking
+
+
+ Iterative Multi-Greedy Docking
+
+
+ split QSAR data set
+
+
+ generate QSAR data set
+
+
+ define interaction constraint
+
+
+ check molecules for errors
+
+
+ generate 3D coordinates for small molecules
+
+
+ split molecule files
+
+
+ create a QSAR model
+
+
+ combine molecular files
+
+
+ create structure diagrams
+
+
+ filter molecule files
+
+
+ predict molecule activities with QSAR model
+
+
+ separate ligand and receptor
+
+
+ retrieve pdb-file from pdb.org
+
+
+ transfer part. charges between files
+
+
+ detect binding pocket
+
+
+ predict activities with QSAR model
+
+
+ modify molecule property tags
+
+
+ plot molecule properties
+
+
+ quality check for proteins structures
+
+
+ protonate protein structures
+
+
+ calculate RMSD between poses
+
+
+ generate ROC or enrichment plots
+
+
+ analyze similarity between molecule files
+
+
+ rescore docking results
+
+
+ define spatial constraint
+
+
+ Target-specific Grid-Rescoring, training
+
+
+ Target-specific Grid-Rescoring
+
+
+ evaluate quality of a QSAR model
+
+
+ search vendors for compounds
+
+
+ find strongly bound waters
+