# HG changeset patch # User g2cmnty@test-web1.g2.bx.psu.edu # Date 1309110656 14400 # Node ID bbc4a2c1d2764ba28a49da93c3f7f9e8eb024c79 # Parent 867bf9f815a0a18b12273a791e7ebc70d530457b Deleted selected files diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/CADDSuite-description.txt --- a/CADDSuite/CADDSuite-description.txt Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -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 - - ConstraintsFinder: find strongly interacting residues - - PocketDetector: detect ligand binding pocket - - GridBuilder: precalculate grids for docking - - IMeedyDock: 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/IMGDock --- a/CADDSuite/IMGDock Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/IMGDock.bin "$@" diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/InteractionConstraintDefiner --- a/CADDSuite/InteractionConstraintDefiner Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/SpatialConstraintDefiner --- a/CADDSuite/SpatialConstraintDefiner Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/AntitargetRescorer.bin Binary file CADDSuite/bin/AntitargetRescorer.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/AutoModel.bin Binary file CADDSuite/bin/AutoModel.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/BindingDBCleaner.bin Binary file CADDSuite/bin/BindingDBCleaner.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/CombiLibGenerator.bin Binary file CADDSuite/bin/CombiLibGenerator.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/ConstraintsFinder.bin Binary file CADDSuite/bin/ConstraintsFinder.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/Converter.bin Binary file CADDSuite/bin/Converter.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/DBExporter.bin Binary file CADDSuite/bin/DBExporter.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 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bbc4a2c1d276 CADDSuite/bin/InputReader.bin Binary file CADDSuite/bin/InputReader.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/InteractionConstraintDefiner.bin Binary file CADDSuite/bin/InteractionConstraintDefiner.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/LigCheck.bin Binary file CADDSuite/bin/LigCheck.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/Ligand3DGenerator.bin Binary file CADDSuite/bin/Ligand3DGenerator.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/LigandFileSplitter.bin Binary file CADDSuite/bin/LigandFileSplitter.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/ModelCreator.bin Binary file CADDSuite/bin/ModelCreator.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/MolCombine.bin Binary file CADDSuite/bin/MolCombine.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/MolDepict.bin Binary file CADDSuite/bin/MolDepict.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/MolFilter.bin Binary file CADDSuite/bin/MolFilter.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/MolPredictor.bin Binary file CADDSuite/bin/MolPredictor.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/PDBCutter.bin Binary file CADDSuite/bin/PDBCutter.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/PDBDownload.bin Binary file CADDSuite/bin/PDBDownload.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/PartialChargesCopy.bin Binary file CADDSuite/bin/PartialChargesCopy.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/PocketDetector.bin Binary file CADDSuite/bin/PocketDetector.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/Predictor.bin Binary file CADDSuite/bin/Predictor.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/PropertyModifier.bin Binary file CADDSuite/bin/PropertyModifier.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/PropertyPlotter.bin Binary file CADDSuite/bin/PropertyPlotter.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/ProteinCheck.bin Binary file CADDSuite/bin/ProteinCheck.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/ProteinProtonator.bin Binary file CADDSuite/bin/ProteinProtonator.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/RMSDCalculator.bin Binary file CADDSuite/bin/RMSDCalculator.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/ScoreAnalyzer.bin Binary file CADDSuite/bin/ScoreAnalyzer.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/SimilarityAnalyzer.bin Binary file CADDSuite/bin/SimilarityAnalyzer.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/SimpleRescorer.bin Binary file CADDSuite/bin/SimpleRescorer.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/SpatialConstraintDefiner.bin Binary file CADDSuite/bin/SpatialConstraintDefiner.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/TaGRes-train.bin Binary file CADDSuite/bin/TaGRes-train.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/TaGRes.bin Binary file CADDSuite/bin/TaGRes.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/Validator.bin Binary file CADDSuite/bin/Validator.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/VendorFinder.bin Binary file CADDSuite/bin/VendorFinder.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/bin/WaterFinder.bin Binary file CADDSuite/bin/WaterFinder.bin has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/changelog.txt --- a/CADDSuite/changelog.txt Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tool_conf.xml --- a/CADDSuite/galaxyconfigs/tool_conf.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ - - - \ No newline at end of file diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml --- a/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml --- a/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml --- a/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - - 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 - Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml --- a/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/Converter.xml --- a/CADDSuite/galaxyconfigs/tools/Converter.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/DBExporter.xml --- a/CADDSuite/galaxyconfigs/tools/DBExporter.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/DBImporter.xml --- a/CADDSuite/galaxyconfigs/tools/DBImporter.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/DockResultMerger.xml --- a/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/EvenSplit.xml --- a/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml --- a/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/GridBuilder.xml --- a/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/IMGDock.xml --- a/CADDSuite/galaxyconfigs/tools/IMGDock.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml --- a/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/LigCheck.xml --- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml --- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml --- a/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/MolCombine.xml --- a/CADDSuite/galaxyconfigs/tools/MolCombine.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/MolDepict.xml --- a/CADDSuite/galaxyconfigs/tools/MolDepict.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/PDBCutter.xml --- a/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/PDBDownload.xml --- a/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml --- a/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/PocketDetector.xml --- a/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/PropertyModifier.xml --- a/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml --- a/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/ProteinCheck.xml --- a/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml --- a/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml --- a/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml --- a/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml --- a/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml --- a/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/TaGRes-train.xml --- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ - - - - 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 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 this 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/TaGRes.xml --- a/CADDSuite/galaxyconfigs/tools/TaGRes.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/VendorFinder.xml --- a/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/WaterFinder.xml --- a/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/galaxyconfigs/tools/upload.xml --- a/CADDSuite/galaxyconfigs/tools/upload.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - - - - 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 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/install.sh --- a/CADDSuite/install.sh Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -#!/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 $INSTALL_DIR." -echo diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libBALL.so.1.4 Binary file CADDSuite/lib/libBALL.so.1.4 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libQtCore.so.4 Binary file CADDSuite/lib/libQtCore.so.4 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libQtNetwork.so.4 Binary file CADDSuite/lib/libQtNetwork.so.4 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libQtSql.so.4 Binary file CADDSuite/lib/libQtSql.so.4 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libQtXml.so.4 Binary file CADDSuite/lib/libQtXml.so.4 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libmysqlclient_r.so.16 Binary file CADDSuite/lib/libmysqlclient_r.so.16 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/lib/libnsl.so.1 Binary file CADDSuite/lib/libnsl.so.1 has changed diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/setPathes.sh --- a/CADDSuite/setPathes.sh Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#!/bin/bash -export LD_LIBRARY_PATH="$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/fonts -export GNUPLOT_DEFAULT_GDFONT=FreeSans - diff -r 867bf9f815a0 -r bbc4a2c1d276 CADDSuite/suite_config.xml --- a/CADDSuite/suite_config.xml Sun Jun 26 13:45:14 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ - - - -CADDSuite: A flexible and open framework for Computer-Aided Drug Design - - - from your computer - - - rescore w/ anti-target dock-results - - - 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 - - - generate galaxy tool-config files - - - create score-grids for docking - - - Iterative Multi-Greedy Docking - - - define interaction constraint - - - check molecules for errors - - - generate 3D coordinates for small molecules - - - split molecule files - - - combine molecular files - - - create structure diagrams - - - filter molecule files - - - separate ligand and receptor - - - retrieve pdb-file from pdb.org - - - transfer part. charges between files - - - detect binding pocket - - - 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 - - - search vendors for compounds - - - find strongly bound waters - - - automatically find best QSAR model - - - run feature-selection on a QSAR model - - - split QSAR data set - - - generate QSAR data set - - - create a QSAR model - - - predict molecule activities with QSAR model - - - predict activities with QSAR model - - - evaluate quality of a QSAR model -