annotate CADDSuite-1.0.1/changelog.txt @ 9:2cff9609f2c7

Uploaded
author marcel
date Tue, 15 Nov 2011 10:40:26 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
1 Version 1.0.1, 11-06-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
2 - In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
3 - Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
4 - Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
5
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
6 Version 1.0, 11-04-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
7 - Added support for advanced parameters and parameter sections
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
8 - Added some missing 'supported_formats' and 'tool_category' tags
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
9 - Fixed tar compression on Mac
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
10 - Fix for use of libsvm 3.1
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
11 - Fix for use of created release packages on MacOS 10.7
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
12 - Added missing flag to MolPredictor.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
13
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
14 Version 0.9.6, 08-20-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
15 - MolFilter: Use union of SMARTS matches instead of intersection
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
16 - Support for reading and writing compressed molecule files (*.gz)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
17 - Added optional parameter for output log-file to DBImporter
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
18 - Added flag for disabling uniqueness-check to LigCheck
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
19 - mol2-files: disabled gaff atom-typing for speed-up
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
20 - drf-files: automatically add new protein-conformations
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
21 - Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
22 - InputReader: made sure to always calculate correct set of features
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
23 - Fixed a nan problem during centering of QSAR data
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
24
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
25 Version 0.9.5, 07-12-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
26 - Let rescoring search for correct LigCheck molecule property-tags
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
27 - Indicate optional parameters in galaxy interface
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
28 - Fixed compilation with disabled QuEasyViz
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
29 - Added missing gnuplot data file to release archive
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
30 - Set some default values for flags for use in GUIs
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
31 - Clarified EvenSplit docu
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
32
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
33 Version 0.9.4, 06-27-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
34 - Fixed tool-startup script for pathes containing whitespaces
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
35 - New tool SpatialConstraintDefiner
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
36 - New tool InteractionConstraintDefiner
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
37 - Removed superficial pathes from startup-script
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
38 - Slight change in ParamFile format (i.e. the files written with -write_par)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
39 - Renamed IMeedyDock to IMGDock
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
40
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
41 Version 0.9.3, 05-30-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
42 - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
43 - Allow to optionally specify output filenames to LigandFileSplitter
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
44 - Fixed creation of galaxy-scripts for tools with inputfile-lists
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
45 - Fixed creation of galaxy-scripts for Converter and DockResultMerger
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
46 - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
47 - New tool MolFilter
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
48 - Fixed some gnuplot issues
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
49 - Added PDBDownload tool
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
50 - Slight change of format of ParamFile
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
51 - Added some missing tool-manuals
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
52 - Disable B-factor check for hydrogens in ProteinCheck
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
53 - Added safeguards to several tools
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
54 - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
55 - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
56 - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
57 - Enhanced several tool manuals
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
58 - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
59
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
60 Version 0.9.2, 05-17-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
61 - Speed-up of ob-mol generation
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
62 - Support build on Windows
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
63 - ProteinCheck now generates protein-quality report as pdf
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
64 - Added info about mandatory parameters and parameter-restrictions to parameter xml-file
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
65 - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
66 - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
67 - 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).
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
68 - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
69 - Write information about supported file-formats to parameter xml-file
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
70 - new tool ProteinProtonator
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
71 - new tool Ligand3DGenerator
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
72 - new tool GalaxyConfigGenerator
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
73 - allow to open file that do not have an extension (by searching for format-specific keywords)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
74
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
75 Version 0.9.1, 04-12-2011:
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
76 - All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par)
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
77
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
78 Version 0.9