Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.0.1/changelog.txt @ 5:e30a41af9d2b
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:53:16 -0500 |
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| 4:af446ca2d5c6 | 5:e30a41af9d2b |
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| 1 Version 1.0.1, 11-06-2011: | |
| 2 - In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules | |
| 3 - Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions | |
| 4 - Display meaningful error if autmatic QSAR model is attempted with data not containing any response variables | |
| 5 | |
| 6 Version 1.0, 11-04-2011: | |
| 7 - Added support for advanced parameters and parameter sections | |
| 8 - Added some missing 'supported_formats' and 'tool_category' tags | |
| 9 - Fixed tar compression on Mac | |
| 10 - Fix for use of libsvm 3.1 | |
| 11 - Fix for use of created release packages on MacOS 10.7 | |
| 12 - Added missing flag to MolPredictor. | |
| 13 | |
| 14 Version 0.9.6, 08-20-2011: | |
| 15 - MolFilter: Use union of SMARTS matches instead of intersection | |
| 16 - Support for reading and writing compressed molecule files (*.gz) | |
| 17 - Added optional parameter for output log-file to DBImporter | |
| 18 - Added flag for disabling uniqueness-check to LigCheck | |
| 19 - mol2-files: disabled gaff atom-typing for speed-up | |
| 20 - drf-files: automatically add new protein-conformations | |
| 21 - Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable | |
| 22 - InputReader: made sure to always calculate correct set of features | |
| 23 - Fixed a nan problem during centering of QSAR data | |
| 24 | |
| 25 Version 0.9.5, 07-12-2011: | |
| 26 - Let rescoring search for correct LigCheck molecule property-tags | |
| 27 - Indicate optional parameters in galaxy interface | |
| 28 - Fixed compilation with disabled QuEasyViz | |
| 29 - Added missing gnuplot data file to release archive | |
| 30 - Set some default values for flags for use in GUIs | |
| 31 - Clarified EvenSplit docu | |
| 32 | |
| 33 Version 0.9.4, 06-27-2011: | |
| 34 - Fixed tool-startup script for pathes containing whitespaces | |
| 35 - New tool SpatialConstraintDefiner | |
| 36 - New tool InteractionConstraintDefiner | |
| 37 - Removed superficial pathes from startup-script | |
| 38 - Slight change in ParamFile format (i.e. the files written with -write_par) | |
| 39 - Renamed IMeedyDock to IMGDock | |
| 40 | |
| 41 Version 0.9.3, 05-30-2011: | |
| 42 - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring) | |
| 43 - Allow to optionally specify output filenames to LigandFileSplitter | |
| 44 - Fixed creation of galaxy-scripts for tools with inputfile-lists | |
| 45 - Fixed creation of galaxy-scripts for Converter and DockResultMerger | |
| 46 - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive | |
| 47 - New tool MolFilter | |
| 48 - Fixed some gnuplot issues | |
| 49 - Added PDBDownload tool | |
| 50 - Slight change of format of ParamFile | |
| 51 - Added some missing tool-manuals | |
| 52 - Disable B-factor check for hydrogens in ProteinCheck | |
| 53 - Added safeguards to several tools | |
| 54 - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator | |
| 55 - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used) | |
| 56 - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file) | |
| 57 - Enhanced several tool manuals | |
| 58 - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles. | |
| 59 | |
| 60 Version 0.9.2, 05-17-2011: | |
| 61 - Speed-up of ob-mol generation | |
| 62 - Support build on Windows | |
| 63 - ProteinCheck now generates protein-quality report as pdf | |
| 64 - Added info about mandatory parameters and parameter-restrictions to parameter xml-file | |
| 65 - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file) | |
| 66 - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions. | |
| 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). | |
| 68 - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script | |
| 69 - Write information about supported file-formats to parameter xml-file | |
| 70 - new tool ProteinProtonator | |
| 71 - new tool Ligand3DGenerator | |
| 72 - new tool GalaxyConfigGenerator | |
| 73 - allow to open file that do not have an extension (by searching for format-specific keywords) | |
| 74 | |
| 75 Version 0.9.1, 04-12-2011: | |
| 76 - All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par) | |
| 77 | |
| 78 Version 0.9 |