Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.5/changelog.txt @ 7:bfab27640f5e draft
CADDSuite version 1.5
| author | Marcel Schumann <schumann.marcel@gmail.com> |
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| date | Tue, 24 Jul 2012 11:13:59 -0400 |
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| 6:decca54699e3 | 7:bfab27640f5e |
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| 1 Version 1.5, 07-18-2012: | |
| 2 - Changed scoring function to include greatly improved solvation term !!! | |
| 3 - Added SurfaceMatcher. It finds the best superposition of two binding pocket surfaces using FFT !! | |
| 4 - Added PocketCutter, which allows to cut receptor atoms contributing to the SES of the binding pocket of a receptor. This output can then be used with SurfaceMatcher. | |
| 5 - Added k-mean clustering to MolDB | |
| 6 - For DBExporter and similarity search, allow to set threshold for max. desired molecules per query mol | |
| 7 - Allow to filter compound library by vendor name using DBExporter | |
| 8 - Allow to restrict similarity search to molecules with molecular weigth similar to the one of query molecule | |
| 9 - Added diversity criteria to DB similarity search and to MolFilter | |
| 10 - Optional automatic detection of ref. ligand (using largest heterosystem) added to PDBCutter | |
| 11 - PDBCutter can now also download ligand sdf with correct topology from PDB server instead just writing a pdb with unkown bond orders | |
| 12 - Adapted default penalty value set by SpatialConstraintDefiner and PocketDetector | |
| 13 | |
| 14 Version 1.1, 01-10-2012: | |
| 15 - Eradicated use of external tool 'tar'. ScoreGridSets are now compressed using boost's gzip support. Multiple ScoreGridSets are automatically. concatenated and saved as one gzipped file | |
| 16 - Added default atom type for grid calculation | |
| 17 - Fixed default state of galaxy check-boxes | |
| 18 - Some small fixes for g++ 4.6 | |
| 19 - Changed some default output formats of many tools to mol2.gz. This will only have an effect if _no_ valid file extension is specified. | |
| 20 - Gave some more tools the ability to delete their input file after sucessful execution | |
| 21 - The last two points together allow to reduce required disk space for common docking pipeline by about 95%. | |
| 22 | |
| 23 Version 1.0.1, 11-06-2011: | |
| 24 - In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules | |
| 25 - Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions | |
| 26 - Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables | |
| 27 | |
| 28 Version 1.0, 11-04-2011: | |
| 29 - Added support for advanced parameters and parameter sections | |
| 30 - Added some missing 'supported_formats' and 'tool_category' tags | |
| 31 - Fixed tar compression on Mac | |
| 32 - Fix for use of libsvm 3.1 | |
| 33 - Fix for use of created release packages on MacOS 10.7 | |
| 34 - Added missing flag to MolPredictor. | |
| 35 | |
| 36 Version 0.9.6, 08-20-2011: | |
| 37 - MolFilter: Use union of SMARTS matches instead of intersection | |
| 38 - Support for reading and writing compressed molecule files (*.gz) | |
| 39 - Added optional parameter for output log-file to DBImporter | |
| 40 - Added flag for disabling uniqueness-check to LigCheck | |
| 41 - mol2-files: disabled gaff atom-typing for speed-up | |
| 42 - drf-files: automatically add new protein-conformations | |
| 43 - Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable | |
| 44 - InputReader: made sure to always calculate correct set of features | |
| 45 - Fixed a nan problem during centering of QSAR data | |
| 46 | |
| 47 Version 0.9.5, 07-12-2011: | |
| 48 - Let rescoring search for correct LigCheck molecule property-tags | |
| 49 - Indicate optional parameters in galaxy interface | |
| 50 - Fixed compilation with disabled QuEasyViz | |
| 51 - Added missing gnuplot data file to release archive | |
| 52 - Set some default values for flags for use in GUIs | |
| 53 - Clarified EvenSplit docu | |
| 54 | |
| 55 Version 0.9.4, 06-27-2011: | |
| 56 - Fixed tool-startup script for pathes containing whitespaces | |
| 57 - New tool SpatialConstraintDefiner | |
| 58 - New tool InteractionConstraintDefiner | |
| 59 - Removed superficial pathes from startup-script | |
| 60 - Slight change in ParamFile format (i.e. the files written with -write_par) | |
| 61 - Renamed IMeedyDock to IMGDock | |
| 62 | |
| 63 Version 0.9.3, 05-30-2011: | |
| 64 - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring) | |
| 65 - Allow to optionally specify output filenames to LigandFileSplitter | |
| 66 - Fixed creation of galaxy-scripts for tools with inputfile-lists | |
| 67 - Fixed creation of galaxy-scripts for Converter and DockResultMerger | |
| 68 - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive | |
| 69 - New tool MolFilter | |
| 70 - Fixed some gnuplot issues | |
| 71 - Added PDBDownload tool | |
| 72 - Slight change of format of ParamFile | |
| 73 - Added some missing tool-manuals | |
| 74 - Disable B-factor check for hydrogens in ProteinCheck | |
| 75 - Added safeguards to several tools | |
| 76 - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator | |
| 77 - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used) | |
| 78 - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file) | |
| 79 - Enhanced several tool manuals | |
| 80 - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles. | |
| 81 | |
| 82 Version 0.9.2, 05-17-2011: | |
| 83 - Speed-up of ob-mol generation | |
| 84 - Support build on Windows | |
| 85 - ProteinCheck now generates protein-quality report as pdf | |
| 86 - Added info about mandatory parameters and parameter-restrictions to parameter xml-file | |
| 87 - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file) | |
| 88 - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions. | |
| 89 - 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). | |
| 90 - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script | |
| 91 - Write information about supported file-formats to parameter xml-file | |
| 92 - new tool ProteinProtonator | |
| 93 - new tool Ligand3DGenerator | |
| 94 - new tool GalaxyConfigGenerator | |
| 95 - allow to open file that do not have an extension (by searching for format-specific keywords) | |
| 96 | |
| 97 Version 0.9.1, 04-12-2011: | |
| 98 - All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par) | |
| 99 | |
| 100 Version 0.9 |