Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.0/changelog.txt @ 14:55c32b55c2c2
Uploaded Version 1.1
| author | marcel |
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| date | Thu, 12 Jan 2012 11:00:43 -0500 |
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| 13:cce3667779c2 | 14:55c32b55c2c2 |
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| 1 Version 1.1, 01-10-2012: | |
| 2 - 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 | |
| 3 - Added default atom type for grid calculation | |
| 4 - Fixed default state of galaxy check-boxes | |
| 5 - Some small fixes for g++ 4.6 | |
| 6 - Changed some default output formats of many tools to mol2.gz. This will only have an effect if _no_ valid file extension is specified. | |
| 7 - Gave some more tools the ability to delete their input file after sucessful execution | |
| 8 - The last two points together allow to reduce required disk space for common docking pipeline by about 95%. | |
| 9 | |
| 10 Version 1.0.1, 11-06-2011: | |
| 11 - In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules | |
| 12 - Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions | |
| 13 - Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables | |
| 14 | |
| 15 Version 1.0, 11-04-2011: | |
| 16 - Added support for advanced parameters and parameter sections | |
| 17 - Added some missing 'supported_formats' and 'tool_category' tags | |
| 18 - Fixed tar compression on Mac | |
| 19 - Fix for use of libsvm 3.1 | |
| 20 - Fix for use of created release packages on MacOS 10.7 | |
| 21 - Added missing flag to MolPredictor. | |
| 22 | |
| 23 Version 0.9.6, 08-20-2011: | |
| 24 - MolFilter: Use union of SMARTS matches instead of intersection | |
| 25 - Support for reading and writing compressed molecule files (*.gz) | |
| 26 - Added optional parameter for output log-file to DBImporter | |
| 27 - Added flag for disabling uniqueness-check to LigCheck | |
| 28 - mol2-files: disabled gaff atom-typing for speed-up | |
| 29 - drf-files: automatically add new protein-conformations | |
| 30 - Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable | |
| 31 - InputReader: made sure to always calculate correct set of features | |
| 32 - Fixed a nan problem during centering of QSAR data | |
| 33 | |
| 34 Version 0.9.5, 07-12-2011: | |
| 35 - Let rescoring search for correct LigCheck molecule property-tags | |
| 36 - Indicate optional parameters in galaxy interface | |
| 37 - Fixed compilation with disabled QuEasyViz | |
| 38 - Added missing gnuplot data file to release archive | |
| 39 - Set some default values for flags for use in GUIs | |
| 40 - Clarified EvenSplit docu | |
| 41 | |
| 42 Version 0.9.4, 06-27-2011: | |
| 43 - Fixed tool-startup script for pathes containing whitespaces | |
| 44 - New tool SpatialConstraintDefiner | |
| 45 - New tool InteractionConstraintDefiner | |
| 46 - Removed superficial pathes from startup-script | |
| 47 - Slight change in ParamFile format (i.e. the files written with -write_par) | |
| 48 - Renamed IMeedyDock to IMGDock | |
| 49 | |
| 50 Version 0.9.3, 05-30-2011: | |
| 51 - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring) | |
| 52 - Allow to optionally specify output filenames to LigandFileSplitter | |
| 53 - Fixed creation of galaxy-scripts for tools with inputfile-lists | |
| 54 - Fixed creation of galaxy-scripts for Converter and DockResultMerger | |
| 55 - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive | |
| 56 - New tool MolFilter | |
| 57 - Fixed some gnuplot issues | |
| 58 - Added PDBDownload tool | |
| 59 - Slight change of format of ParamFile | |
| 60 - Added some missing tool-manuals | |
| 61 - Disable B-factor check for hydrogens in ProteinCheck | |
| 62 - Added safeguards to several tools | |
| 63 - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator | |
| 64 - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used) | |
| 65 - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file) | |
| 66 - Enhanced several tool manuals | |
| 67 - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles. | |
| 68 | |
| 69 Version 0.9.2, 05-17-2011: | |
| 70 - Speed-up of ob-mol generation | |
| 71 - Support build on Windows | |
| 72 - ProteinCheck now generates protein-quality report as pdf | |
| 73 - Added info about mandatory parameters and parameter-restrictions to parameter xml-file | |
| 74 - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file) | |
| 75 - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions. | |
| 76 - 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). | |
| 77 - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script | |
| 78 - Write information about supported file-formats to parameter xml-file | |
| 79 - new tool ProteinProtonator | |
| 80 - new tool Ligand3DGenerator | |
| 81 - new tool GalaxyConfigGenerator | |
| 82 - allow to open file that do not have an extension (by searching for format-specific keywords) | |
| 83 | |
| 84 Version 0.9.1, 04-12-2011: | |
| 85 - All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par) | |
| 86 | |
| 87 Version 0.9 |