Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.1/changelog.txt @ 6:decca54699e3
Uploaded Version 1.1
author | marcel |
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date | Thu, 12 Jan 2012 11:07:03 -0500 |
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5:e30a41af9d2b | 6:decca54699e3 |
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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 |