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