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annotate CADDSuite-1.0.1/changelog.txt @ 26:2f19ad95a19d

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Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
author greg
date Tue, 15 Nov 2011 11:55:29 -0500
parents 389056b8864a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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23
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
1 Version 1.0.1, 11-06-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
2 - In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
3 - Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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4 - Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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5
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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6 Version 1.0, 11-04-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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7 - Added support for advanced parameters and parameter sections
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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8 - Added some missing 'supported_formats' and 'tool_category' tags
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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9 - Fixed tar compression on Mac
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
10 - Fix for use of libsvm 3.1
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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11 - Fix for use of created release packages on MacOS 10.7
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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12 - Added missing flag to MolPredictor.
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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13
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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14 Version 0.9.6, 08-20-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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15 - MolFilter: Use union of SMARTS matches instead of intersection
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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16 - Support for reading and writing compressed molecule files (*.gz)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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17 - Added optional parameter for output log-file to DBImporter
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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18 - Added flag for disabling uniqueness-check to LigCheck
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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19 - mol2-files: disabled gaff atom-typing for speed-up
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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20 - drf-files: automatically add new protein-conformations
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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21 - Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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22 - InputReader: made sure to always calculate correct set of features
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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23 - Fixed a nan problem during centering of QSAR data
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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24
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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25 Version 0.9.5, 07-12-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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26 - Let rescoring search for correct LigCheck molecule property-tags
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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27 - Indicate optional parameters in galaxy interface
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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28 - Fixed compilation with disabled QuEasyViz
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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29 - Added missing gnuplot data file to release archive
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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30 - Set some default values for flags for use in GUIs
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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31 - Clarified EvenSplit docu
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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32
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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33 Version 0.9.4, 06-27-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
34 - Fixed tool-startup script for pathes containing whitespaces
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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35 - New tool SpatialConstraintDefiner
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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36 - New tool InteractionConstraintDefiner
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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37 - Removed superficial pathes from startup-script
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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38 - Slight change in ParamFile format (i.e. the files written with -write_par)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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39 - Renamed IMeedyDock to IMGDock
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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40
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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41 Version 0.9.3, 05-30-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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42 - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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43 - Allow to optionally specify output filenames to LigandFileSplitter
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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44 - Fixed creation of galaxy-scripts for tools with inputfile-lists
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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45 - Fixed creation of galaxy-scripts for Converter and DockResultMerger
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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46 - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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47 - New tool MolFilter
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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48 - Fixed some gnuplot issues
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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49 - Added PDBDownload tool
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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50 - Slight change of format of ParamFile
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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51 - Added some missing tool-manuals
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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52 - Disable B-factor check for hydrogens in ProteinCheck
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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53 - Added safeguards to several tools
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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54 - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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55 - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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56 - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
57 - Enhanced several tool manuals
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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58 - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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59
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
60 Version 0.9.2, 05-17-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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61 - Speed-up of ob-mol generation
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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62 - Support build on Windows
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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63 - ProteinCheck now generates protein-quality report as pdf
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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64 - Added info about mandatory parameters and parameter-restrictions to parameter xml-file
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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65 - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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66 - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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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).
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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68 - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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69 - Write information about supported file-formats to parameter xml-file
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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70 - new tool ProteinProtonator
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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71 - new tool Ligand3DGenerator
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
72 - new tool GalaxyConfigGenerator
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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73 - allow to open file that do not have an extension (by searching for format-specific keywords)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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diff changeset
74
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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diff changeset
75 Version 0.9.1, 04-12-2011:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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76 - All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par)
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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77
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
greg
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78 Version 0.9