annotate CADDSuite-1.5/changelog.txt @ 15:ac342506cd4e draft

CADDSuite version 1.5

Version 1.5, 07-18-2012:
	- Changed scoring function to include greatly improved solvation term !!!
	- Added SurfaceMatcher. It finds the best superposition of two binding pocket surfaces using FFT !!
	- 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.
	- Added k-mean clustering to MolDB
	- For DBExporter and similarity search, allow to set threshold for max. desired molecules per query mol
	- Allow to filter compound library by vendor name using DBExporter
	- Allow to restrict similarity search to molecules with molecular weigth similar to the one of query molecule
	- Added diversity criteria to DB similarity search and to MolFilter
	- Optional automatic detection of ref. ligand (using largest heterosystem) added to PDBCutter
	- PDBCutter can now also download ligand sdf with correct topology from PDB server instead just writing a pdb with unkown bond orders
	- Adapted default penalty value set by SpatialConstraintDefiner and PocketDetector 

Version 1.1, 01-10-2012:
	- 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
	- Added default atom type for grid calculation
	- Fixed default state of galaxy check-boxes
	- Some small fixes for g++ 4.6
	- Changed some default output formats of many tools to mol2.gz. This will only have an effect if _no_ valid file extension is specified.
	- Gave some more tools the ability to delete their input file after sucessful execution
	- The last two points together allow to reduce required disk space for common docking pipeline by about 95%.

Version 1.0.1, 11-06-2011:
	- In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules
	- Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions
	- Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables

Version 1.0, 11-04-2011:
	- Added support for advanced parameters and parameter sections
	- Added some missing 'supported_formats' and 'tool_category' tags
	- Fixed tar compression on Mac
	- Fix for use of libsvm 3.1
	- Fix for use of created release packages on MacOS 10.7
	- Added missing flag to MolPredictor.

Version 0.9.6, 08-20-2011:
	- MolFilter: Use union of SMARTS matches instead of intersection
	- Support for reading and writing compressed molecule files (*.gz)
	- Added optional parameter for output log-file to DBImporter
	- Added flag for disabling uniqueness-check to LigCheck
	- mol2-files: disabled gaff atom-typing for speed-up
	- drf-files: automatically add new protein-conformations
	- Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable
	- InputReader: made sure to always calculate correct set of features
	- Fixed a nan problem during centering of QSAR data

Version 0.9.5, 07-12-2011:
	- Let rescoring search for correct LigCheck molecule property-tags
	- Indicate optional parameters in galaxy interface
	- Fixed compilation with disabled QuEasyViz
	- Added missing gnuplot data file to release archive
	- Set some default values for flags for use in GUIs
	- Clarified EvenSplit docu

Version 0.9.4, 06-27-2011:
	- Fixed tool-startup script for pathes containing whitespaces
	- New tool SpatialConstraintDefiner
	- New tool InteractionConstraintDefiner
	- Removed superficial pathes from startup-script
	- Slight change in ParamFile format (i.e. the files written with -write_par)
	- Renamed IMeedyDock to IMGDock

Version 0.9.3, 05-30-2011:
	- Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
	- Allow to optionally specify output filenames to LigandFileSplitter
	- Fixed creation of galaxy-scripts for tools with inputfile-lists
	- Fixed creation of galaxy-scripts for Converter and DockResultMerger
	- Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
	- New tool MolFilter
	- Fixed some gnuplot issues
	- Added PDBDownload tool
	- Slight change of format of ParamFile
	- Added some missing tool-manuals
	- Disable B-factor check for hydrogens in ProteinCheck
	- Added safeguards to several tools
	- Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
	- Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
	- Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
	- Enhanced several tool manuals
	- Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.

Version 0.9.2, 05-17-2011:
	- Speed-up of ob-mol generation
	- Support build on Windows
	- ProteinCheck now generates protein-quality report as pdf
	- Added info about mandatory parameters and parameter-restrictions to parameter xml-file
	- Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
	- Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
	- 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).
	- Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
	- Write information about supported file-formats to parameter xml-file
	- new tool ProteinProtonator
	- new tool Ligand3DGenerator
	- new tool GalaxyConfigGenerator
	- allow to open file that do not have an extension (by searching for format-specific keywords)

Version 0.9.1, 04-12-2011:
	- All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par)

Version 0.9