The main features of this release are improved PDBML format support (particularly SEQRES equivalent support), support for defining atom types and future support for secondary structure. There are also some small bug fixes and general enhancements:
- Update unit tests for pdb->atomType to pdb->atomInfo change.
- Improved MAKERESID macro
- Added '.' to MAKERESID()
- pdb.h added PDBEXTRASPTR() and RESIDMATCH()
- Added atomtype.c Added BuildConect.c/blIsConected()
- hbond.c - Added blSetMaxProteinHBondDADistance(), blListAllHBonds() hbond.h - Added HBLIST
- Added some comments to pdb.h about structure size
- Renamed blDistPtVect() to blDistPtLine() and added deprecation
- Added PDB.secstr field
- Fixed return value when run without XML_SUPPORT. This didn't give any error message on Linux, but did on Mac
- Added output of pdbml-formatted SEQRES records.
- Added part distribution information
- Split ParseHeaderPDBML() into smaller functions.
This release contains significant changes to support reading headers from the WHOLEPDB structure, proper support for CONECT records (including regenerating them, dealing with deleted/inserted atoms, etc), proper MASTER and TER record support, and much improved PDBML support. In addition there are a number of bug fixes and new general purpose routines including a general purpose set of hash/dictionary functions.
V3.2 adds new functions:
- blEigen() / eigen()
- blCalculateCovarianceMatrix() / CalculateCovarianceMatrix()
- blCalculateBestFitLine() / CalculateBestFitLine()
- blFindCentroid() / FindCentroid()
- blExtractZoneSpecPDBAsCopy() / ExtractZoneSpecPDB()
(Note that the deprecated function names have also been provied)
An option has also been added for compiling code that uses BiopLib that prevents it reading the contents of deprecated.h thus providing warnings about use of deprecated functions at compile time (-D NODEPRECATION on the compile line)
V3.0 adds reading and writing of PDB-XML files and handling of multi-character chain names.
(Almost) all functions have been renamed to have a 'bl' prefix and function naming is now much more consistent. For example, routines that clone a PDB linked list all have 'AsCopy' in their names.
A set of 'deprecation' files are provided so that the old function names can still be used with an option to warn the user that deprecated routines are in use.
A number of new functions have also been added.
Work on this release was funded by a BBSRC Sparking Impact award and has largely been the work of Dr. Craig Porter