Fix in blExtractZonePDBAsCopy()

@AndrewCRMartin AndrewCRMartin released this Feb 17, 2016 · 47 commits to master since this release

blExtractZonePDBAsCopy() was core dumping if there was an exact match to the first residue in the file. 'prev' wasn't being set correctly to NULL.


cp compatibility

@AndrewCRMartin AndrewCRMartin released this Feb 15, 2016 · 48 commits to master since this release

In Makefile, changed

cp -Rcp


cp -Rp

The -c doesn't work on all version of cp


Support for secondary structure and various PDBML enhancements

@AndrewCRMartin AndrewCRMartin released this Aug 4, 2015 · 67 commits to master since this release

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.


Enhanced header support, CONECT support and bug fixes

@AndrewCRMartin AndrewCRMartin released this Jun 26, 2015 · 86 commits to master since this release

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.


Additional Functions

@AndrewCRMartin AndrewCRMartin released this Oct 24, 2014 · 198 commits to master since this release

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)


Automated overview documentation

@AndrewCRMartin AndrewCRMartin released this Oct 18, 2014 · 200 commits to master since this release

This is largely a cosmetic release which automates the generation of overview documentation from formatted comments in the source code. Some minor changes to where the documentation goes as well.


First V3 Release

@AndrewCRMartin AndrewCRMartin released this Oct 9, 2014 · 209 commits to master since this release

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