Added ForceExtractZone functions and various cleanup

• BuildConect.c Added check on MAXCONECT
• Some fixes for strncpy() terminating strings
• Increased some buffer sizes to avoid possible overwrites in sprintf()
• Increased MAXCONECT from 8 to 16 for 1A3L
• Added ForceExtractZone routines
• Fix to deprecated.h
• Added levenshtein.c
• Updated ReadPDB.c for more checks on defining popen()
• Changed calls to fabs() to abs() in secstr.c

Fixed blListHBonds()

blListHbonds() was only listing the first HBond found between two residues rather than creating a list of all HBonds between the two residues as advertised.

Clean compile with optimization

Turning on optimization with gcc 7.3.1 gave a non-clean compile. Most of these were not real problems, but some real out-of-bounds potential errors were found. Fixed all these.

Improved blCheckProgName

Simple improvement to blCheckProgName() for pdbatomselect

Added sequtil and ability to free the MDM for alignment

• Initialized some variables
• Added sequtil.c
• Added BLOSUM90 matrix
• Stripping hydrogens also removes deuterium
• Corrections to ABS() calls in blWritePDB()
• Added blFreeMDM()

Added blDeleteResiduePDB()

• Fixed possible undefined variable in ReadPDB.c
• Added blDeleteResiduePDB()

V3.5.0 - Added secondary structure calculation

Adds secstr.c and secstr.h

Fix in blExtractZonePDBAsCopy()

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

In Makefile, changed

cp -Rcp

to

cp -Rp

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

Support for secondary structure and various PDBML enhancements

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.