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Releases: ACRMGroup/bioptools

Lots of updates!

04 Feb 16:38
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  • Added pdbhphob
  • Added problem example to checkpdb
  • Added pdbline
  • Added 1zeh test example for pdbsymm
  • pdb2pir - valgrind clean
  • Various fixes for GCC V8 which finds some possible buffer overflows
  • Added pdbfindnearres
  • pdbgetresidues: fix to array boundary
  • pdbgetzone: -f with -v now forces extraction even if residues are not found
  • Added -v option to pdbchain
  • scorecons: Fixed bug in not reading specified matrix
  • Added rangecontacts
  • Updated to require bioplib V3.11

Added checkpdb

16 Aug 10:22
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checkpdb is a new tool for checking a PDB file. Currently it just checks for:

  • all backbone atoms are present
  • residues within a chain are connected

The idea is to expand this with lots more features.

Replaced pdbatomsel with pdbatomselect

03 Aug 09:32
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pdbatomselect does the same job as pdbatomsel but the style of calling is now more compatible with other programs. Rather than specifying atoms as

pdbatomsel -N -CA -C -O

it uses

pdbatomselect -a N,CA,C,O

The install provides a symbolic link to the old names (pdbatomsel and atomsel) which behave in the old way for backwards compatibility.

Added pdbfit and sixft. Fixed automatic bioplib install when working in a cloned repository

12 Jul 12:55
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  • Added pdbfit
  • Added sixft
  • Added -x option to pdbsolv
  • Update to BiopLib V3.8
  • Removed non-working git submodules
  • Fixed ./ -bioplib when working from a git clone
  • Added script to install all data from BiopLib if not present

V1.5 Various enhancements

24 Oct 09:49
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  • pdbhbond: updated output format
  • Removed unneeded include from pdblistss
  • Updated pdbpatchnumbering to skip up to 5 residues at the start of the chain
  • Bumped to require Bioplib V3.6
  • Added builddist for pdbaddhet
  • Added builddist for pdbtorsions
  • Added builddist for pdbcheckforres
  • Added builddist for pdbhbond
  • Added builddist for pdbsolv
  • Added builddist for pdbchain
  • Added builddist for pdbpatchnumbering
  • Added builddist for pdbhbond

V1.4 Added pdbsymm and chaincontacts

08 Aug 11:37
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  • Added pdbsymm and chaincontacts programs
  • Added some more builddist config files
  • Rewrote distmat

V1.3 - added secondary structure calculation

11 Aug 14:46
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Added pdbsecstr for secondary structure calculation
Requires Bioplib V3.5

Bioplib fix for pdbgetzone

17 Feb 15:03
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Fix in BiopLib to fix bug in pdbgetzone which was core dumping when the zone started with the first residue in the file.

Now required BiopLib V3.4.2

Fixed makemake bug

15 Feb 19:17
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The sub-directory needed when running -bioplib

wasn't created.

Enhancements and header support

29 Jun 14:19
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This release requires BiopLib V3.3. It provides significantly enhanced header support - where possible, all tools now retain headers and correctly update CONECT records. Some additional tools and bugfixes too.