Changelog

Release 0.11.1

13 September 2018

  • Fixed bug pertaining to residues with ID 0.
  • Fixed bug pertaining to SEQRES parsing when chain ID is numeric.
  • Changed format of residue IDs to include colon.
  • Considerable speed improvements in .mmcif parsing.

Release 0.11.0

22 August 2018

  • Added .mmcif parsing.
  • Changed how parsing in general is done under the hood.
  • Added atom angle calculation.
  • Fixed bug where modified residues were treated as ligands if authors used HETATM records.

Release 0.10.2

29 July 2018

  • Added function for getting PDBs over SSH.
  • Fixed biological assembly parsing bug.
  • Fixed chain copying of sequence bug.

Release 0.10.1

25 June 2018

  • Added function for returning best biological assembly.
  • Fixed bug with sorting None energy assemblies.
  • Fixed bug pertaining to excessive atom duplication when creating assembly.

Release 0.10.0

22 June 2018

  • Parsing of .pdb keywords.
  • Parsing of atom anisotropy.
  • Parsing of .pdb sequence information.
  • More R-factor information.
  • Biological assembly parsing and generation.
  • More powerful transformations rather than just simple rotation.
  • Backend simplifications.
  • Powerful new atom querying syntax.

Release 0.9.1

17 May 2018

  • Added Residue one-letter codes.
  • Fixed stray print statement.

Release 0.9.0

10 April 2018

  • Turned many methods into properties.
  • Added full residue name generation.
  • Made bind site detection more picky.
  • Added coordinate rounding to deal with floating point rounding errors.
  • Atomic structures now ‘copy’able.
  • Refactored atom querying.
  • Added grid generation.
  • Implemented Kabsch superposition/rotation.
  • Implemented RMSD comparison.
  • Created Complex class (for later).

Release 0.8.0

2 December 2017

  • Added option to get water residues in binding sites.

  • Added extra PDB meta information parsing, such as:

    • Classification
    • Experimental Technique
    • Source Organism
    • Expression Organism
    • R-factor

Release 0.7.0

2 November 2017

  • PDBs with multiple occupancy can now be parsed correctly.
  • Added pairwise atom generator.
  • PDB parser now extracts resolution.
  • Further speed increased to PDB parser.
  • Miscellaneous bug fixes.
  • Implemented Continuous Integration.

Release 0.6.0

3 October 2017

  • Now allows for fetching and opening of PDB data dictionaries.
  • Added parsing/saving of HEADER and TITLE records in PDB files.
  • Added ability to exclude elements from atom search.
  • Added ability to get nearby atoms in a model.
  • Added bind site identification.
  • Fixed chain length bottleneck in PDB model saving.
  • Overhauled PDB parsing by replacing classes with built in Python types.
  • Fixed bug where numerical residue names were interpreted as integers.
  • Changed atoms so that they can allow negative B factors.
  • Added loading of .xyz data dictionaries.
  • Miscellaneous speed increases.

Release 0.5.0

16 September 2017

  • Added atom temperature factors.
  • Added bond vector production.
  • Added parse time tests and reduced parse time by over a half.
  • Changed way atoms are stored in structures to make ID lookup orders of magnitude faster.
  • Made IDs immutable.
  • Added multiple model parsing and saving.
  • Added option to fetch PDBs from PDBe rather than RCSB.

Release 0.4.0

26 August 2017

  • Added PDB parsing.
  • Added PDB saving.
  • Gave atoms ability to get specific bond with other atom.
  • Added bond angle calculation.
  • Added ability to filter out water molecules.

Release 0.3.0

11 August 2017

  • Added classes for Molecules, Chains, Residues, and their interfaces.
  • Added charges to atoms and structures.
  • Add ability to create AtomicStructures from AtomicStructures.

Release 0.2.0

14 June 2017

  • Made all Atomic Structures savable.
  • Added Atom IDs and uniqueness constraints.
  • Added Atom Bonds.

Release 0.1.1

1 June 2017

  • Fixed setup.py
  • Minor typos

Release 0.1.0

1 June 2017

  • Added basic Model and Atom classes.
  • Added .xyz parsing.