Changelog

Release 1.0.10

29 May 2021

  • Fixed secondary structure parsing for multi character asym IDs in mmCIF.

Release 1.0.9

4 February 2021

  • Fixed temperature factor zero-padding in PDB saving.

  • Fixed MMTF decode bug in Ubuntu.

Release 1.0.8

9 December 2020

  • HETATM identity now preserved when parsing PDB files

Release 1.0.7

5 November 2020

  • Fixed blank ANISOU values in PDB saving.

  • Fixed negative residue IDs in PDB saving.

  • Fixed SyntaxWarning messages on PDB saving.

Release 1.0.6

8 September 2020

  • Added handling of new branched entities in MMCIF/MMTF.

Release 1.0.5

21 July 2020

  • Added ability to open compressed .gz files.

Release 1.0.4

1 May 2020

  • Made TER records more compliant in saved PDB files.

  • Specified required msgpack version to fix MMTF parsing issue.

Release 1.0.3

5 December 2019

  • Made quality information detection more broad.

  • Improved documentation.

Release 1.0.2

1 October 2019

  • Added distance optimiser for proximity checks.

  • Improved test coverage.

Release 1.0.1

26 September 2019

  • Added a pdb2json script for converting local structure files to JSON.

  • Improved speed comparison checks.

Release 1.0.0

23 June 2019

  • Saving now issues warning if the stucture has duplicate IDs.

  • Missing residues parsed for all three file types.

  • Crystallographic information now parsed.

  • Refactor of atomic structures.

  • Refactor of .mmtf parsing.

  • Structure copying now retains all properties.

  • Fixed bug in parsing .cif expression systems.

  • Full names of ligands and modified residues now parsed.

  • Secondary structure information parsed and available now.

  • Atoms now have covalent radius property for calculating bond cutoffs.

  • .pdb parsing can now handle heavy water (DOD).

  • General speed improvements.

Release 0.12.2

4 February 2019

  • Angle between superimposed atoms now possible.

  • Fixed source speices lookup in .cif files.

  • Fixed bug relating to embedded quotes in .cif files.

Release 0.12.1

13 January 2019

  • Fixed assembly parsing bug in small number of .cif files.

Release 0.12.0

2 January 2019

  • Refactored parse utilities to improve speed.

  • Added support for .mmtf files.

  • Added file writing for all three file types (.pdb, .cif, .mmtf).

  • Made .cif the default file type.

  • General library restructuring.

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.