27 November 2021
Optimised distance lookup for finding atoms within sphere.
29 May 2021
Fixed secondary structure parsing for multi character asym IDs in mmCIF.
4 February 2021
Fixed temperature factor zero-padding in PDB saving.
Fixed MMTF decode bug in Ubuntu.
9 December 2020
HETATM identity now preserved when parsing PDB files
5 November 2020
Fixed blank ANISOU values in PDB saving.
Fixed negative residue IDs in PDB saving.
Fixed SyntaxWarning messages on PDB saving.
8 September 2020
Added handling of new branched entities in MMCIF/MMTF.
21 July 2020
Added ability to open compressed .gz files.
1 May 2020
Made TER records more compliant in saved PDB files.
Specified required msgpack version to fix MMTF parsing issue.
5 December 2019
Made quality information detection more broad.
1 October 2019
Added distance optimiser for proximity checks.
Improved test coverage.
26 September 2019
Added a pdb2json script for converting local structure files to JSON.
Improved speed comparison checks.
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.
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.
13 January 2019
Fixed assembly parsing bug in small number of .cif files.
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.
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.
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.
29 July 2018
Added function for getting PDBs over SSH.
Fixed biological assembly parsing bug.
Fixed chain copying of sequence bug.
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.
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.
Powerful new atom querying syntax.
17 May 2018
Added Residue one-letter codes.
Fixed stray print statement.
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).
2 December 2017
Added option to get water residues in binding sites.
Added extra PDB meta information parsing, such as:
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.
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.
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.
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.
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.
14 June 2017
Made all Atomic Structures savable.
Added Atom IDs and uniqueness constraints.
Added Atom Bonds.
1 June 2017
1 June 2017
Added basic Model and Atom classes.
Added .xyz parsing.