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.
- Improved documentqtion.
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.
- Backend simplifications.
- 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:
- Experimental Technique
- Source Organism
- Expression Organism
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
- Fixed setup.py
- Minor typos
1 June 2017
- Added basic Model and Atom classes.
- Added .xyz parsing.