Changelog --------- Release 1.0.11 ~~~~~~~~~~~~~~ `27 November 2021` * Optimised distance lookup for finding atoms within sphere. 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.