29 January 2017
- Added PDB writing to file.
- Structures can now be translated and transformed.
- Complexes added.
- Models can now duplicate structures within them.
- Added center of mass and radius of gyration metrics.
- Atom distances can now be to a structure as well as another atom.
- Renamed different Atom types (there are now ‘ghost atoms’)
15 August 2016
- Fixed bug relating to CONECT bonds sometimes bound to same atom.
- Fixed PDB datafile’s string representation.
12 August 2016
- Fixed bug relating to bind site construction from invalid chain.
- Fixed bug relating to disulphide bonds sometimes bound to same atom.
4 August 2016
- Version number fix.
4 August 2016
- A backwards-incompatible redesign of molecuPy.
- Attributes are now methods.
- Bind site calculation is now done at the atomic structure level.
- Tests are now fully mocked and easier to establish.
- Atoms can now detect nearby atoms as long as they are in the same model.
11 July 2016
- Fixed bug where occasionally covalent bonds would be made over missing residues.
20 June 2016
- Added Alpha Helix class.
- Added Beta Strand class.
Residue distance matrices
- Chains can now generate SVG distance matrices showing the distances between residues.
- Chains can now produce a combined list of all residue IDs, missing and present.
1 June 2016
- Covalent bonds are now added, and atoms now know about their neighbours.
- Residues are now aware of which residue they are covalently bound to in their chain.
- Added methods for calculating the internal and external atomic contacts of any atomic structure.
- Fixed bug where PDB files could not have site mapping parsed where there was no space between the chain ID and residue ID.
19 May 2016
- Residuic Sequences can now return their amino acid sequence as a string
- Added a class for binding sites
- Mapped sites to ligands
- Added methods for getting sites for ligands
- Incorporated insert codes into residue IDs
16 May 2016
- Basic PDB parsing
- Small Molecules