Release 1.1.0

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’)

Release 1.0.3

15 August 2016

  • Fixed bug relating to CONECT bonds sometimes bound to same atom.
  • Fixed PDB datafile’s string representation.

Release 1.0.2

12 August 2016

  • Fixed bug relating to bind site construction from invalid chain.
  • Fixed bug relating to disulphide bonds sometimes bound to same atom.

Release 1.0.1

4 August 2016

  • Version number fix.

Release 1.0.0

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.

Release 0.4.1

11 July 2016

  • Bug fix

    • Fixed bug where occasionally covalent bonds would be made over missing residues.

Release 0.4.0

20 June 2016

  • Secondary Structure

    • Added Alpha Helix class.
    • Added Beta Strand class.
  • Residue distance matrices

    • Chains can now generate SVG distance matrices showing the distances between residues.
  • Missing residues

    • Chains can now produce a combined list of all residue IDs, missing and present.

Release 0.3.0

1 June 2016

  • Atom connectivity

    • Covalent bonds are now added, and atoms now know about their neighbours.
  • Residue connectivity

    • Residues are now aware of which residue they are covalently bound to in their chain.
  • Atomic contacts

    • Added methods for calculating the internal and external atomic contacts of any atomic structure.
  • Bug fixes

    • Fixed bug where PDB files could not have site mapping parsed where there was no space between the chain ID and residue ID.

Release 0.2.0

19 May 2016

  • Protein Sequences

    • Residuic Sequences can now return their amino acid sequence as a string
  • Binding Sites

    • Added a class for binding sites
    • Mapped sites to ligands
    • Added methods for getting sites for ligands
  • Insert codes

    • Incorporated insert codes into residue IDs

Release 0.1.0

16 May 2016

  • Basic PDB parsing
    • Models
    • Chains
    • Residues
    • Atoms
    • Small Molecules