Biotite 0.12.0

Changelog

Additions

• Added new structure.info subpackage that contains all kinds of basic structure-related data
  • structure.info.mass() function provides weight for elements, residue name and enitre structures
  • structure.info.vdw_radius_single() and structure.info.vdw_radius_protor() function provides Van-der-Waals radii for single elements or atoms with bonded hydrogens, respectively
  • structure.info.bond_order() and structure.info.bonds_in_residue() provide information about bonded atoms
  • structure.full_name() provides the full name of an up to 3-letter residue/compound name
  • structure.link_type() provides the link type for a residue name
• Added structure.rdf() function for calculation of the radial distribution function of positions in an AtomArray or AtomArrayStack
• Added structure.residue_iter() function, that yields each residue in an AtomArray or AtomArrayStack as an subarray (stack)

Changes

• Removed structure.mass_of_element() and structure.atom_masses()
• When writing MMTF files, the chemCompType in groupList is determined via structure.link_type()

Fixes

• PDB files can be written for structures with more than 100,000 atoms
  • When the amount of 99,999 atoms is exceeded, the atom ID starts over again
• dir() function gives proper results for AtomArray and AtomArrayStack
• Fixed ProtOr radii in structure.sasa()
• structure.stack() includes the box attribute when stacking AtomArray objects