Changelog

Additions

• Added interfaces to other packages in the bioinformatics ecosystem via the new interface subpackage. (#762)
  • interface.rdkit allows conversion between AtomArray and Mol objects from the RDKit package. (#736, #741, #742)
  • interface.pymol allows conversion between AtomArray and PyMOL objects, supporting NumPy-style indices as atom selections. (#749)
  • interface.openmm allows conversion between AtomArray and OpenMM Toplology, System and State objects. (#750)
• Added database.alphafold subpackage for accessing structures from AlphaFold DB. (#492)
  • The IDs of computational models obtained via database.rcsb.search() can be passed directly to database.alphafold.fetch().
• Added new metrics for measuring similarity of two structures.
  • structure.lddt() computes the Local Distance Difference Test and can be highly customized with filtering and binning options. (#699)
  • structure.tm_score() computes the TM-score. Curresponding structure alignments can be performed with superimpose_structural_homologs(). (#705)
• Added functions related to aromatic rings. (#751)
  • structure.find_aromatic_rings() finds atom indices of aromatic rings in a structure.
  • structure.find_stacking_interactions() finds pi-stacking interactions between aromatic rings.
• Added structure.BondType.AROMATIC bond type, for bonds where the kekulized form is unknown. (#738)
• structure.info.residue() and structure.io.pdbx.get_component() now support chemical components without valid coordinates. (#730)
• label_entity_id annotation can now be written to PDBx files via structure.io.pdbx.set_structure(). (#732)
• structure.info.vdw_radius_single() now supports more elements. (#745)
• Improved performance of structure.spread_residue_wise() and structure.spread_chain_wise(). (#770)

Fixes

• Now only finite coordinates can be given to structure.CellList() (#733).
• Fixed structure.array() truncating string annotations. (#755)
• structure.io.pdbx.get_structure() with include_bonds=True is now much faster and more memory efficient for very large structures. (#765)
• Fixed serialization (and string representation) of structure.io.pdbx.CIFBlock objects raising an exception. (#767)
• Now structure.io.mol.set_structure() checks if the input coordinates fit into the fixed number of columns in MOL/SDF files. (#772)
• The height of letters in sequence.graphics.plot_feature_map.plot_sequence_logo() is now more accurate. (#769)