Changelog

Additions

Added structure.find_pi_cation_interactions() to identify pi-cation interactions in a structure. (#810)
Added more convenient bond type conversion methods for structure.BondList objects. (#808)
- remove_kekulization() changes AROMATIC_<order> bonds to generic AROMATIC bonds.
- convert_bond_type() maps the given bond type to a new bond type.

Deprecated include_bonds parameter in structure.io.pdbx.set_structure(). (#804)
- Intra-residue bonds are now always written to chem_comp_bond category.
interface.rdkit.from_mol() writes the altloc into the altloc_id annotation
instead of label_alt_id. (#807)

Fixed altloc filtering in structure.io.pdbx.set_structure() for PDBx files where each atom has an altloc. (#806)
Fixed warning in structure.lddt() that was raised, if no contact exists. (#811)
Fixed selection parameter interface.pymol.PyMOLObject methods that errored if a slice index was passed. (#801)
Fixed the amount parameter in structure.repeat_box_coord() not being used. (#800)
Fixed spurious bonds added to the structure returned by structure.io.pdb.PDBFile.get_structure(). (#810)
- Appeared when an altloc atom that participated in a non-canonical bond, was removed during parsing.
Fixed exception in structure.io.pdb.PDBFile.get_assembly(), if the file contains multiple assemblies. (#810)