Releases · ihmwg/python-ihm

Output mmCIF files containing non-polymers should now validate against the PDBx dictionary (#76).
Bugfix: non-polymers that are erroneously marked as polymers in the input mmCIF can now be read in without causing a Python exception (#78).
Bugfix: strings starting with an underscore (e.g. chain names) are now quoted in mmCIF output to conform to the CIF syntax (#75).

ihm.Citation now takes a is_primary argument, which can be used to denote the most pertinent publication for the modeling.
Improved support for non-standard residues, and for standard amino acids used as nonpolymers.

Minor documentation improvements.
Add support for the _struct.pdbx_structure_determination_methodology mmCIF data item.

ihm.dumper.write and ihm.reader.read both now take a variant argument which can be used to control the set of tables that are read/written. This can be used by other libraries (such as python-ma) to support other mmCIF extensions.

ihm.dictionary.Dictionary.validate will now report errors for any keywords or categories in the file that are not present in the dictionary.
ihm.LPeptideAlphabet now supports the ASX and GLX ambiguous residue types.

ihm.AsymUnit now supports insertion codes in its auth_seq_id_map. The target of this mapping can either be an author-provided residue number (as previously) or a 2-element tuple containing this number and an insertion code.
ihm.AsymUnit now allows the PDB or author-provided strand/chain ID to be different from the regular ID.
Bugfix: if two ihm.dictionary.Dictionary objects both contain information about a given category, adding the two dictionaries together now combines the category information, rather than just using that from one dictionary.
Bugfix: ihm.dictionary.Dictionary should now be able to validate BinaryCIF files containing integer or float values (#66).

Bugfix: _struct_ref.pdbx_seq_one_letter_code is now treated as the subset of the reference (e.g. UniProt) sequence that overlaps with our Entities, not the entire sequence (#64).

The ihm.Software class now allows a citation for the software to be provided.
A new ihm.citations module contains citations for some packages that are commonly used in integrative modeling.

BinaryCIF files now use UTF8 msgpack strings for all text, rather than raw bytes. This should make python-ihm's BinaryCIF files interoperable with those used by, e.g., CoordinateServer.
Output mmCIF files now include author-provided numbering (auth_seq_id) for atoms in the atom_site table. This should help packages that don't read the pdbx_poly_seq_scheme table to show the desired residue numbering (#61).

Support for Python 2.6 has been dropped. The library needs Python 2.7 or Python 3.
Bugfix: correctly read in multiline reference sequence one-letter codes.
Bugfix: the reader is now more tolerant of omitted or unknown values (. or ?) in input mmCIF files.

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