python-modelcif 1.3 release

• The new modelcif.CustomTemplate class allows for custom templates (that have not been deposited in a database such as PDB) to be referenced, together with their atomic coordinates (#1).
• Model quality scores can now be defined that act on single features or pairs of features using the modelcif.qa_metric.Feature and modelcif.qa_metric.FeaturePairwise classes, respectively. Features can be defined as groups of atoms, residues, or asyms (#38).
• The modelcif.associated.QAMetricsFile class should now be used to reference files that contain model quality scores. The old name (LocalPairwiseQAScoresFile) is deprecated. This allows for all types of QA scores, not just local pairwise scores, to be stored in a separate file.
• Sanity checks when writing out a file can now be disabled if desired, using the new check argument to modelcif.dumper.write.
• modelcif.reference.TargetReference now takes an is_primary argument which can be used to denote the most pertinent sequence database reference.
• Information on model groups (modelcif.model.ModelGroup) is now written to the new ma_model_group and ma_model_group_link mmCIF tables, instead of ma_model_list, to match the latest ModelCIF dictionary. Old-style information in ma_model_list will still be used when reading a file if these new tables are missing.

Full Changelog: 1.2...1.3

python-modelcif 1.2 release

• Data that have been split over multiple mmCIF or BinaryCIF files can now be combined into a single modelcif.System object using the new add_to_system argument to modelcif.reader.read (#10).
• A new example, associated.py, has been added to demonstrate reading in data that has been split into multiple "associated" mmCIF files using modelcif.associated.CIFFile.

Full Changelog: 1.1...1.2

python-modelcif 1.1 release

• The new class modelcif.model.NotModeledResidueRange allows for the annotation of residue ranges that were explicitly not modeled. Any residue marked as not-modeled in all models will be excluded from the pdbx_poly_seq_scheme table.
• The util/make-mmcif.py script is now included in the installed package, so can be run if desired with python3 -m modelcif.util.make_mmcif.
• The make_mmcif utility script will now automatically add any missing modelcif.model.NotModeledResidueRange objects for not-modeled residue ranges.

Full Changelog: 1.0...1.1

python-modelcif 1.0 release

• Reference information in the struct_ref mmCIF table is now supported in addition to the ModelCIF-specific tables such as ma_target_ref_db_details. modelcif.reference.TargetReference now inherits from ihm.reference.Sequence and allows for the full database sequence, plus any differences between it and the modeled sequence, to be recorded. The align_begin and align_end arguments are now deprecated (#34).

Full Changelog: 0.9...1.0

python-modelcif 0.9 release

• Bugfix: modelcif.SoftwareGroup now allows for parameters to be associated with each piece of software in the group, rather than with the group as a whole (#33).

Full Changelog: 0.8...0.9

python-modelcif 0.8 release

• modelcif.associated.File now takes an optional data argument to allow describing any modeling input/output that is stored in that file.
• RPM packages are now provided for Fedora and RedHat Enterprise Linux.

Full Changelog: 0.7...0.8

python-modelcif 0.7 release

• More examples have been added to demonstrate interconversion between mmCIF and BinaryCIF, and to validate mmCIF files.
• A utility script util/make-mmcif.py has been added which can add minimal ModelCIF-related tables to an mmCIF file, to add in deposition.
• The reader is now more robust when handling files that are not ModelCIF compliant (#31).
• The exptl table is no longer written to output mmCIF files, to conform with wwPDB's recommendation. Instead, the struct.pdbx_structure_determination_methodology data item denotes that the model is computational (#29).

Full Changelog: 0.6...0.7

python-modelcif 0.6 release

• ihm.ChemComp now allows for custom chemical components to be defined in a chemical component dictionary (CCD) outside of the wwPDB CCD, such as the ModelArchive CCD, or in the file itself using descriptors such as SMILES or InChI in the modelcif.descriptor module.
• The ma_struct_assembly category is no longer written out to mmCIF files, as this is deprecated by ModelCIF (all models are required to have the same composition).
• Templates can now be described in AlphaFoldDB or PubChem using new modelcif.reference.TemplateReference subclasses.
• HHblits e-values can now be used as alignment scores, using modelcif.alignment.HHblitsEValue.
• Bugfix: modelcif.associated.CIFFile now writes local files (if requested via categories or copy_categories) even if it is placed inside a modelcif.associated.ZipFile (#26).

Full Changelog: 0.5...0.6

python-modelcif 0.5 release

• A new class modelcif.ReferenceDatabase allows describing collections of sequences that were used as part of the modeling protocol.
• Lists of ints or floats can now be given as software parameters to the modelcif.SoftwareParameter class.

python-modelcif 0.4 release

• Sequence information for templates is now only written to template-specific categories in the mmCIF/BinaryCIF, not to the entity, entity_poly etc. tables, to properly comply with the ModelCIF dictionary.
• modelcif.Template now takes a entity_id argument which can be used to provide the entity ID (if known) of the template in its own mmCIF file.
• External files (e.g. alignments, or quality scores) can now be referenced from the main file (using the modelcif.associated module). Selected CIF categories can automatically be written to these external files instead of the main file, in either mmCIF or BinaryCIF format (see modelcif.associated.CIFFile).
• Non-polymer models can now be linked to their template using the modelcif.NonPolymerFromTemplate class.
• Add classes for the PLDDT, PTM, and IpTM quality metrics.
• modelcif.reference.TargetReference now supports the version and CRC64 checksum of the reference sequence.