Change history

0.9 - 2023-10-02

• 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).

0.8 - 2023-08-04

• 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.

0.7 - 2023-01-25

• 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).

0.6 - 2022-08-03

• 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).

0.5 - 2022-05-10

• 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.

0.4 - 2022-04-14

• 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.

0.3 - 2022-03-21

• Add a package to conda-forge so the library can be installed using conda install -c conda-forge modelcif

• modelcif.Template now takes a strand_id argument which can be used to provide the author-provided (e.g. PDB) chain ID.

• Non-polymers can now be used as templates.

0.2 - 2022-01-27

• Minor packaging and documentation improvements.

• Add a basic “theoretical model” exptl category to output files.

• Bugfix: fix output of alignments with an empty list of pairs.

0.1 - 2022-01-26

• First stable release. This provides support for single-chain single-template models using the ModelCIF extension dictionary, and will read and write mmCIF and BinaryCIF files that are compliant with the PDBx and modelcif.alignment.HHblitsEValue.