Change history

0.40 - 2023-09-25

• Basic support for oligosaccharides is now provided. New classes are provided to describe saccharide chemical components (ihm.SaccharideChemComp and subclasses). Unlike polymers and non-polymers, oligosaccharides can be branched, and a new ihm.BranchLink class allows the linkage between individual components to be described.
• A summary report of the system can now be produced by calling ihm.System.report(). This can help to reveal errors or inconsistencies, and will warn about missing data that may not be technically required for a compliant mmCIF file, but is usually expected to be present.
• ihm.metadata.MRCParser now uses the new EMDB API to extract version information and details for electron density map datasets.
• RPM packages are now available for recent versions of Fedora and RedHat Enterprise Linux.

0.39 - 2023-08-04

• ihm.location.DatabaseLocation no longer accepts a db_name parameter. Derived classes (such as ihm.location.PDBLocation) should be used instead; the base class should only be used for “other” databases that are not described in the IHM dictionary (#116).
• Bugfix: AlphaFold models in PDB format are no longer categorized by ihm.metadata.PDBParser as being deposited in the PDB database with an empty accession code.

0.38 - 2023-05-26

• Convenience classes are added to describe datasets stored in the Model Archive, iProX, and AlphaFoldDB repositories (ihm.location.ModelArchiveLocation, ihm.location.IProXLocation, and ihm.location.AlphaFoldDBLocation respectively).
• The new class ihm.metadata.CIFParser can be used to extract metadata from starting models in mmCIF format. It is currently in development and only supports model metadata from PDB or Model Archive at this time.
• Line wrapping of output mmCIF files can now be turned if desired using ihm.dumper.set_line_wrap() (by default files are wrapped to 80 characters if possible).
• The make-mmcif.py utility script now allows for the name of the output mmCIF file to be overridden (#115).

0.37 - 2023-02-03

• Convenience classes are added to describe ensemble FRET datasets (ihm.dataset.EnsembleFRETDataset) and datasets stored in the jPOSTrepo repository (ihm.location.JPOSTLocation).
• Related depositions can now be grouped using the ihm.Collection class (#108).
• The ihm.model.Ensemble class has a new superimposed attribute to indicate whether the grouped models are structurally aligned.

0.36 - 2023-01-25

• When reading a file that references external files, preserve any information on the size of those files (#104).
• When reading a file containing models not in a model group, preserve any information on the number of models deposited (#105).
• Bugfix: ihm.dictionary.read() now correctly handles dictionaries that define a category after data items in that category (#107).

0.35 - 2022-09-16

• Author names now use PDB style (“Lastname, A.B.”) by default rather than PubMed style (“Lastname AB”) (#95).
• Asyms containing multiple water molecules should now be correctly handled (previously every water molecule in the output atom_site table was given the same auth_seq_id). Use the new ihm.WaterAsymUnit to create an asym containing waters (#98).
• Masses for all elements are now included, so that _entity.formula_weight can be correctly populated for ligands (#99).
• Bugfix: ihm.analysis.Analysis objects are now read correctly from input files when two objects share the same ID but are part of different protocols (#101).

0.34 - 2022-08-03

• Strings that start with STAR reserved words such as stop_ are now quoted to help some readers such as the GEMMI library (ihmwg/python-modelcif#25).
• If an input file defines a chemical descriptor with an empty name but also defines linker_type, use that to fill in the name (#91).
• ihm.ChemComp now allows for chemical components to be defined in a chemical component dictionary (CCD) outside of the wwPDB CCD. This is not used in python-ihm itself but can be used in python-modelcif.
• Bugfix: if a read mmCIF file defines a complete assembly, do not overwrite its name and description on output (#92).
• Bugfix: only allow clustering methods/features that are supported by the underlying IHM dictionary for ihm.model.Ensemble (#94).
• Bugfix: categories such as _struct that are not typically looped now support multi-line strings (ihmwg/python-modelcif#27).

0.33 - 2022-06-27

• Improve reading of mmCIF files with incomplete data (#86, #87) or with categories in an unexpected order (#85).
• Bugfix: fix sanity check for multiple atoms with the same atom_id and seq_id to handle bulk water (where such duplicates are OK) (#88).

0.32 - 2022-05-31

• ihm.protocol.Step now takes an ensemble flag, to indicate whether the modeling involved an ensemble, and which defaults to True if the system contains at least one ihm.model.Ensemble (#83).
• When reading an incomplete mmCIF file, such as that generated by some versions of PyMOL, python-ihm will now fill in missing entity-related information by guessing the sequence from the atom_site table (#67).
• Bugfix: ihm.flr.RefMeasurementGroup objects are now read from mmCIF files correctly.

0.31 - 2022-04-14

• The ihm.dumper.IgnoreVariant class can now be used to exclude selected categories from the mmCIF/BinaryCIF output.
• The _pdbx_nonpoly_scheme CIF table should now fully comply with the PDBx dictionary.
• Atoms are now checked at file-output time to ensure that a given model chain does not contain multiple atoms with the same atom_id and seq_id (#81).

0.30 - 2022-04-05

• Add support for a long description of the system (like an abstract) using struct.pdbx_model_details (#80).
• Bugfix: correctly read mmCIF files with missing entity.type.

0.29 - 2022-04-01

• 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).

0.28 - 2022-03-21

• 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.

0.27 - 2022-01-27

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

0.26 - 2022-01-12

• 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.

0.25 - 2021-12-03

• 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.

0.24 - 2021-12-01

• 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).

0.23 - 2021-11-01

• 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).

0.22 - 2021-10-22

• 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.

0.21 - 2021-07-14

• 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).

0.20 - 2021-05-06

• 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.

0.19 - 2021-04-16

• A convenience class is added to describe datasets stored in the ProXL database (ihm.location.ProXLLocation).

0.18 - 2020-11-06

• Update to match latest FLR dictionary.
• Add a simple utility (util/make-mmcif.py) to make a minimal compliant IHM mmCIF file, given an mmCIF file (potentially just coordinates) as input.
• Bugfix: the full residue range spanned by a starting model is now reported, rather than just the subset that is mapped to one or more templates (#55).
• Bugfix: handle TrEMBL UniProt sequences (#57).

0.17 - 2020-07-10

• Convenience classes are added to describe hydrogen/deuterium exchange data (ihm.dataset.HDXDataset) and datasets stored in the PDB-Dev database (ihm.location.PDBDevLocation).
• Multiple ihm.restraint.CrossLinkPseudoSite objects can now be assigned to a given ihm.restraint.CrossLink.
• Bugfix: the ihm.dataset.Dataset base class now has a type of “Other” rather than “unspecified” to conform with the latest IHM dictionary.

0.16 - 2020-05-29

• ihm.reader.read() no longer discards models read from non-IHM mmCIF files; they are instead placed in their own ihm.model.ModelGroup.
• Bugfix: both the pure Python and C-accelerated mmCIF readers are now more robust, able to handle files in binary mode (e.g. from opening a URL) and in Unicode (mmCIF files are supposed to be ASCII but python-ihm should handle any encoding Python supports).

0.15 - 2020-04-14

• ihm.dataset.Dataset objects that derive from another dataset can now record any transformation involved; see ihm.dataset.TransformedDataset.
• ihm.metadata.PDBParser now extracts basic metadata from PDB files generated by SWISS-MODEL.
• An ihm.Entity can now be linked to one or more reference databases (e.g. UniProt). See the classes in the ihm.reference module.

0.14 - 2020-02-26

• A cross-link can now use pseudo sites to represent one or both ends of the link. The new ihm.restraint.CrossLinkPseudoSite object is used when the end of the cross-link is not represented in the model but its position is known (e.g. it may have been approximated given the position of nearby residues).
• ihm.restraint.PseudoSiteFeature now references an underlying ihm.restraint.PseudoSite, allowing a single pseudo site to be shared between a feature and a cross-link if desired.
• ihm.model.Ensemble now supports describing subsamples from which the ensemble was constructed; see ihm.model.Subsample.
• Bugfix: ihm.Citation.from_pubmed_id() now works correctly when the journal volume or page range are empty, or the page “range” is just a single page.

0.13 - 2019-11-14

• ihm.reader.read() has a new optional reject_old_file argument. If set, it will raise an exception if asked to read a file that conforms to too old a version of the IHM extension dictionary.
• Definitions for the DHSO and BMSO cross-linkers are now provided in the ihm.cross_linkers module.

0.12 - 2019-10-16

• ihm.restraint.ResidueFeature objects can now act on one or more Residue objects, which act equivalently to 1-residue ranges (AsymUnitRange or EntityRange).
• The new ihm.dataset.GeneticInteractionsDataset class and the mic_value argument to ihm.restraint.DerivedDistanceRestraint can be used to represent restraints from genetic interactions, such as point-mutant epistatic miniarray profile (pE-MAP) data.

0.11 - 2019-09-05

• ihm.Assembly objects can now only contain AsymUnit and AsymUnitRange objects (not Entity or EntityRange).
• Bugfix: ensembles that don’t reference a ihm.model.ModelGroup no longer cause the reader to create bogus empty model groups.

0.10 - 2019-07-09

• Features (ihm.restraint.AtomFeature, ihm.restraint.ResidueFeature, and ihm.restraint.NonPolyFeature), which previously could select part or all of an ihm.AsymUnit, can now also select parts of an Entity. A restraint acting on an entity-feature is assumed to apply to all instances of that entity.

0.9 - 2019-05-31

• Add support for the latest version of the IHM dictionary.

0.8 - 2019-05-28

• ihm.reader.read() can now be asked to warn if it encounters categories or keywords in the mmCIF or BinaryCIF file that it doesn’t know about (and will ignore).
• Predicted contacts (ihm.restraint.PredictedContactRestraint) are now supported.
• ihm.reader.read() will now read starting model coordinates and sequence difference information into the ihm.startmodel.StartingModel class. Applications that don’t require coordinates can instruct the reader to ignore them with the new read_starting_model_coord flag.
• The new ihm.flr module allows for information from Fluorescence / FRET experiments to be stored. This follows the definitions in the FLR dictionary.

0.7 - 2019-04-24

• Authors of the mmCIF file itself (_audit_author category) can now be set by manipulating ihm.System.authors. (If this list is empty on output, the set of all citation authors is used instead, as before.)
• Any grants that supported the modeling can now be listed in ihm.System.grants.
• A copy of SWIG is no longer needed to install releases of python-ihm via pip as pre-generated SWIG outputs are included in the PyPI package. SWIG is still needed to build directly from source code though.

0.6 - 2019-03-22

• Entity now takes an optional ihm.source.Source object to describe the method by which the sample for the entity was produced. ihm.metadata.PDBParser will also extract this information from input PDB files.
• ihm.reader.read() and ihm.dumper.write() now support reading or writing additional user-defined mmCIF categories.

0.5 - 2019-01-17

• ihm.restraint.CrossLinkRestraint now takes an ihm.ChemDescriptor object rather than the name of the cross-linker used. This allows the use of novel cross-linkers (beyond those currently listed in a fixed enumeration in the IHM dictionary). ihm.ChemDescriptor allows for the chemical structure of the cross-linker to be uniquely specified, as a SMILES or INCHI string. The ihm.cross_linkers module provides chemical descriptors for some commonly-used cross-linkers.
• Pseudo sites are now supported. ihm.restraint.PseudoSiteFeature allows points or spheres with arbitrary coordinates to be designated as features, which can then be used in ihm.restraint.DerivedDistanceRestraint.

0.4 - 2018-12-17

• Certain restraints can now be grouped using the ihm.restraint.RestraintGroup class. Due to limitations of the underlying dictionary, this only works for some restraint types (currently only ihm.restraint.DerivedDistanceRestraint) and all restraints in the group must be of the same type.
• Bugfix: the model’s representation (see ihm.representation) need not be a strict subset of the model’s ihm.Assembly. However, any ihm.model.Atom or ihm.model.Sphere objects must be covered by both the representation and the model’s ihm.Assembly.
• Bugfix: the reader no longer fails to read files that contain _entity.formula_weight.

0.3 - 2018-11-21

• The library now includes basic support for nonpolymers and water molecules. In addition to the previous support for polymers (amino or nucleic acid chains), ihm.Entity objects can now comprise ligands, water molecules, and user-defined chemical components.
• The library can now read mmCIF dictionaries and validate mmCIF or BinaryCIF files against them. See ihm.dictionary.
• Any ihm.model.Atom or ihm.model.Sphere objects are now checked against the model’s representation (see ihm.representation); for example, an ihm.model.Atom must correspond to an ihm.representation.AtomicSegment. The representation in turn must be a subset of the model’s ihm.Assembly.
• More examples are now provided, of creating and using non-standard residue types (chemical components); representing nonpolymers; and using the C mmCIF parser in other C programs.

0.2 - 2018-09-06

• This release should fix installation of the package using pip: pip install ihm should now work correctly.

0.1 - 2018-09-06

• First stable release. This provides largely complete support for the current version of the wwPDB IHM mmCIF extension dictionary, and will read and write mmCIF and BinaryCIF files that are compliant with the PDBx and IHM dictionaries.