Releases: ihmwg/python-ihm
python-ihm 0.9 release
- Add support for the latest version of the IHM dictionary.
python-ihm 0.8 release
ihm.reader.readcan 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.readwill now read starting model coordinates and sequence difference information into theihm.startmodel.StartingModelclass. Applications that don't require coordinates can instruct the reader to ignore them with the newread_starting_model_coordflag.- The new
ihm.flrmodule allows for information from Fluorescence / FRET experiments to be stored. This follows the definitions in the FLR dictionary.
python-ihm 0.7 release
- Authors of the mmCIF file itself (
_audit_authorcategory) can now be set by manipulatingihm.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 stable releases of python-ihm (e.g. those installed via
pip) as pre-generated SWIG outputs are included. SWIG is still needed to build directly from source code though.
python-ihm 0.6 release
Entitynow takes an optionalihm.source.Sourceobject to
describe the method by which the sample for the entity was produced.
ihm.metadata.PDBParserwill also extract this information
from input PDB files.ihm.reader.readandihm.dumper.writenow support reading
or writing additional user-defined mmCIF categories.
python-ihm 0.5 release
-
ihm.restraint.CrossLinkRestraintnow takes anihm.ChemDescriptorobject 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.ChemDescriptorallows for the chemical structure of the cross-linker to be uniquely specified, as a SMILES or INCHI string. Theihm.cross_linkersmodule provides chemical descriptors for some commonly-used cross-linkers. -
Pseudo sites are now supported.
ihm.restraint.PseudoSiteFeatureallows points or spheres with arbitrary coordinates to be designated as features, which can then be used inihm.restraint.DerivedDistanceRestraint.
python-ihm 0.4 release
- Certain restraints can now be grouped using the
ihm.restraint.RestraintGroupclass. Due to limitations of the
underlying dictionary, this only works for some restraint types (currently
onlyihm.restraint.DerivedDistanceRestraint) and all restraints
in the group must be of the same type. - Bugfix: the the model's representation (see
ihm.representation)
need not be a strict subset of the model'sihm.Assembly. However,
anyihm.model.Atomorihm.model.Sphereobjects must be
covered by both the representation and the model'sihm.Assembly. - Bugfix: the reader no longer fails to read files that contain
_entity.formula_weight.
python-ihm 0.3 release
- 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.Entityobjects 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.Atomorihm.model.Sphereobjects are now checked against the model's representation (seeihm.representation); for example, anihm.model.Atommust correspond to anihm.representation.AtomicSegment. The representation in turn must be a subset of the model'sihm.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.
python-ihm 0.2 release
This release should fix installation of the package
using pip: pip install ihm should now work correctly.
python-ihm 0.1 release
This is the first stable release of the python-ihm package.
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.