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| author | Steffen Moeller <moeller@debian.org> | 2025-10-03 16:07:11 +0100 |
|---|---|---|
| committer | git-ubuntu importer <ubuntu-devel-discuss@lists.ubuntu.com> | 2025-10-28 22:36:18 +0000 |
| commit | 8ed8247f0973f900898167c0eebf94825504b2ce (patch) | |
| tree | 9ab3f04e1ae81543bbd7fdce37786a2cc34f35c7 /modelcif/reference.py | |
1.5-1 (patches unapplied)HEADimport/1.5-1ubuntu/resolute-proposedubuntu/resolute-develubuntu/resoluteubuntu/develdebian/sid
Imported using git-ubuntu import.
Notes
Notes:
Diffstat (limited to 'modelcif/reference.py')
| -rw-r--r-- | modelcif/reference.py | 179 |
1 files changed, 179 insertions, 0 deletions
diff --git a/modelcif/reference.py b/modelcif/reference.py new file mode 100644 index 0000000..1655c78 --- /dev/null +++ b/modelcif/reference.py @@ -0,0 +1,179 @@ +"""Classes for linking back to a sequence or structure database.""" + +import warnings +import ihm.reference +from ihm.reference import Alignment, SeqDif # noqa: F401 + + +class TargetReference(ihm.reference.Sequence): + """Point to the sequence of a target :class:`modelcif.Entity` in a sequence + database. Typically a subclass such as :class:`UniProt` is used, + although to use a custom database, make a new subclass and provide + a docstring to describe the database, e.g.:: + + class CustomRef(TargetReference): + "my custom database" + + Compare with :class:`modelcif.ReferenceDatabase`, which describes + multiple sequences used in template searches or alignment + construction; this class relates to just the modeled sequence itself. + + See also :attr:`alignments` to describe the correspondence between + the database and entity sequences. + + :param str code: The name of the sequence in the database. + :param str accession: The database accession. + :param int align_begin: Beginning index of the sequence in the database. + Deprecated; use :attr:`alignments` instead. + :param int align_end: Ending index of the sequence in the database. + Deprecated; use :attr:`alignments` instead. + :param str isoform: Sequence isoform, if applicable. + :param str ncbi_taxonomy_id: Taxonomy identifier provided by NCBI. + :param str organism_scientific: Scientific name of the organism. + :param sequence_version_date: Versioning date, e.g. for UniProtKB + sequences this is usually the date of last + modification from the DT line of an entry. + :type sequence_version_date: :class:`datetime.date` or + :class:`datetime.datetime` + :param str sequence_crc64: The CRC64 sum of the original database + sequence. + :param str sequence: The complete database sequence, as a string of + one-letter codes. If omitted, will default to the canonical + sequence of the associated :class:`~modelcif.Entity`. + :param str details: Longer text describing the sequence. + :param bool is_primary: True iff this is the main input used in the + modeling. + """ + + name = 'Other' + + def __init__(self, code, accession, align_begin=None, align_end=None, + isoform=None, ncbi_taxonomy_id=None, + organism_scientific=None, sequence_version_date=None, + sequence_crc64=None, sequence=None, details=None, + is_primary=None): + super(TargetReference, self).__init__( + db_name=self.name, db_code=code, accession=accession, + sequence=sequence, details=details) + self.align_begin, self.align_end = align_begin, align_end + self.isoform = isoform + self.ncbi_taxonomy_id = ncbi_taxonomy_id + self.organism_scientific = organism_scientific + self.sequence_version_date = sequence_version_date + self.sequence_crc64 = sequence_crc64 + if align_begin or align_end: + warnings.warn( + "align_begin and align_end are deprecated, and will be " + "removed in a future python-modelcif release. Specify the " + "database sequence and provide one or more " + "modelcif.reference.Alignment objects instead.", stacklevel=2) + if sequence is None: + warnings.warn( + "No sequence provided. The canonical sequence of the Entity " + "will be used instead.", stacklevel=2) + #: All alignments between the reference and entity sequences, as + #: :class:`Alignment` objects. If none are provided, a simple 1:1 + #: alignment is assumed. + self.alignments = [] + self.is_primary = is_primary + + code = property(lambda self: self.db_code) + + def _get_other_details(self): + if (type(self) is not TargetReference + and self.name == TargetReference.name): + return self.__doc__.split('\n')[0] + + other_details = property( + _get_other_details, + doc="More information about a custom reference type. " + "By default it is the first line of the docstring.") + + +class UniProt(TargetReference): + """Point to the sequence of an :class:`modelcif.Entity` in UniProt. + + These objects are typically passed to the :class:`modelcif.Entity` + constructor for target sequences (for templates, see + :class:`TemplateReference`). + + See :class:`TargetReference` for a description of the parameters. + """ + name = 'UNP' + other_details = None + + +class TemplateReference: + """Point to the structure of a :class:`modelcif.Template` in a structure + database. + + These objects are typically passed to the :class:`modelcif.Template` + constructor for template sequences (for target sequences, see + :class:`TargetReference`). + + Typically a subclass such as :class:`PDB` is used, + although to use a custom database, make a new subclass and provide + a docstring to describe the database, e.g.:: + + class CustomRef(TemplateReference): + "my custom database" + + :param str accession: The database accession. + :param db_version_date: Versioning date, e.g. for PDB entries this is + usually the value of + ``_pdbx_audit_revision_history.revision_date``. + :type db_version_date: :class:`datetime.date` or + :class:`datetime.datetime` + """ + name = 'Other' + + def __init__(self, accession, db_version_date=None): + self.accession = accession + self.db_version_date = db_version_date + + def _get_other_details(self): + if (type(self) is not TemplateReference + and self.name == TemplateReference.name): + return self.__doc__.split('\n')[0] + + other_details = property( + _get_other_details, + doc="More information about a custom reference type. " + "By default it is the first line of the docstring.") + + +class PDB(TemplateReference): + """Point to the structure of a :class:`modelcif.Template` in PDB. + + These objects are typically passed to the :class:`modelcif.Template` + constructor. + + See :class:`TemplateReference` for a description of the parameters. + """ + name = 'PDB' + other_details = None + + +class AlphaFoldDB(TemplateReference): + """Point to the structure of a :class:`modelcif.Template` in AlphaFold DB. + + These objects are typically passed to the :class:`modelcif.Template` + constructor. + + See :class:`TemplateReference` for a description of the parameters. + """ + name = 'AlphaFoldDB' + other_details = None + + +class PubChem(TemplateReference): + """Point to the structure of a :class:`modelcif.Template` in PubChem. + + These objects are typically passed to the :class:`modelcif.Template` + constructor. + + See :class:`TemplateReference` for a description of the parameters. Use + the PubChem CID as the accession code. + """ + name = 'PubChem' + other_details = None |