The ihm.reference
Python module¶
Classes for providing extra information about an ihm.Entity
- class ihm.reference.Reference[source]¶
Base class for extra information about an
ihm.Entity
.This class is not used directly; instead, use a subclass such as
Sequence
orUniProtSequence
. These objects are then typically passed to theihm.Entity
constructor.
- class ihm.reference.Sequence(db_name, db_code, accession, sequence, details=None)[source]¶
Point to the sequence of an
ihm.Entity
in a sequence database; convenience subclasses are provided for common sequence databases such asUniProtSequence
.These objects are typically passed to the
ihm.Entity
constructor.See also
alignments
to describe the correspondence between the database and entity sequences.- Parameters:
db_name (str) – The name of the database.
db_code (str) – The name of the sequence in the database.
accession (str) – The database accession.
sequence (str) – The complete sequence, as a string of one-letter codes.
details (str) – Longer text describing the sequence.
- class ihm.reference.UniProtSequence(db_code, accession, sequence, details=None)[source]¶
Point to the sequence of an
ihm.Entity
in UniProt.These objects are typically passed to the
ihm.Entity
constructor.- Parameters:
db_code (str) – The UniProt name (e.g. NUP84_YEAST)
accession (str) – The UniProt accession (e.g. P52891)
See
Sequence
for a description of the remaining parameters.- classmethod from_accession(accession)[source]¶
Create
UniProtSequence
from just an accession. This is done by querying the UniProt web API, so requires network access.- Parameters:
accession (str) – The UniProt accession (e.g. P52891)
- class ihm.reference.Alignment(db_begin=1, db_end=None, entity_begin=1, entity_end=None, seq_dif=[])[source]¶
A sequence range that aligns between the database and the entity. This describes part of the sequence in the sequence database (
Sequence
) and in theihm.Entity
. The two ranges must be the same length and have the same primary sequence (any differences must be described withSeqDif
objects).- Parameters:
db_begin (int) – The first residue in the database sequence that is used (defaults to the entire sequence).
db_end (int) – The last residue in the database sequence that is used (or None, the default, to use the entire sequence).
entity_begin (int) – The first residue in the
Entity
sequence that is taken from the reference (defaults to the entire entity sequence).entity_end (int) – The last residue in the
Entity
sequence that is taken from the reference (or None, the default, to use the entire sequence).seq_dif (Sequence of
SeqDif
objects.) – Single-point mutations made to the sequence.
- class ihm.reference.SeqDif(seq_id, db_monomer, monomer, details=None)[source]¶
Annotate a sequence difference between a reference and entity sequence. See
Alignment
.- Parameters:
seq_id (int) – The residue index in the entity sequence.
db_monomer (
ihm.ChemComp
) – The monomer type (as aChemComp
object) in the reference sequence.monomer (
ihm.ChemComp
) – The monomer type (as aChemComp
object) in the entity sequence.details (str) – Descriptive text for the sequence difference.