The modelcif.alignment
Python module¶
Classes to handle alignments between template structure(s) and target sequence(s).
To create an alignment, first declare a class for the given kind of
alignment by deriving from subclasses of AlignmentMode
(e.g. Global
) and AlignmentType
(e.g. Pairwise
).
For example, a typical pairwise global alignment could be declared using:
class Alignment(modelcif.alignment.Global, modelcif.alignment.Pairwise):
pass
- class modelcif.alignment.Identity(value)[source]¶
Percent sequence identity between the template sequence and the target sequence being modeled. Use the correct subclass that corresponds to the denominator used when calculating the identity, for example
ShorterSequenceIdentity
, or if the denominator is not covered here, subclass this class and provide a docstring to describe the denominator, e.g.:class CustomIdentity(Identity): "my custom sequence identity denominator"
- Parameters:
value (float) – The percent sequence identity value.
- property other_details¶
More information about a custom sequence identity denominator. By default it is the first line of the docstring.
- class modelcif.alignment.ShorterSequenceIdentity(value)[source]¶
Sequence identity calculated using the length of the shorter sequence as the denominator. See
Identity
for more information.
- class modelcif.alignment.AlignedPositionsIdentity(value)[source]¶
Sequence identity calculated using the number of aligned positions (including gaps) as the denominator. See
Identity
for more information.
- class modelcif.alignment.Pair(template, target, identity, score)[source]¶
A single pairwise alignment between a single target and template chain. See
AlignmentMode
. An alignment consists of one or more of these pairs.- Parameters:
template (
modelcif.TemplateSegment
) – The template segment that is aligned, i.e. the seq_id range for the template and the sequence (including gaps) of one-letter codes.target (output from
ihm.AsymUnit.segment()
) – The target segment that is aligned.identity (
Identity
) – The sequence identity between target and template.score (
Score
) – A measure of the quality of the alignment.
- class modelcif.alignment.AlignmentMode(name, pairs, software=None)[source]¶
Base class for all alignments. Actual alignments should derive from both a subclass of this class (e.g.
Global
) and a subclass ofAlignmentType
.- Parameters:
name (str) – A short description of this alignment.
pairs (list of
Pair
objects) – List of individual target-template alignments.software (
modelcif.Software
ormodelcif.SoftwareGroup
) – The software that was used to build the alignment.
- class modelcif.alignment.Global(name, pairs, software=None)[source]¶
Base class for global alignments. See
AlignmentMode
for more details.
- class modelcif.alignment.AlignmentType[source]¶
Base class for all alignment types. Actual alignments should derive from both a subclass of this class (e.g.
Pairwise
) and a subclass ofAlignmentMode
.
- class modelcif.alignment.Pairwise[source]¶
An alignment between a single target and template. See
AlignmentType
for more details.
- class modelcif.alignment.Score(value)[source]¶
Base class for a quality score for a given target-template alignment. Usually a derived class such as
BLASTEValue
is used, and passed toPair
objects.- Parameters:
value (float) – The actual score value.