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)

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)

Sequence identity calculated using the length of the shorter sequence as the denominator. See Identity for more information.

class modelcif.alignment.AlignedPositionsIdentity(value)

Sequence identity calculated using the number of aligned positions (including gaps) as the denominator. See Identity for more information.

class modelcif.alignment.AlignedResiduePairsIdentity(value)

Sequence identity calculated using the number of aligned residue pairs (not including gaps) as the denominator. See Identity for more information.

class modelcif.alignment.MeanSequenceIdentity(value)

Sequence identity calculated using the arithmetic mean of the sequence lengths as the denominator. See Identity for more information.

class modelcif.alignment.Pair(template, target, identity=None, score=None)

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, if known.

• score (Score) – A measure of the quality of the alignment, if known.

class modelcif.alignment.AlignmentMode(name, pairs, software=None)

Base class for all alignments. Actual alignments should derive from both a subclass of this class (e.g. Global) and a subclass of AlignmentType.

Parameters:

• name (str) – A short description of this alignment.

• pairs (list of Pair objects) – List of individual target-template alignments.

• software (modelcif.Software or modelcif.SoftwareGroup) – The software that was used to build the alignment.

class modelcif.alignment.Global(name, pairs, software=None)

Base class for global alignments. See AlignmentMode for more details.

class modelcif.alignment.Local(name, pairs, software=None)

Base class for local alignments. See AlignmentMode for more details.

class modelcif.alignment.AlignmentType

Base class for all alignment types. Actual alignments should derive from both a subclass of this class (e.g. Pairwise) and a subclass of AlignmentMode.

class modelcif.alignment.Pairwise

An alignment between a single target and template. See AlignmentType for more details.

class modelcif.alignment.Multiple

A multiple sequence alignment between target and template. See AlignmentType for more details.

class modelcif.alignment.Score(value)

Base class for a quality score for a given target-template alignment. Usually a derived class such as BLASTEValue is used, and passed to Pair objects.

Parameters:

value (float) – The actual score value.

class modelcif.alignment.BLASTEValue(value)

BLAST e-value for an alignment. See Score for more details.

class modelcif.alignment.HHblitsEValue(value)

E-value computed by HHblits for an alignment. See Score for more details.