schrodinger.application.msv.converters module

Utilities for converting between different sequence and sequence group objects.

There are currently three different sequence-related objects that need to be converted between: a) legacy: This refers to the Sequence and SequenceGroup classes that live in schrodinger/ui/sequencealignment

b) biopython: This refers to Seq and related classes in the biopython package. Lightweight converter code should make it easy to benefit from a lot of this code-base.

c) msv: This refers to the new msv code that currently lives in schrodinger/application/msv

class schrodinger.application.msv.converters.LegacySequenceConverter(legacy_seq)

Bases: object

An object that knows how to convert a legacy Sequence object into an msv ProteinSequence, complete with annotations.

getSequence()

class schrodinger.application.msv.converters.SequenceConverter(seq)

Bases: object

An object that knows how to construct a legacy sequence from an msv ProteinSequence.

This is a simple, incomplete utility class useful for testing at the moment.

getLegacySequence()

Return type:schrodinger.ui.sequencealignment.sequence.Sequence

class schrodinger.application.msv.converters.SequenceGroupConverter(sequence_group)

Bases: object

An object that knows how to convert a legacy SequenceGroup object into an alignment, i.e., an msv object that holds a collection a sequences together with alignment information for them.

getAlignment()