Module seqio

Classes

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SequenceReaderException

StructureConverter

LegacySequenceConverter
Knows how to make a sequence.ProteinSequence from a sequencealignment.Sequence object

BaseProteinAlignmentReader
Base class for reading protein sequence alignments from files.

ClustalAlignmentReader
Class for reading Clustal *.aln files.

BaseProteinAlignmentWriter
Class for writing protein alignments to files.

ClustalAlignmentWriter
Class for writing Clustal *.aln files.

MMSequenceConverter
Converts sequence between mmseq and MSV sequence formats.

FastaAlignmentReader

Functions

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get_disulfide_bond_indices(ct)
Returns: list of bonded atom CYS sulfur atom indices in provided ct

_partition_by_predicate(arr, pred)
Utility function to groups a list into lists, with each sublist beginning with an element that matches the supplied predicate

Variables

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CAPPING_GROUPS = ['NH2']

STANDARD_ID_REGEX = re.compile(r'^>\s*(?P<name>.+)[:_]\s*(?P<i...

SPACE_ID_REGEX = re.compile(r'^>\s*(?P<name>\w+)\s*.*$')

__package__ = 'schrodinger.application.msv.io'

Function Details

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get_disulfide_bond_indices(ct)

Returns:: list of bonded atom CYS sulfur atom indices in provided ct

_partition_by_predicate(arr, pred)

Utility function to groups a list into lists, with each sublist beginning with an element that matches the supplied predicate

Note that many file reading functions below would benefit from using this function.

Parameters:

arr (list) - A list to split into sublists
pred (function
This is not efficient, since we loop through the array twice, but it probably doesn't matter.
) - A function that takes a list item and returns True if the list item meets a criteria and False otherwise

Variables Details

[hide private]

STANDARD_ID_REGEX

Value:

re.compile(r'^>\s*(?P<name>.+)[:_]\s*(?P<id>\w)\s*')