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2016-4 Schrodinger Python API
Package schrodinger :: Package application :: Package msv :: Package io :: Module seqio :: Class BaseProteinAlignmentReader
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Class BaseProteinAlignmentReader

object --+
         |
        BaseProteinAlignmentReader
Known Subclasses:

Base class for reading protein sequence alignments from files.

Instance Methods [hide private]

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods [hide private]
ProteinAlignment
_makeProteinAlignment(cls, sequences, AlnClass=<class 'schrodinger.application.msv.domain.alignment.ProteinAl...)
Helper function that creates ProteinAlignment from a dictionary of sequence elements and list of sequence names.
 
read(cls, file_name)
Reads alignment from a file.
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

_makeProteinAlignment(cls, sequences, AlnClass=<class 'schrodinger.application.msv.domain.alignment.ProteinAl...)
Class Method

 

Helper function that creates ProteinAlignment from a dictionary of sequence elements and list of sequence names.

Parameters:
  • sequences (collections.OrderedDict) - Ordered dictionary of sequence elements.
  • AlnClass (alignment.ProteinAlignment) - The Alignment class to use in constructing alignments
Returns: ProteinAlignment
Protein alignment.

read(cls, file_name)
Class Method

 

Reads alignment from a file.

Parameters:
  • file_name (str) - Source file name.

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2016-4 Schrodinger Python API
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