Module clans

source code

Classes for parsing/manipulating/writing CLANS (by Tancred Frickey) files

This module defines ClansParser and ClansFileWriter for parsing and writing CLANS format files, respectively. Further, class Clans and several helper classes are used to hold and handle the parsed data.

The most commenly used CLANS data can be accessed in an Clans instance via

• .entries <ClansEntryCollection containing ClansEntry instances>
  • .name
  • .seq <the amino acid sequence>
  • .hsps <connections of this ClansEntry to others>
  • .groups <ClansSeqgroups the entry belongs to>
• .seqgroups <ClansSeqgroupCollection containing ClansSeqgroup instances>
• .params <ClansParams>

Parse a file into Clans instance clans_instance by

>>> clans_instance = ClansParser().parse_file('input.clans')

Create a new entry e with name "my entry", sequence AAAA and coordinates (x=1, y=1, z=1)

>>> e = ClansEntry(name='my entry', seq='AAAA', coords=(1, 1, 1))

and add it to an existing Clans instance clans_instance

>>> clans_instance.add_entry(e)

Entries can be accessed using indices of Clans instances

>>> clans_instance[0]  # access to first entry

and deleted by

>>> clans_instance.remove_entry(e)

Equivalent functions exist for ClansSeqgroups.

Author: Klaus Kopec MPI fuer Entwicklungsbiologie, Tuebingen