conkit.io.pcons module¶

Parser module specific to Pcons predictions

This module can be used to parse all versions of the Pcons programs, i.e. PconsC, PconsC2, and PconsC3.

class PconsParser[source]¶

Bases: conkit.io._parser.ContactFileParser

Class to parse a Pcons output

This module can be used to parse all versions of the Pcons programs, i.e. PconsC, PconsC2, and PconsC3.

Methods

read(f_handle[, f_id])	Read a contact file
write(f_handle, hierarchy[, write_header_footer])	Write a contact file instance to to file

read(f_handle, f_id=’pcons’)[source]¶

Read a contact file

Parameters:	f_handle Open file handle [read permissions] f_id : str, optional Unique contact file identifier
Returns:	ContactFile

write(f_handle, hierarchy, write_header_footer=True)[source]¶

Write a contact file instance to to file

Default format is PconsC3 style, including comments and sequence information (if provided).

Parameters:	f_handle Open file handle [write permissions] hierarchy : ContactFile, ContactMap or Contact write_header_footer : bool Write a PconsC3-typical header
Raises:	RuntimeError More than one contact map in the hierarchy