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

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.

read(f_handle, f_id='pcons')

Read a contact file

Parameters:

• f_handle – Open file handle [read permissions]
• f_id (str, optional) – Unique contact file identifier

Returns:

Return type:

ContactFile

write(f_handle, hierarchy, write_header_footer=True)

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