ample.parsers.psipred_parser module¶

A parser object for Psipred Ss2 files

class PsipredSs2Parser(ss2file=None)[source]¶

Bases: object

Parser for psipred ss2 file

Attributes:	secondary_structure The secondary structure

Methods

checkContent()	Check the secondary structure composition
check_content()	Check the secondary structure composition
getSecondaryStructure()	Get the secondary structure content
parse(ss2file)	Parse a secondary structure file

checkContent()[source]¶

Check the secondary structure composition

check_content()[source]¶

Check the secondary structure composition

getSecondaryStructure()[source]¶

Get the secondary structure content

parse(ss2file)[source]¶

Parse a secondary structure file

Parameters:	ss2file : str The path to the Psipred ss2 file

secondary_structure¶

The secondary structure

Returns:	str The secondary structure one-letter codes