ample.parsers.tm_parser module¶

class TMalignLogParser[source]¶

Bases: object

Class to mine information from a TMalign log

Warning

TMalign parser cannot distinguish which TM-score to use. Please run TMalign with the -a flag.

Attributes:	tm : float TemplateModelling score rmsd : float RMSD score nr_residues_common : int Number of residues in common between structures seq_id : float Sequence identity [n_identical/n_aligned]

Methods

parse(logfile)	Read a TMalign logfile to extract the scores
reset()	Reset the TMalign parser
set(tm, seq_id, rmsd, nr_residues_common)	Manually set the TMalign parser parameters

parse(logfile)[source]¶

Read a TMalign logfile to extract the scores

Parameters:	logfile : str Path to the TMalign logfile

reset()[source]¶

Reset the TMalign parser

set(tm, seq_id, rmsd, nr_residues_common)[source]¶

Manually set the TMalign parser parameters

class TMscoreLogParser[source]¶

Bases: object

Class to mine information from a TMscore log

Attributes:	tm : float TemplateModelling score maxsub : float MaxSub score gdtts : float GDT-TS score gdtha : float GDT-HA score rmsd : float RMSD score nr_residues_common : int Number of residues in common between structures

Methods

parse(logfile)	Read a TMscore logfile to extract the scores
reset()	Reset the TMscore parser
set(tm, maxsub, gdtts, gdtha, rmsd, …)	Manually set the TMscore parser parameters

parse(logfile)[source]¶

Read a TMscore logfile to extract the scores

Parameters:	logfile : str Path to the TMscore logfile

reset()[source]¶

Reset the TMscore parser

set(tm, maxsub, gdtts, gdtha, rmsd, nr_residues_common)[source]¶

Manually set the TMscore parser parameters