ample.parsers.tm_parser module¶

class TMalignLogParser[source]¶

Bases: object

Class to mine information from a TMalign log

tm¶

TemplateModelling score

Type:	float

rmsd¶

RMSD score

Type:	float

nr_residues_common¶

Number of residues in common between structures

Type:	int

seq_id¶

Sequence identity [n_identical/n_aligned]

Type:	float

Warning

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

parse(logfile)[source]¶

Read a TMalign logfile to extract the scores

Parameters:	logfile (str) – Path to the TMalign logfile

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

tm¶

TemplateModelling score

Type:	float

maxsub¶

MaxSub score

Type:	float

gdtts¶

GDT-TS score

Type:	float

gdtha¶

GDT-HA score

Type:	float

rmsd¶

RMSD score

Type:	float

nr_residues_common¶

Number of residues in common between structures

Type:	int

parse(logfile)[source]¶

Read a TMscore logfile to extract the scores

Parameters:	logfile (str) – Path to the TMscore logfile

set(tm, maxsub, gdtts, gdtha, rmsd, nr_residues_common)[source]¶: Manually set the TMscore parser parameters