ample.util.theseus module¶

Created on 26 May 2015

@author: jmht

class Theseus(work_dir=None, theseus_exe=None)[source]¶

Bases: object

Class to run THESEUS to superpose pdb files and determine the per-residue variances.

Methods

alignment_file(models[, alignment_file])	Create an alignment file for the models - this is based on the assumption they are all the same length
superpose_models(models[, work_dir, …])	Superpose models and return the ensemble.

parse_variances

alignment_file(models, alignment_file=None)[source]¶

Create an alignment file for the models - this is based on the assumption they are all the same length but may have different residues

parse_variances()[source]¶

superpose_models(models, work_dir=None, basename=’theseus’, homologs=False, alignment_file=None)[source]¶

Superpose models and return the ensemble. Also set superposed_models and var_by_res variables.

This also sets the superposed_models and var_by_res parameters.

Parameters:	models : list List of pdb files to be superposed. work_dir: str The directory to run theseus in and generate all the output files basename : str The stem that will be used to name all files homologs : bool True if the pdbs are homologous models as opposed to ab initio ones alignment_file : str An externally generated alignment file for homolgous models in FASTA format
Returns:	superposed_models : a pdb file containing an ensemble of the superposed models

class TheseusVariances¶

Bases: tuple

Attributes:	core Alias for field number 6 idx Alias for field number 0 resName Alias for field number 1 resSeq Alias for field number 2 rmsd Alias for field number 5 stdDev Alias for field number 4 variance Alias for field number 3

Methods

count(…)
index((value, [start, …)	Raises ValueError if the value is not present.

core¶

Alias for field number 6

idx¶

Alias for field number 0

resName¶

Alias for field number 1

resSeq¶

Alias for field number 2

rmsd¶

Alias for field number 5

stdDev¶

Alias for field number 4

variance¶

Alias for field number 3