ample.util.theseus module¶

Created on 26 May 2015

@author: jmht

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

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

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
Return type:	a pdb file containing an ensemble of the superposed models

class TheseusVariances(idx, resName, resSeq, variance, stdDev, rmsd, core)¶