schrodinger.trajectory.trajectory_gui_dir.custom_analyzers module

class schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.AbstractTorsionAnalyzer(*args, **kwargs)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Abstract class. Adds gids contained in self.torsions to calculation and results

getTorsions(*args, **kwargs)

Should return a list of relevant dihedrals, defined as a sequence of four atom IDs

class schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions(*args, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.AbstractTorsionAnalyzer

__init__(msys_model, cms_model, asl, **kwargs)

getTorsions(st, aids)

Should return a list of relevant dihedrals, defined as a sequence of four atom IDs

createLabels() → list

Create unique labels for all torsions, starting with the smallest labels possible

a, b, c … aa, ab … aaa, etc.

reduce(results, *_, **__)

class schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.ResiduesTorsions(*args, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.AbstractTorsionAnalyzer

Analyzer for amino acids

__init__(msys_model, cms_model, res_asl, **kwargs)

getTorsions(residue)

Gets torsions for residues. Each residue has psi/phi angles and up to 5 chi angles, depending on the residue.

reduce(results, *_, **__)

class schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.NucleotideTorsions(*args, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.AbstractTorsionAnalyzer

Analyzer for nucleotide specific torsions

__init__(msys_model, cms_model, res_asl, **kwargs)

getTorsions(res)

Should return a list of relevant dihedrals, defined as a sequence of four atom IDs

reduce(results, *_, **__)

schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.get_nucleotide_dihedrals(res)

Returns dihedrals for a given nucleotide. If any dihedral atom in a torsion is missing (ex. the first nucleotide won’t have an alpha because there is no nucleotide before it), the torsion will be marked as None