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