schrodinger.trajectory.trajectory_gui_dir.custom_analyzers module¶

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

Bases: 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: 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: 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: 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: Residue) → list[list[schrodinger.structure._structure.StructureAtom] | None]¶

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

Parameters:: res – The nucleotide residue for which the dihedrals are calculated.
Returns:: A list of dihedrals.

schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.get_ordered_dihedral_idxs(st: Structure, atom_idxs: list[int]) → list[int]¶

Retrieve the ordered atom indexes for a given set of atoms forming a dihedral angle.

This function identifies the dihedral angle corresponding to the provided atom indexes in a nucleotide. The atom indexes for a specific dihedral angle are guaranteed to be unique. If the provided atom_idxs do not match any dihedral angle in the nucleotide, the function returns the original atom_idxs.

Parameters:

st – The molecular structure containing the nucleotide.
atom_idxs – A list of atom indexes representing the dihedral angle.

Returns:

A list of ordered atom indexes corresponding to the dihedral angle. Returns the original atom_idxs if no match is found.

Raises:

ValueError – If the provided atom_idxs do not contain exactly 4 atoms.