Package schrodinger :: Package trajectory :: Module analysis
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Module analysis

A module of classes to analyze Desmond trajectories.

Please see the AnalysisTool documentation for a description of the API that handles interaction between AnalysisTool objects and schrodinger.trajectory.desmondsimulation.DesmondSimulation instances.

Copyright Schrodinger, LLC. All rights reserved.

Classes [hide private]
  _PBCMeasureMananger
A class to measure distance, angle, dihedral and planar angle under periodic boundary conditions.
  Angle
A tool to calculate angles between selected atom sets.
  Distance
A tool to calculate distances between selected atom sets.
  Dihedral
A tool to calculate dihedral angles from selected atom sets.
  PlanarAngle
A tool calculate inter-planar angles from selected atoms
  Position
A tool to track positions of atoms.
  RadiusOfGyration
A tool to calculate radius of gyration for a set of atoms.
  HydrogenBondFinder
A tool to find hydrogen bonds present between two sets of molecules.
  HydrogenBondTracker
A tool to track the state of hydrogen bonds between atom sets.
  SecondaryStructure
A tool to track secondary protein structure.
  Ramachandran
A tool to look at Ramachandran information and plots.
  _RamachandranCallback
This class implements a callback to print information about selected Ramachandran plot points.
  RMSD
A tool to calculate Root Mean Square Deviation from reference positions.
  CenterOfMotion
A tool to calculate center of motion of selected atoms.
  CenterOfMass
A tool to calculate center of mass of selected atoms.
  Superimposer
  AverageStructure
A tool to calculate average position over time for each atom in a set.
  CovarianceMatrix
A tool to calculate covmatiant matrix.
  RMSF
A tool to calculate Root Mean Square Fluctation from reference positions.
  Grid3D
A class for representing a function of 3D Cartesian coordinates discretize onto a grid.
  VolumeMapper
A tool to map atomic volume onto a grid.
Functions [hide private]
 
_get_atoms(frame, index, selections)
Return a tuple of _StructureAtom instances for the provided index in each of the provided selections.
 
_get_connected_pair(ct, iatom, at1name, at2name)
Return a pair of atom indexes, where at1name is attached to iatom and at2name is attached to at1name.
 
_find_connected_atom(ct, iatom, atname)
Return the atom index with PDB atom type atname attached to iatom in ct, or -1 if no connection is found.From rama.py
 
_is_valid_atom(atid, atom_set=None)
 
get_phi_psi_atoms(st, ca_asl_expr='atom.ptype " CA "', atom_list=None)
Return phi_psi atoms that can be used in Ramachandran class
 
superimpose(p, coords, reference_coords)
Variables [hide private]
  degrees_per_rad = 57.2957795131
  __package__ = 'schrodinger.trajectory'
Function Details [hide private]

_get_atoms(frame, index, selections)

 

Return a tuple of _StructureAtom instances for the provided index in each of the provided selections.

Parameters:
  • index (int) - The 0-based index of the selection to choose.
  • selections (iterable of AtomSelection class)

_get_connected_pair(ct, iatom, at1name, at2name)

 

Return a pair of atom indexes, where at1name is attached to iatom and at2name is attached to at1name. From rama.py

get_phi_psi_atoms(st, ca_asl_expr='atom.ptype " CA "', atom_list=None)

 

Return phi_psi atoms that can be used in Ramachandran class

Parameters:
  • st (Structure) - A Structure instance to be operated on
  • ca_asl_expr (string) - ASL expression for CA
  • atom_list (list) - An atom index list that used to determine if the selected atom is valid. By default, it is set to None, which means any selected atom is valid.