Package schrodinger :: Package trajectory :: Module analysis

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.

Classes

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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.

LigandRMSD
A tool to calculate Root Mean Square Deviation from reference positions of a small molecule.

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.

SolventAccessibleSurfaceAreaByResidue
A class which calculates Solvent Accessible Surface Area and returns results groupped by residues.

MolecularSurfaceArea
A tool to calculate molecular (connolly) surface area.

SolventAccessibleSurfaceArea
A class which calculates Solvent Accessible Surface Area.

PolarSurfaceArea
A tool to calculate Polar Surface Area.

Functions

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import_pylab()
Do a lazy import of pylab here.

_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

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degrees_per_rad = 57.2957795131

pylab = None
hash(x)

__package__ = 'schrodinger.trajectory'

Function Details

[hide private]

import_pylab()

Do a lazy import of pylab here. We want to usually use agg backend to do non interactive drawing. We will only successfully set this if no one has already used matplotlib functions.

_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.

Module analysis

import_pylab()

_get_atoms(frame, index, selections)

_get_connected_pair(ct, iatom, at1name, at2name)

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

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