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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__metaclass__
type(object) -> the object's type type(name, bases, dict) -> a new type

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

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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_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 = 180./ numpy.pi

Function Details

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_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.