Conformation

This module defines classes handling individual conformations.

class Conformation(ensemble, index)[source]

A class to provide methods on a conformation in an ensemble. Instances of this class do not keep coordinate and weights data.

getAtoms()

Returns associated atom group.

getCoords()

Returns a copy of the coordinates of the conformation. If a subset of atoms are selected in the ensemble, coordinates for selected atoms will be returned.

getDeviations()

Returns deviations from the ensemble reference coordinates. Deviations are calculated for (selected) atoms.

getEnsemble()

Returns the ensemble that this conformation belongs to.

getIndex()

Returns conformation index.

getRMSD()

Returns RMSD from the ensemble reference coordinates. RMSD is calculated for (selected) atoms.

getWeights()

Returns coordinate weights for (selected) atoms.

numAtoms()

Returns number of atoms.

numSelected()

Returns number of selected atoms.

class PDBConformation(ensemble, index)[source]

This class is the same as Conformation, except that the conformation has a name (or identifier), e.g. PDB identifier.

getAtoms()

Returns associated atom group.

getCoords()

Returns a copy of the coordinates of the conformation. If a subset of atoms are selected in the ensemble, coordinates for selected atoms will be returned.

Warning

When there are atoms with weights equal to zero (0), their coordinates will be replaced with the coordinates of the ensemble reference coordinate set.

getDeviations()

Returns deviations from the ensemble reference coordinates. Deviations are calculated for (selected) atoms.

getEnsemble()

Returns the ensemble that this conformation belongs to.

getIndex()

Returns conformation index.

getLabel()

Returns the label of the conformation.

getRMSD()

Returns RMSD from the ensemble reference coordinates. RMSD is calculated for (selected) atoms.

getTransformation()

Returns the Transformation used to superpose this conformation onto reference coordinates. The transformation can be used to superpose original PDB file onto the reference PDB file.

getWeights()

Returns coordinate weights for (selected) atoms.

numAtoms()

Returns number of atoms.

numSelected()

Returns number of selected atoms.

setLabel(label)

Set the label of the conformation.