schrodinger.trajectory.prody.ensemble module

class schrodinger.trajectory.prody.ensemble.Ensemble(dsim, asl_sel=None)

Bases: object

A class for analysis of arbitrary conformational ensembles. Adopted from ProDy project (prody.csb.pitt.edu)

getCoords()

Return a copy of reference coordinates for selected atoms.

getDeviations()

Return deviations from reference coordinates for selected atoms. Conformations can be aligned using one of superpose() or iterpose() methods prior to calculating deviations.

getWeights()

Return a copy of weights of selected atoms.

get_selected_st()

return maestro structure of selected atoms.

get_solute_st()

return maestro structure of solute atoms.

iterpose(rmsd=1e-05)

Iteratively superpose the ensemble until convergence.

1. Conformations are aligned with the reference coordinates
2. mean coordiantes are calculated
3. mean coordiantes are used as reference coordinates
4. repeat until mean coordinates do not change

At the end of the procedure, the reference coordinates set will be averate of conformations in the ensemble.

numAtoms()

Return number of atoms.

numConfs()

Return number of frames.

numSelected()

setConfs()

setCoords()

Coodinates is a reference structure

setSoluteCoords()

Coordinate of the solute

setWeight(weights)

Set atomic weights.

set_solute_structure()

Sets structure of the solute molecule (sans water, ions, membrane)

solute_asl = <schrodinger.trajectory.atomselection.FrameAslSelection object>

superpose()

Superpose the ensemble onto the reference coordinates.

write_reference_structure(name='ref.mae')

Writes maestro structure

schrodinger.trajectory.prody.ensemble.checkWeights(weights, natoms, ncsets=None, dtype=<type 'float'>)

Return weights if it has correct shape ([ncsets, ]natoms, 1). after its shape and data type is corrected. otherwise raise an exception. All items of weights must be greater than zero.

schrodinger.trajectory.prody.ensemble.getRMSD(ref, tar, weights=None)

schrodinger.trajectory.prody.ensemble.importLA()

Return one of scipy.linalg or numpy.linalg.