schrodinger.trajectory.prody.ensemble module

schrodinger.trajectory.prody.ensemble.importLA()

Return one of scipy.linalg or numpy.linalg.

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

class schrodinger.trajectory.prody.ensemble.Ensemble(cms_model, tr, asl_sel='(protein and atom.ptype " CA ")')

Bases: object

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

solute_asl = 'not ((water) or (ions) or (membrane))'

__init__(cms_model, tr, asl_sel='(protein and atom.ptype " CA ")')

Initialize self. See help(type(self)) for accurate signature.

__len__()

set_solute_structure()

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

setSoluteCoords()

Coordinate of the solute

setCoords()

Coodinates is a reference structure

getCoords()

Return a copy of reference coordinates for selected atoms.

setWeight(weights)

Set atomic weights.

getWeights()

Return a copy of weights of selected atoms.

setConfs()

superpose()

Superpose the ensemble onto the reference coordinates.

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.

getDeviations()

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

write_reference_structure(name='ref.mae')

Writes maestro structure

get_solute_st()

return maestro structure of solute atoms.

get_selected_st()

return maestro structure of selected atoms.

numAtoms()

Return number of atoms.

numConfs()

Return number of frames.

numSelected()