schrodinger.trajectory.prody.ensemble module¶
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schrodinger.trajectory.prody.ensemble.
importLA
()¶ Return one of
scipy.linalg
ornumpy.linalg
.
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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.
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schrodinger.trajectory.prody.ensemble.
getRMSD
(ref, tar, weights=None)¶
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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)
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__init__
(cms_model, tr, asl_sel='(protein and atom.ptype " CA ")')¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
()¶
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setSoluteCoords
()¶ Coordinate of the solute
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setCoords
()¶ Coodinates is a reference structure
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getCoords
()¶ Return a copy of reference coordinates for selected atoms.
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setWeight
(weights)¶ Set atomic weights.
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getWeights
()¶ Return a copy of weights of selected atoms.
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setConfs
()¶
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superpose
()¶ Superpose the ensemble onto the reference coordinates.
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iterpose
(rmsd=1e-05)¶ - Iteratively superpose the ensemble until convergence.
- Conformations are aligned with the reference coordinates
- mean coordiantes are calculated
- mean coordiantes are used as reference coordinates
- 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.
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getDeviations
()¶ Return deviations from reference coordinates for selected atoms. Conformations can be aligned using one of
superpose()
oriterpose()
methods prior to calculating deviations.
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solute_st
¶ return maestro structure of solute atoms.
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selected_st
¶ return maestro structure of selected atoms.
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numAtoms
()¶ Return number of atoms.
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numConfs
()¶ Return number of frames.
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numSelected
()¶
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