Package schrodinger :: Package trajectory :: Package prody :: Module ensemble :: Class Ensemble

Class Ensemble

object --+
         |
        Ensemble

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

Instance Methods

[hide private]

__init__(self, dsim, asl_sel=None)
x.__init__(...) initializes x; see help(type(x)) for signature

__len__(self)

__str__(self)
str(x)

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

setSoluteCoords(self)
Coordinate of the solute

setCoords(self)
Coodinates is a reference structure

getCoords(self)
Return a copy of reference coordinates for selected atoms.

setWeight(self, weights)
Set atomic weights.

getWeights(self)
Return a copy of weights of selected atoms.

setConfs(self)

_getCoordsets(self, indices=None)
Returns a copy of coordinate sets() at given *indices*, which may be an integer, a list of integers or ``None``.

superpose(self)
Superpose the ensemble onto the reference coordinates.

_superpose(self, **kwargs)
Superpose conformations and upate coordinates.

iterpose(self, rmsd=1e-05)
Iteratively superpose the ensemble until convergence.

getDeviations(self)
Return deviations from reference coordinates for selected atoms.

write_reference_structure(self, name='ref.mae')
Writes maestro structure

get_solute_st(self)
return maestro structure of solute atoms.

get_selected_st(self)
return maestro structure of selected atoms.

numAtoms(self)
Return number of atoms.

numConfs(self)
Return number of frames.

numSelected(self)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables

[hide private]

solute_asl = atomselection.FrameAslSelection('not ((water) or ...

Properties

[hide private]

_indices
Returns a list of atom indices

Inherited from object: __class__

Method Details

[hide private]

init(self, dsim, asl_sel=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

_getCoordsets(self, indices=None)

Returns a copy of coordinate sets() at given *indices*, which may be an integer, a list of integers or ``None``. ``None`` returns all coordinate sets.

iterpose(self, 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(self)

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

Class Variable Details

[hide private]

solute_asl

Value:

atomselection.FrameAslSelection('not ((water) or (ions) or (membrane))
')

Property Details

[hide private]

_indices

Returns a list of atom indices

Get Method:: unreachable._indices(self) - Returns a list of atom indices

Class Ensemble

__init__(self, dsim, asl_sel=None) (Constructor)

__str__(self) (Informal representation operator)

_getCoordsets(self, indices=None)

iterpose(self, rmsd=1e-05)

getDeviations(self)

solute_asl

_indices

init(self, dsim, asl_sel=None)
(Constructor)

str(self)
(Informal representation operator)