PDB Structure Ensemble¶
This module defines a class for handling ensembles of PDB conformations.

class
PDBEnsemble
(title='Unknown')[source]¶ This class enables handling coordinates for heterogeneous structural datasets and stores identifiers for individual conformations.
See usage usage in Heterogeneous Xray Structures, Multimeric Structures, and Homologous Proteins.
Note
This class is designed to handle conformations with missing coordinates, e.g. atoms that are note resolved in an Xray structure. For unresolved atoms, the coordinates of the reference structure is assumed in RMSD calculations and superpositions.

addCoordset
(coords, weights=None, label=None, **kwargs)[source]¶ Add coordinate set(s) to the ensemble. coords must be a Numpy array with suitable shape and dimensionality, or an object with
getCoordsets()
. weights is an optional argument. If provided, its length must match number of atoms. Weights of missing (not resolved) atoms must be0
and weights of those that are resolved can be anything greater than0
. If not provided, weights of all atoms for this coordinate set will be set equal to1
. label, which may be a PDB identifier or a list of identifiers, is used to label conformations.

delData
(label)¶ Return data associated with label and remove from the instance. If data associated with label is not found, return None.

deselect
()¶ Undoes the selection.

getAtoms
(selected=True)¶ Returns associated/selected atoms.

getCoords
(selected=True)¶ Returns a copy of reference coordinates for selected atoms.

getCoordsets
(indices=None, selected=True)[source]¶ Returns a copy of coordinate set(s) at given indices for selected atoms. indices may be an integer, a list of integers or None. None returns all coordinate sets.
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.

getData
(label)¶ Returns a copy of the data array associated with label, or None if such data is not present.

getDataLabels
(which=None)¶ Returns data labels. For
which='user'
, return only labels of user provided data.

getDataType
(label)¶ Returns type of the data (i.e.
data.dtype
) associated with label, or None label is not used.

getDefvecs
(pairwise=False)¶ Calculate and return deformation vectors (defvecs). Note that you might need to align the conformations using
superpose()
oriterpose()
before calculating defvecs.Parameters: pairwise (bool) – if True then it will return pairwise defvecs as an nbyn matrix. n is the number of conformations.

getDeviations
()¶ Returns deviations from reference coordinates for selected atoms. Conformations can be aligned using one of
superpose()
oriterpose()
methods prior to calculating deviations.

getIndices
()¶ Returns a copy of indices of selected columns

getMSFs
()[source]¶ Calculate and return mean square fluctuations (MSFs). Note that you might need to align the conformations using
superpose()
oriterpose()
before calculating MSFs.

getRMSDs
(pairwise=False)[source]¶ Calculate and return root mean square deviations (RMSDs). Note that you might need to align the conformations using
superpose()
oriterpose()
before calculating RMSDs.Parameters: pairwise (bool) – if True then it will return pairwise RMSDs as an nbyn matrix. n is the number of conformations.

getRMSFs
()¶ Returns root mean square fluctuations (RMSFs) for selected atoms. Conformations can be aligned using one of
superpose()
oriterpose()
methods prior to RMSF calculation.

getTitle
()¶ Returns title of the ensemble.

getTransformations
()[source]¶ 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
(selected=True)¶ Returns a copy of weights of selected atoms.

isDataLabel
(label)¶ Returns True if data associated with label is present.

isSelected
()¶ Returns if a subset of atoms are selected.

iterCoordsets
()[source]¶ Iterate over coordinate sets. A copy of each coordinate set for selected atoms is returned. Reference coordinates are not included.

iterpose
(rmsd=0.0001)[source]¶ Iteratively superpose the ensemble until convergence. Initially, all conformations are aligned with the reference coordinates. Then mean coordinates are calculated, and are set as the new reference coordinates. This is repeated until reference coordinates do not change. This is determined by the value of RMSD between the new and old reference coordinates. Note that at the end of the iterative procedure the reference coordinate set will be average of conformations in the ensemble.
Parameters: rmsd (float) – change in reference coordinates to determine convergence, default is 0.0001 Å RMSD

numAtoms
(selected=True)¶ Returns number of atoms.

numConfs
()¶ Returns number of conformations.

numCoordsets
()¶ Returns number of conformations.

numSelected
()¶ Returns number of selected atoms. Number of all atoms will be returned if a selection is not made. A subset of atoms can be selected by passing a selection to
setAtoms()
.

select
(selection)¶ Selects columns corresponding to a part of the atoms.

setAtoms
(atoms)¶ Set atoms or specify a selection of atoms to be considered in calculations and coordinate requests. When a selection is set, corresponding subset of coordinates will be considered in, for example, alignments and RMSD calculations. Setting atoms also allows some functions to access atomic data when needed. For example,
Ensemble
andConformation
instances become suitable arguments forwritePDB()
. Passing None as atoms argument will deselect atoms.

setCoords
(coords)¶ Set coords as the ensemble reference coordinate set. coords may be an array with suitable data type, shape, and dimensionality, or an object with
getCoords()
method.

setData
(label, data)¶ Store atomic data under label, which must:
 start with a letter
 contain only alphanumeric characters and underscore
 not be a reserved word (see
listReservedWords()
)
data must be a
list()
or andarray
and its length must be equal to the number of atoms. If the dimension of the data array is 1, i.e.data.ndim==1
, label may be used to make atom selections, e.g."label 1 to 10"
or"label C1 C2"
. Note that, if data with label is present, it will be overwritten.

setTitle
(title)¶ Set title of the ensemble.

superpose
(**kwargs)[source]¶ Superpose the ensemble onto the reference coordinates obtained by
getCoords()
.
