Atom Pointer

This module defines atom pointer base class.

class AtomPointer(ag, acsi)[source]

A base for classes pointing to atoms in AtomGroup instances. Derived classes are:

copy()

Returns a copy of atoms (and atomic data) in an AtomGroup instance.

getACSIndex()[source]

Returns index of the coordinate set.

getACSLabel()[source]

Returns active coordinate set label.

getAtomGroup()[source]

Returns associated atom group.

getCSLabels()[source]

Returns coordinate set labels.

getDataLabels(which=None)[source]

Returns data labels. For which='user', return only labels of user provided data.

getDataType(label)[source]

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

getFlagLabels(which=None)[source]

Returns flag labels. For which='user', return labels of user or parser (e.g. hetatm) provided flags, for which='all' return all possible Atom Flags labels in addition to those present in the instance.

getSequence(**kwargs)

Returns one-letter sequence string for amino acids. When allres keyword argument is True, sequence will include all residues (e.g. water molecules) in the chain and X will be used for non-standard residue names.

getTitle()

Returns title of the instance.

isDataLabel(label)[source]

Returns True if data associated with label is present.

isFlagLabel(label)[source]

Returns True if flags associated with label are present.

numCoordsets()[source]

Returns number of coordinate sets.

select(selstr, **kwargs)

Returns atoms matching selstr criteria. See select module documentation for details and usage examples.

setACSIndex(index)[source]

Set coordinates at index active.

toAtomGroup()

Returns a copy of atoms (and atomic data) in an AtomGroup instance.