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()

Returns index of the coordinate set.

getACSLabel()

Returns active coordinate set label.

getAtomGroup()

Returns associated atom group.

getCSLabels()

Returns coordinate set labels.

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.

getFlagLabels(which=None)

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)

Returns True if data associated with label is present.

isFlagLabel(label)

Returns True if flags associated with label are present.

numCoordsets()

Returns number of coordinate sets.

select(selstr, **kwargs)

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

setACSIndex(index)

Set coordinates at index active.