Atom Pointer

This module defines atom pointer base class.

class AtomPointer(ag, acsi)

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

• Atom
• AtomSubset
• AtomMap

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.

getAnisous()

Returns a copy of anisotropic temperature factors from the active coordinate set.

getAtomGroup()

Returns associated atom group.

getBonds()

Returns bonds. Use setBonds() or inferBonds() from parent AtomGroup for setting bonds.

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.

iterAcceptors()

Yield acceptors formed by the atom. Use setAcceptors() for setting acceptors.

iterAngles()

Yield angles formed by the atom. Use setAngles() for setting angles.

iterBonds()

Yield bonds formed by the atom. Use setBonds() or inferBonds() for setting bonds.

iterCrossterms()

Yield crossterms formed by the atom. Use setCrossterms() for setting crossterms.

iterDihedrals()

Yield dihedrals formed by the atom. Use setDihedrals() for setting dihedrals.

iterDonors()

Yield donors formed by the atom. Use setDonors() for setting donors.

iterImpropers()

Yield impropers formed by the atom. Use setImpropers() for setting impropers.

iterNBExclusions()

Yield nbexclusions formed by the atom. Use setNBExclusions() for setting nbexclusions.

numBonds()

Returns number of bonds. Use setBonds() or inferBonds() from parent AtomGroup for setting bonds.

numCoordsets()

Returns number of coordinate sets.

numResidues()

Returns number of residues.

select(selstr, **kwargs)

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

setACSIndex(index)

Set coordinates at index active.

toAtomGroup()

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

toBioPythonStructure(header=None, **kwargs)

Returns a Bio.PDB.Structure object

Parameters:

• atoms (Atomic) – an object with atom and coordinate data
• csets – coordinate set indices, default is all coordinate sets

toTEMPyAtoms()

Returns a TEMPy.protein.prot_rep_biopy.Atom or list of them as appropriate

toTEMPyStructure()

Returns a protein.prot_rep_biopy.Structure object