Atomic Base

This module defines base class Atomic that all other atomic classes are derived from.

class Atomic[source]

Base class for all atomic classes that can be used for type checking.

copy()[source]

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

getSequence(**kwargs)[source]

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()[source]

Returns title of the instance.

numResidues()[source]

Returns number of residues.

select(selstr, **kwargs)[source]

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

toAtomGroup()

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

toBioPythonStructure(header=None, **kwargs)[source]

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()[source]

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

toTEMPyStructure()[source]

Returns a protein.prot_rep_biopy.Structure object