Atomic Base

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

class prody.atomic.atomic.Atomic

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

__copy__()

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

copy()

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

getSequence(**kwargs)

Returns one-letter sequence string for amino acids, unless longSeq is True. 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.

numResidues()

Returns number of residues.

select(selstr, **kwargs)

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)

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