Topology representations

This module provides different topological representations to translate from external toolkits the different molecular parameters for PELE.

Primary objects

Molecule	It represent wraps up all the tools to parameterize a molecule with the OpenForceField toolkit for PELE.
Topology	It represents the topology of a molecule.

Secondary objects

Atom	It represents the properties of an atom.
Bond	It represents a bond in the topology.
Angle	It represents an angle in the topology.
Dihedral	It represents a dihedral in the topology.
Proper	It represents a proper dihedral in the topology.
Improper	It represents an improper dihedral in the topology.
elements.DummyAtom	It represents a dummy atom.
elements.OFFDihedral	It represents a dihedral in the Open Force Field’s topology.
elements.OFFProper	It represents a proper dihedral in the Open Force Field’s topology.
elements.OFFImproper	It represents an improper dihedral in the Open Force Field’s topology.
ZMatrix	It generates the zmatrix of a molecule as a numpy.array.
rotamer.Rotamer	It represents the conformational space of a rotatable bond, discretized with a certain resolution.
rotamer.RotamerLibrary	It represents a set of rotamers found in the same molecule.
rotamer.MolecularGraph	It represents the structure of a Molecule as a networkx.Graph.