Molecular representations (rmgpy.molecule)

The rmgpy.molecule subpackage contains classes and functions for working with molecular representations, particularly using chemical graph theory.

Graphs

Class Description
Vertex A generic vertex (node) in a graph
Edge A generic edge (arc) in a graph
Graph A generic graph data type

Graph isomorphism

Class Description
VF2 Graph isomorphism using the VF2 algorithm

Elements and atom types

Class/Function Description
Element A model of a chemical element
getElement() Return the Element object for a given atomic number or symbol
AtomType A model of an atom type: an element and local bond structure
getAtomType() Return the AtomType object for a given atom in a molecule

Molecules

Class Description
Atom An atom in a molecule
Bond A bond in a molecule
Molecule A molecular structure represented using a chemical graph

Functional groups

Class Description
GroupAtom An atom in a functional group
GroupBond A bond in a functional group
Group A functional group structure represented using a chemical graph

Adjacency lists

Function Description
fromAdjacencyList() Convert an adjacency list to a set of atoms and bonds
toAdjacencyList() Convert a set of atoms and bonds to an adjacency list

Symmetry numbers

Class Description
calculateAtomSymmetryNumber() Calculate the atom-centered symmetry number for an atom in a molecule
calculateBondSymmetryNumber() Calculate the bond-centered symmetry number for a bond in a molecule
calculateAxisSymmetryNumber() Calculate the axis-centered symmetry number for a double bond axis in a molecule
calculateCyclicSymmetryNumber() Calculate the ring-centered symmetry number for a ring in a molecule
calculateSymmetryNumber() Calculate the total internal + external symmetry number for a molecule

Molecule and reaction drawing

Class Description
MoleculeDrawer Draw the skeletal formula of a molecule
ReactionDrawer Draw a chemical reaction

Exceptions

Exception Description
ElementError Raised when an error occurs while working with chemical elements
AtomTypeError Raised when an error occurs while working with atom types
InvalidAdjacencyListError Raised when an invalid adjacency list is encountered
ActionError Raised when an error occurs while working with a reaction recipe action