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 |
---|---|
A generic vertex (node) in a graph |
|
A generic edge (arc) in a graph |
|
A generic graph data type |
Graph isomorphism¶
Class |
Description |
---|---|
Graph isomorphism using the VF2 algorithm |
Elements and atom types¶
Class/Function |
Description |
---|---|
A model of a chemical element |
|
Return the |
|
A model of an atom type: an element and local bond structure |
|
Return the |
Molecules¶
Class |
Description |
---|---|
An atom in a molecule |
|
A bond in a molecule |
|
A molecular structure represented using a chemical graph |
Functional groups¶
Class |
Description |
---|---|
An atom in a functional group |
|
A bond in a functional group |
|
A functional group structure represented using a chemical graph |
Molecule Utilities¶
Class |
Description |
---|---|
Resonance structure generation methods |
|
Kekule structure generation |
|
Resonance structure filtration methods |
|
Resonance path enumeration |
|
Molecule object converter (RDKit/OpenBabel) |
|
Molecule string representation translator |
Adjacency lists¶
Function |
Description |
---|---|
Convert an adjacency list to a set of atoms and bonds |
|
Convert a set of atoms and bonds to an adjacency list |
Symmetry numbers¶
Class |
Description |
---|---|
Calculate the atom-centered symmetry number for an atom in a molecule |
|
Calculate the bond-centered symmetry number for a bond in a molecule |
|
Calculate the axis-centered symmetry number for a double bond axis in a molecule |
|
Calculate the ring-centered symmetry number for a ring in a molecule |
|
Calculate the total internal + external symmetry number for a molecule |
Molecule and reaction drawing¶
Class |
Description |
---|---|
Draw the skeletal formula of a molecule |
|
Draw a chemical reaction |