ExplicitMoleculeComponent

class gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent(rdkit: rdkit.Chem.rdchem.Mol, name: str = '')

Base class for explicit molecules.

This provides basic serialization and conversion to different representations. Specific file formats, such as SDF for small molecules or PDB for proteins, should be implemented in subclasses.

Methods

from_json
from_rdkit	Create a Component, copying from an RDKit Mol
to_json
to_rdkit	Return an RDKit copied representation of this molecule

Attributes

name
smiles
total_charge	Net formal charge for the Component, if defined.

classmethod from_json(json_str)

classmethod from_rdkit(rdkit: rdkit.Chem.rdchem.Mol, name: str = '')

Create a Component, copying from an RDKit Mol

property name: str

property smiles: str

to_json()

to_rdkit() → rdkit.Chem.rdchem.Mol

Return an RDKit copied representation of this molecule

property total_charge

Net formal charge for the Component, if defined.