MoleculeAttributes
- pydantic model openff.qcsubmit.common_structures.MoleculeAttributes[source]
A class to hold and validate the molecule attributes associated with a QCArchive entry, All attributes are required to be entered into a dataset.
Note
The attributes here are not exhaustive but are based on those given by cmiles and can all be obtain through the openforcefield toolkit Molecule class.
Show JSON schema
{ "title": "MoleculeAttributes", "description": "A class to hold and validate the molecule attributes associated with a QCArchive entry, All attributes are required\nto be entered into a dataset.\n\nNote:\n The attributes here are not exhaustive but are based on those given by cmiles and can all be obtain through the openforcefield toolkit Molecule class.", "type": "object", "properties": { "canonical_smiles": { "title": "Canonical Smiles", "type": "string" }, "canonical_isomeric_smiles": { "title": "Canonical Isomeric Smiles", "type": "string" }, "canonical_explicit_hydrogen_smiles": { "title": "Canonical Explicit Hydrogen Smiles", "type": "string" }, "canonical_isomeric_explicit_hydrogen_smiles": { "title": "Canonical Isomeric Explicit Hydrogen Smiles", "type": "string" }, "canonical_isomeric_explicit_hydrogen_mapped_smiles": { "title": "Canonical Isomeric Explicit Hydrogen Mapped Smiles", "description": "The fully mapped smiles where every atom should have a numerical tag so that the molecule can be rebuilt to match the order of the coordinates.", "type": "string" }, "molecular_formula": { "title": "Molecular Formula", "description": "The hill formula of the molecule as given by the openfftoolkit.", "type": "string" }, "standard_inchi": { "title": "Standard Inchi", "description": "The standard inchi given by the inchi program ie not fixed hydrogen layer.", "type": "string" }, "inchi_key": { "title": "Inchi Key", "description": "The standard inchi key given by the inchi program.", "type": "string" }, "fixed_hydrogen_inchi": { "title": "Fixed Hydrogen Inchi", "description": "The non-standard inchi with a fixed hydrogen layer to distinguish tautomers.", "type": "string" }, "fixed_hydrogen_inchi_key": { "title": "Fixed Hydrogen Inchi Key", "description": "The non-standard inchikey with a fixed hydrogen layer.", "type": "string" }, "unique_fixed_hydrogen_inchi_keys": { "title": "Unique Fixed Hydrogen Inchi Keys", "description": "The list of unique non-standard inchikey with a fixed hydrogen layer.", "type": "array", "items": { "type": "string" }, "uniqueItems": true } }, "required": [ "canonical_smiles", "canonical_isomeric_smiles", "canonical_explicit_hydrogen_smiles", "canonical_isomeric_explicit_hydrogen_smiles", "canonical_isomeric_explicit_hydrogen_mapped_smiles", "molecular_formula", "standard_inchi", "inchi_key" ] }
- Config
extra: str = allow
- Fields
- field canonical_smiles: str [Required]
- field canonical_isomeric_smiles: str [Required]
- field canonical_explicit_hydrogen_smiles: str [Required]
- field canonical_isomeric_explicit_hydrogen_smiles: str [Required]
- field canonical_isomeric_explicit_hydrogen_mapped_smiles: str [Required]
The fully mapped smiles where every atom should have a numerical tag so that the molecule can be rebuilt to match the order of the coordinates.
- field molecular_formula: str [Required]
The hill formula of the molecule as given by the openfftoolkit.
- field standard_inchi: str [Required]
The standard inchi given by the inchi program ie not fixed hydrogen layer.
- field inchi_key: str [Required]
The standard inchi key given by the inchi program.
- field fixed_hydrogen_inchi: Optional[str] = None
The non-standard inchi with a fixed hydrogen layer to distinguish tautomers.
- field fixed_hydrogen_inchi_key: Optional[str] = None
The non-standard inchikey with a fixed hydrogen layer.
- field unique_fixed_hydrogen_inchi_keys: Optional[Set[str]] = None
The list of unique non-standard inchikey with a fixed hydrogen layer.
- classmethod from_openff_molecule(molecule)[source]
Create the Cmiles metadata for an OpenFF molecule object.
- Parameters
molecule (openff.toolkit.topology.molecule.Molecule) – The molecule for which the cmiles data will be generated.
- Returns
The Cmiles identifiers generated for the input molecule.
- Return type
Note
The Cmiles identifiers currently include:
canonical_smiles
canonical_isomeric_smiles
canonical_explicit_hydrogen_smiles
canonical_isomeric_explicit_hydrogen_smiles
canonical_isomeric_explicit_hydrogen_mapped_smiles
molecular_formula
standard_inchi
inchi_key
fixed_hydrogen_inchi
fixed_hydrogen_inchi_key
unique_fixed_hydrogen_inchi_keys
- to_openff_molecule()[source]
Create an openff molecule from the CMILES information.
- Return type