vibesketch.chem.species¶

Identity and properties of one species, from an RDKit molecule.

Module Attributes

TRANSITION_METALS

their spin state cannot be read off a drawing.

Functions

`identity`(mol)	The identity of a sanitized RDKit molecule.
`mol_from_smiles`(smiles)	An RDKit molecule from SMILES; raises `ValueError` when RDKit refuses it.
`properties`(mol)	Formula, masses and InChI of a sanitized RDKit molecule.
`without_hydrogens`(mol)	A copy without explicit hydrogens, quietly: a lone H or H+ stays, unremarked.

Classes

`Identity`(smiles, inchikey, charge, ...)	What identifies a species and what a calculation needs from the drawing.
`Properties`(formula, average_mass, ...)

class vibesketch.chem.species.Identity(smiles, inchikey, charge, multiplicity, electrons, has_transition_metal, has_stereo)¶

Bases: object

What identifies a species and what a calculation needs from the drawing.

Parameters:

smiles (str)
inchikey (str | None)
charge (int)
multiplicity (int)
electrons (int)
has_transition_metal (bool)
has_stereo (bool)

smiles: str¶

inchikey: str | None¶

charge: int¶

multiplicity: int¶

unpaired radical electrons + 1.

Type:: The multiplicity the drawing implies

electrons: int¶

has_transition_metal: bool¶

has_stereo: bool¶

property key: str¶: What two drawings of the same species share.

class vibesketch.chem.species.Properties(formula: 'str', average_mass: 'float', monoisotopic_mass: 'float', inchi: 'str | None')¶

Bases: object

Parameters:

formula (str)
average_mass (float)
monoisotopic_mass (float)
inchi (str | None)

formula: str¶

average_mass: float¶

monoisotopic_mass: float¶

inchi: str | None¶

vibesketch.chem.species.TRANSITION_METALS = frozenset({21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112})¶

their spin state cannot be read off a drawing.

Type:: d-block and f-block elements

vibesketch.chem.species.identity(mol)¶

The identity of a sanitized RDKit molecule.

Parameters:: mol (Any)
Return type:: Identity

vibesketch.chem.species.mol_from_smiles(smiles)¶

An RDKit molecule from SMILES; raises ValueError when RDKit refuses it.

Parameters:: smiles (str)
Return type:: Any

vibesketch.chem.species.properties(mol)¶

Formula, masses and InChI of a sanitized RDKit molecule.

Parameters:: mol (Any)
Return type:: Properties