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.
DRAWN_RADICAL	An atom property marking a radical the drawing or file states, which is kept as given.

Functions

identity(mol)	The identity of a sanitized RDKit molecule.
inert_pair_radicals(mol[, drawn])	Mark the radicals drawn(index) says were drawn, and set the others to unpaired().
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.
unpaired(atom)	An atom's unpaired electrons, with the inert pair of Ga to Bi kept paired (#147).
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.DRAWN_RADICAL = 'vibesketchDrawnRadical'

An atom property marking a radical the drawing or file states, which is kept as given.

vibesketch.chem.species.inert_pair_radicals(mol, drawn=None)

Mark the radicals drawn(index) says were drawn, and set the others to unpaired().

The counts set last only until RDKit sanitizes the molecule again; unpaired() gives them at any time.

Parameters:

• mol (Any)

• drawn (Any)

Return type:

None

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

vibesketch.chem.species.unpaired(atom)

An atom’s unpaired electrons, with the inert pair of Ga to Bi kept paired (#147).

RDKit’s valence model gives a bare Pb²⁺ two radical electrons, a triplet, and re-assigns them whenever a molecule is sanitized; the ion is [Xe]4f¹⁴5d¹⁰6s², a singlet. For the elements above, the electrons left after the charge and the bonds fill the ns² pair first and then the np shell by Hund’s rule: Pb²⁺, Sn²⁺, In⁺ and Bi³⁺ have none unpaired, a Pb atom two (³P), a Bi atom three (⁴S), a Ga atom one (²P). A radical marked as drawn (DRAWN_RADICAL) is kept as given.

Parameters:

atom (Any)

Return type:

int