Molecule¶

Represents a chemical molecule as a symbolic expression of atoms and bonds. A molecule can be constructed from a chemical name:

$ wo 'Molecule["water"]'
Molecule[{Atom[O], Atom[H], Atom[H]}, {Bond[{1, 2}, Single], Bond[{1, 3}, Single]}]

… from a SMILES string (hydrogen atoms are added to fill the normal valences):

$ wo 'Molecule["C=O"]'
Molecule[{Atom[C], Atom[O], Atom[H], Atom[H]}, {Bond[{1, 2}, Double], Bond[{1, 3}, Single], Bond[{1, 4}, Single]}]

… or from explicit atom and bond lists:

$ wo 'Molecule[{"C", "O"}, {Bond[{1, 2}, "Single"]}]'
Molecule[{Atom[C], Atom[O], Atom[H], Atom[H], Atom[H], Atom[H]}, {Bond[{1, 2}, Single], Bond[{1, 3}, Single], Bond[{1, 4}, Single], Bond[{1, 5}, Single], Bond[{2, 6}, Single]}]

Aromatic rings, formal charges, and isotopes are supported:

$ wo 'Molecule["[NH4+]"]'
Molecule[{Atom[N, FormalCharge -> 1], Atom[H], Atom[H], Atom[H], Atom[H]}, {Bond[{1, 2}, Single], Bond[{1, 3}, Single], Bond[{1, 4}, Single], Bond[{1, 5}, Single]}]

MoleculeQ¶

Tests whether an expression is a valid molecule:

$ wo 'MoleculeQ[Molecule["ethanol"]]'
True

$ wo 'MoleculeQ[5]'
False

AtomList and BondList¶

Return the atoms and bonds of a molecule:

$ wo 'AtomList[Molecule["methane"]]'
{Atom[C], Atom[H], Atom[H], Atom[H], Atom[H]}

$ wo 'BondList[Molecule["ammonia"]]'
{Bond[{1, 2}, Single], Bond[{1, 3}, Single], Bond[{1, 4}, Single]}

MoleculeValue¶

Computes properties of a molecule ("AtomCount", "BondCount", "AtomList", "BondList", "MolecularFormula", and "NetCharge"):

$ wo 'MoleculeValue[Molecule["caffeine"], "MolecularFormula"]'
C8H10N4O2

Properties can also be accessed by applying the molecule to a property name:

$ wo 'Molecule["benzene"]["AtomCount"]'
12

Information tile¶

In visual hosts (the playground and Woxi Studio) a molecule displays as a compact information tile: a structure thumbnail beside the molecular formula, atom count, and bond count. The same tile is available anywhere via ExportString[mol, "SVG"]:

$ wo 'StringTake[ExportString[Molecule["caffeine"], "SVG"], 4]'
<svg

The tile reports the formula and counts as text:

$ wo 'StringContainsQ[ExportString[Molecule["water"], "SVG"], "Formula: "]'
True

MoleculePlot¶

MoleculePlot[mol] draws the full 2-D skeletal structure diagram as a Graphics object. Atoms are laid out with a spring embedder; single, double, triple, and aromatic bonds, heteroatom labels, formal charges, and isotope mass numbers are all drawn. It accepts a molecule or any specification Molecule itself accepts:

$ wo 'MoleculePlot["caffeine"]'
-Graphics-

Carbon atoms with heavy-atom neighbors are drawn as bare vertices (implicit hydrogens omitted), so an aromatic ring like benzene needs no atom labels — its twelve strokes are the six ring bonds plus the six inner aromatic lines:

$ wo 'StringCount[ExportString[MoleculePlot["benzene"], "SVG"], "<line"]'
12