Molecule¶

Represents a chemical molecule as a symbolic expression of atoms and bonds. The canonical form is Molecule[{atoms…}, {bonds…}, {metadata…}]. An atom is a bare element symbol, or Atom["El", "Prop" -> value, …] when it carries extra properties. A molecule can be constructed from a chemical name (whose hydrogens are materialized as explicit atoms):

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

… from a SMILES string (organic-subset hydrogens stay implicit):

$ wo 'Molecule["C=O"]'
Molecule[{C, O}, {Bond[{1, 2}, Double]}, {}]

… or from explicit atom and bond lists (also kept implicit):

$ wo 'Molecule[{"C", "O"}, {Bond[{1, 2}, "Single"]}]'
Molecule[{C, O}, {Bond[{1, 2}, Single]}, {}]

Aromatic rings, formal charges, and isotopes are supported. A bracket-atom hydrogen count rides along as a HydrogenCount property:

$ wo 'Molecule["[NH4+]"]'
Molecule[{Atom[N, FormalCharge -> 1, HydrogenCount -> 4]}, {}, {}]

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]}

BondQ¶

BondQ[mol, bond] tests whether bond is a bond of mol. The atom pair is unordered, and it indexes the same hydrogen-complete atom list AtomList returns — so ethanol's implicit hydrogens (atoms 4 to 9) are addressable:

$ wo 'BondQ[Molecule["CCO"], Bond[{2, 1}]]'
True

$ wo 'BondQ[Molecule["CCO"], Bond[{1, 4}]]'
True

$ wo 'BondQ[Molecule["CCO"], Bond[{1, 3}]]'
False

Omitting the bond type matches a bond of any type; giving one requires an exact match:

$ wo 'BondQ[Molecule["c1ccccc1"], Bond[{1, 2}, "Aromatic"]]'
True

$ wo 'BondQ[Molecule["c1ccccc1"], Bond[{1, 2}, "Single"]]'
False

ConnectedMoleculeQ and ConnectedMoleculeComponents¶

ConnectedMoleculeQ[mol] tests whether the atoms of mol are all joined by bonds. A . in a SMILES string separates fragments, so a salt is not connected:

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

$ wo 'ConnectedMoleculeQ[Molecule["[Na+].[Cl-]"]]'
False

ConnectedMoleculeComponents[mol] returns each connected fragment as its own molecule, with the bonds renumbered against the fragment's atoms:

$ wo 'ConnectedMoleculeComponents[Molecule["CC.O"]]'
{Molecule[{C, C}, {Bond[{1, 2}, Single]}, {}], Molecule[{O}, {}, {}]}

Both take any specification Molecule accepts, not just a molecule:

$ wo 'ConnectedMoleculeQ["CCO"]'
True

MoleculeValue¶

Computes properties of a molecule ("AtomCount", "BondCount", "AtomList", "BondList", "MolecularFormula", and "NetCharge"). The molecular formula is returned as a typeset Row of element symbols with the counts as subscripts:

$ wo 'MoleculeValue[Molecule["caffeine"], "MolecularFormula"]'
Subscript[C, 8]Subscript[H, 10]Subscript[N, 4]Subscript[O, 2]

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

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

Structure diagram¶

In visual hosts (the playground and Woxi Studio) a molecule displays as its 2-D structure diagram. The same diagram is available anywhere via ExportString[mol, "SVG"], a standalone SVG document (with an XML declaration):

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

It is a structure drawing, not a text summary, so it carries no Formula: label:

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

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-

Bonds are drawn as vector polylines rather than <line> elements, matching the markup wolframscript emits, so a benzene diagram contains no <line>:

$ wo 'StringCount[ExportString[MoleculePlot["benzene"], "SVG"], "<line"]'
0