The Molecule is a symbolic representation of a chemical species and is a fully computable first-class member of the Wolfram Language. More than 20 new functions allow users to create, analyze and modify chemical species. A wide range of computed properties such as stereochemistry, symmetry elements, molecular graphs and molecular mechanics energies facilitate problem solving across all chemical disciplines. Built-in support for organic and inorganic nomenclature allows fast creation of molecule objects from chemical names. Molecule folds seamlessly into existing functionality, e.g. Graph , to enable novel computations.

Symbolic Chemical Representation

Molecule — a molecule specified by atoms and bonds, name or SMILES string

BioMolecule — a large biopolymer composed of peptide, DNA or RNA units

ChemicalFormula — symbolic representation for a chemical formula

Atom — symbolic representation of an atom in a molecule

Bond — symbolic representation of single, double, aromatic, etc. bond

Molecule Options

IncludeHydrogens — whether to implicitly add hydrogen atoms for unfilled valences

StereochemistryElements — specify local stereochemical arrangements of atoms

AtomCoordinates — explicitly specify 3D coordinates of atoms in a molecule

AtomDiagramCoordinates — explicitly specify 2D coordinates to use in diagrams

IncludeAromaticBonds — whether to include aromatic bonds or use single/double form

Molecular Structure

AtomList   ▪ AtomCount   ▪ BondList   ▪ BondCount   ▪ BondQ

MoleculeQ — test for a valid molecule

Molecular Visualization

MoleculePlot — annotatable 2D molecular structure diagram with automatic layout

MoleculePlot3D — 3D molecular rendering allowing automatically generated coordinates

MoleculeMesh — a 3D boundary mesh representation of a molecule or biomolecule

BioMoleculePlot3D — display a biomolecule as a ribbon diagram

AtomLabels   ▪ BondLabels

Style — specify highlighting and other styles for molecular substructures

RGBColor   ▪ Opacity   ▪ EdgeForm   ▪ FaceForm   ▪ ...

PlotTheme — specify overall appearance ("SpaceFilling", "BallAndStick", "Tubes", ...)

Molecular Graphs

MoleculeGraph — get an annotated graph for a molecule

ConnectedMoleculeQ — test for a single covalently bound structure

ConnectedMoleculeComponents — give a list of independent covalently bound structures

FindCycle   ▪ FindPath   ▪ FindHamiltonianPath   ▪ ...

Molecular Recognition

MoleculeRecognize — recognize a molecule from an image

MoleculeName — find the name for a molecule

FindIsomers — find molecules with the same chemical formula

MoleculeDraw — sketch freehand molecules and interpret them

Molecular Property Computation

MoleculeValue — find structural or computed properties of molecules

MoleculeProperty — symbolic representation of a molecular property

BioMoleculeValue — find properties of biomolecules

Molecular Comparison & Substructure

MoleculeMatchQ — test whether a molecule matches a pattern or another molecule

MoleculeContainsQ — test whether a molecule contains a specified structure

MoleculeFreeQ — test whether a molecule is free from a specified structure

FindMoleculeSubstructure — find where a substructure occurs in a molecule

MoleculeMaximumCommonSubstructure — identify substructure common to molecules

MoleculeSubstructureCount — count occurrences of a molecule substructure

MoleculePattern — symbolic or SMARTS pattern representing a molecular substructure

Modifying Molecules

MoleculeModify — create a new molecule by editing an existing molecule

MoleculeAlign — align molecules in 3D

ValenceErrorHandling — how to handle valence errors when a molecule is edited

Chemical Reactions

ChemicalReaction — symbolic representation for a chemical reaction

ReactionBalance — balance a chemical reaction

ReactionBalancedQ — check if a chemical reaction is balanced

PatternReaction — symbolic representation of a reaction between molecule patterns

ApplyReaction — apply a pattern reaction to molecules

Chemical Quantities

ChemicalInstance — symbolic representation of an amount of a chemical

ChemicalConvert — convert between different chemical amounts

Import , Export — import and export molecular structures

"MOL"   ▪ "MOL2"   ▪ "SDF"   ▪ "XYZ"   ▪ "Cube"   ▪ "PDB"   ▪ "GaussianLog"

"PDB"   ▪ "MMCIF"   ▪ "MMJSON"

Known Chemicals & Properties

Chemical — known chemicals and their properties

Protein Mineral Food

External Services

ServiceConnect , ServiceExecute — connect to external services

"PubChem"   ▪ "ChemSpider"   ▪ "RCSBProteinDataBank"   ▪ "ESMAtlas"

Molecular Dynamics

NBodySimulation — classical n-body simulation with arbitrary potentials