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description=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.;

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resources for software developers tech support contact us support faqs support faqs contact us company about wolfram career center all sites resources connect follow contact us work with us student ambassador initiative wolfram for startups student opportunities jobs using wolfram language educational programs for adults summer school winter school educational programs for youth middle school camp high school research program computational adventures read stephen wolfram s writings wolfram blog wolfram tech books wolfram media complex systems educational resources wolfram mathworld wolfram in stem wolfram challenges wolfram problem generator wolfram initiatives wolfram science wolfram foundation history of mathematics project events stephen wolfram livestreams online in person events contact us connect follow for ais wolfram cloud your account your account user portal wolfram cloud search close navigation menu products wolfram one mathematica system modeler compute services use with 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solutions technology for education research universities colleges teaching universities high schools resources for students education initiatives next gen edtech computer based math more solutions for education contact us learning support get started wolfram language introduction fast intro for programmers fast intro for math students wolfram language documentation grow your skills wolfram u courses in computing science life and more community learn solve problems and share ideas blog news views and insights from wolfram resources for software developers tech support contact us support faqs more learning highlighted core areas demonstrations youtube daily study groups wolfram schools and programs books support faqs contact us company about wolfram career center all sites resources connect follow contact us work with us student ambassador initiative wolfram for startups student opportunities jobs using wolfram language educational programs for adults summer school winter school educational programs for youth middle school camp high school research program computational adventures read stephen wolfram s writings wolfram blog wolfram tech books wolfram media complex systems educational resources wolfram mathworld wolfram in stem wolfram challenges wolfram problem generator wolfram initiatives wolfram science wolfram foundation history of mathematics project events stephen wolfram livestreams online in person events contact us connect follow for ais wolfram cloud your account user portal enable javascript to interact with content and submit forms on wolfram websites learn how wolfram language system documentation center close molecular structure computation functions applyreaction atom atomcoordinates atomcount atomdiagramcoordinates atomlabels atomlist biomolecule biomoleculealign biomoleculeplot3d biomoleculeq biomoleculevalue bond bondcount bondlabels bondlist bondq chemicalconvert chemicalformula chemicalformulaq chemicalinstance chemicalreaction chemicalreactionq connectedmoleculecomponents connectedmoleculeq edgeform export faceform findcycle findhamiltonianpath findisomers findpath import includearomaticbonds includehydrogens molecule moleculealign moleculecontainsq moleculedraw moleculefreeq moleculegraph moleculematchq moleculemaximumcommonsubstructure moleculemesh moleculemodify moleculename moleculepattern moleculepatternq moleculeplot moleculeplot3d moleculeproperty moleculeq moleculerecognize moleculesubstructure moleculesubstructurecases moleculesubstructurecount moleculesubstructureq moleculevalue nbodysimulation opacity patternreaction patternreactionq periodictableplot plottheme reactionbalance reactionbalancedq rgbcolor serviceconnect serviceexecute stereochemistryelements style valenceerrorhandling functions applyreaction atom atomcoordinates atomcount atomdiagramcoordinates atomlabels atomlist biomolecule biomoleculealign biomoleculeplot3d biomoleculeq biomoleculevalue bond bondcount bondlabels bondlist bondq chemicalconvert chemicalformula chemicalformulaq chemicalinstance chemicalreaction chemicalreactionq connectedmoleculecomponents connectedmoleculeq edgeform export faceform findcycle findhamiltonianpath findisomers findpath import includearomaticbonds includehydrogens molecule moleculealign moleculecontainsq moleculedraw moleculefreeq moleculegraph moleculematchq moleculemaximumcommonsubstructure moleculemesh moleculemodify moleculename moleculepattern moleculepatternq moleculeplot moleculeplot3d moleculeproperty moleculeq moleculerecognize moleculesubstructure moleculesubstructurecases moleculesubstructurecount moleculesubstructureq moleculevalue nbodysimulation opacity patternreaction patternreactionq periodictableplot plottheme reactionbalance reactionbalancedq rgbcolor serviceconnect serviceexecute stereochemistryelements style valenceerrorhandling guide functions applyreaction atom atomcoordinates atomcount atomdiagramcoordinates atomlabels atomlist biomolecule biomoleculealign biomoleculeplot3d biomoleculeq biomoleculevalue bond bondcount bondlabels bondlist bondq chemicalconvert chemicalformula chemicalformulaq chemicalinstance chemicalreaction chemicalreactionq connectedmoleculecomponents connectedmoleculeq edgeform export faceform findcycle findhamiltonianpath findisomers findpath import includearomaticbonds includehydrogens molecule moleculealign moleculecontainsq moleculedraw moleculefreeq moleculegraph moleculematchq moleculemaximumcommonsubstructure moleculemesh moleculemodify moleculename moleculepattern moleculepatternq moleculeplot moleculeplot3d moleculeproperty moleculeq moleculerecognize moleculesubstructure moleculesubstructurecases moleculesubstructurecount moleculesubstructureq moleculevalue nbodysimulation opacity patternreaction patternreactionq periodictableplot plottheme reactionbalance reactionbalancedq rgbcolor serviceconnect serviceexecute stereochemistryelements style valenceerrorhandling functions applyreaction atom atomcoordinates atomcount atomdiagramcoordinates atomlabels atomlist biomolecule biomoleculealign biomoleculeplot3d biomoleculeq biomoleculevalue bond bondcount bondlabels bondlist bondq chemicalconvert chemicalformula chemicalformulaq chemicalinstance chemicalreaction chemicalreactionq connectedmoleculecomponents connectedmoleculeq edgeform export faceform findcycle findhamiltonianpath findisomers findpath import includearomaticbonds includehydrogens molecule moleculealign moleculecontainsq moleculedraw moleculefreeq moleculegraph moleculematchq moleculemaximumcommonsubstructure moleculemesh moleculemodify moleculename moleculepattern moleculepatternq moleculeplot moleculeplot3d moleculeproperty moleculeq moleculerecognize moleculesubstructure moleculesubstructurecases moleculesubstructurecount moleculesubstructureq moleculevalue nbodysimulation opacity patternreaction patternreactionq periodictableplot plottheme reactionbalance reactionbalancedq rgbcolor serviceconnect serviceexecute stereochemistryelements style valenceerrorhandling molecular structure computation topic overview 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 moleculepattern symbolic or smarts pattern representing a molecular substructure 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 biomoleculeq test for a valid bio molecule chemicalformulaq moleculepatternq 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 moleculesubstructurecases give all occurrences of a pattern in a molecule moleculesubstructure symbolic representation of a substructure within a molecule moleculesubstructurecount count occurrences of a molecule substructure moleculemaximumcommonsubstructure identify substructure common to molecules moleculesubstructureq modifying molecules moleculemodify create a new molecule by editing an existing molecule moleculealign align molecules in 3d biomoleculealign align bio 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 chemicalreactionq patternreactionq 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 periodictableplot create a visualization of the periodic table of elements chemical known chemicals and their properties protein mineral food external services serviceconnect serviceexecute connect to external services pubchem chemspider rcsbproteindatabank esmatlas encyclopediaofdomains cathdatabase molecular dynamics nbodysimulation classical n body simulation with arbitrary potentials related links wolfram core areas chemistry give feedback top introduction for programmers introductory book wolfram function repository wolfram data repository wolfram data 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