"PubChem" (Service Connection)
"PubChem" (Service Connection)
Connecting & Authenticating
ServiceConnect["PubChem"] creates a connection to the PubChem API. If a previously saved connection can be found, it will be used; otherwise, a new authentication request will be launched.
Requests
ServiceExecute["PubChem","request",params] sends a request to the PubChem API, using parameters params. The following give possible requests.
Compound Names
"CompoundDescription" — get the standard name for one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| Method | None | search method | |
| "InterpretEntities" | False | interpret each result as a chemical Entity |
"CompoundSynonyms" — get other names for one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| Method | None | search method |
List of Compound-Related IDs
"CompoundSID" — get a list of all SubstanceIDs associated with one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| "SIDType" | None | "SubstanceID" type to return | |
| Method | None | search method |
"CompoundAID" — get a list of all AssayIDs associated with one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| "AIDType" | None | "AssayID" type to return | |
| Method | None | search method |
"CompoundCID" — get a list of all CompoundIDs associated with one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| "CIDType" | None | "CompoundID" type to return | |
| Method | None | search method |
List of Compound Properties
"CompoundProperties" — returns properties associated with one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| "Property" | None | one or more properties in a List | |
| Method | None | search method |
List of Compound Cross-References
"CompoundCrossReferences" — returns cross-references associated with one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| "CrossReference" | None | one or more cross-references in a List | |
| Method | None | search method |
Compound Image
"CompoundImage" — get a 2D or 3D image of a single compound
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "ImageType" | "2D" | "2D" or "3D" | |
| "ImageSize" | Large | Small or Large |
Compound SDF
"CompoundSDF" — get the SDF of a single compound
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) |
Only one type of identifier can be used as an input.
All Compound Records
"CompoundFullRecords" — get all the records of one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| "RecordType" | "2D" | "2D" or "3D" | |
| Method | None | search method |
Compound Assay Summary
"CompoundAssaySummary" — get the assay summary for one or more compounds
| "CompoundID" | None | integer compound identifier(s) | |
| "SMILES" | None | SMILES string(s) | |
| "Name" | None | compound name(s) or chemical entities | |
| "InChI" | None | InChI compound identifier(s) | |
| "InChIKey" | None | InChIKey compound identifier(s) | |
| "Formula" | None | molecular formula (only valid with "FormulaSearch" Method) | |
| Method | None | search method |
Substance Similar Names
"SubstanceSynonyms" — get other names for one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities |
List of Substance-Related IDs
"SubstanceCID" — get a list of all CompoundIDs associated with one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities | |
| "CIDType" | None | "CompoundID" type to return |
"SubstanceAID" — get a list of all AssayIDs associated with one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities | |
| "AIDType" | None | "AssayID" type to return |
"SubstanceSID" — get a list of all SubstanceIDs associated with one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities | |
| "SIDType" | None | "SubstanceID" type to return |
Substance Image
"SubstanceImage" — get a 2D or 3D image of the substance
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities | |
| "ImageSize" | Large | either Small or Large |
Only one type of identifier can be used as an input.
Substance SDF
"SubstanceSDF" — get the SDF of a single substance
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities |
Only one type of identifier can be used as an input.
All Substance Records
"SubstanceFullRecords" — get all the records of one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities |
List of Substance Cross-References
"SubstanceCrossReferences" — returns cross-references associated with one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities | |
| "CrossReference" | None | one or more cross-references in a List |
Substance Assay Summary
"SubstanceAssaySummary" — get the assay summary for one or more substances
| "SubstanceID" | None | integer substance identifier(s) | |
| "Name" | None | substance name(s) or chemical entities |
Parameter details
Possible values for Method include:
| "Similarity2DSearch" | search by 2D similarity | |
| "Similarity3DSearch" | search by 3D similarity | |
| "SubstructureSearch" | search by substructure | |
| "SuperstructureSearch" | search by superstructure | |
| "FormulaSearch" | search by formula |
Possible search parameters when using "SubstructureSearch" or "SuperstructureSearch" as Method include:
| "MatchIsotopes" | whether atoms must be of the specified isotope | |
| "MatchCharges" | whether atoms must match the specified charge | |
| "MatchTautomers" | whether to allow match to tautomers of the given structure | |
| "RingsNotEmbedded" | whether rings may not be embedded in a larger system | |
| "SingleDoubleBondsMatch" | whether single or double bonds match aromatic bonds | |
| "ChainsMatchRings" | whether chain bonds in the query may match rings in hits | |
| "StripHydrogen" | whether to remove any explicit hydrogens before searching | |
| "Stereo" | how to handle stereo; one of "Ignore", "Exact", "Relative", "Nonconflicting" |
| "Threshold" | minimum Tanimoto score for a hit |
| "AllowOtherElements" | whether to allow other elements to be present in addition to those specified |
| All | all | |
| "Standardized" | standardized | |
| "Component" | component |
| All | all | |
| "Active" | active | |
| "Inactive" | inactive |
| "Original" | original | |
| "Parent" | parent | |
| "Component" | component | |
| "Similar2D" | 2D similarity | |
| "Similar3D" | 3D similarity | |
| "SameStereo" | same stereo | |
| "SameIsotopes" | same isotopes | |
| "SameConnectivity" | same connectivity | |
| "SameTautomer" | same tautomer | |
| "SameParent" | same parent | |
| "SameParentStereo" | same parent stereo | |
| "SameParentIsotopes" | same parent isotopes | |
| "SameParentConnectivity" | same parent connectivity | |
| "SameParentTautomer" | same parent tautomer |
| "MolecularFormula" | molecular formula | |
| "MolecularWeight" | molecular weight | |
| "CanonicalSMILES" | canonical SMILES | |
| "IsomericSMILES" | includes stereo information | |
| "InChI" | standard InChI | |
| "InChIKey" | InChI key | |
| "IUPACName" | IUPAC name | |
| "XLogP" | XLogP | |
| "ExactMass" | exact mass | |
| "MonoisotopicMass" | monoisotopic mass | |
| "TPSA" | topological polar surface area | |
| "Complexity" | complexity | |
| "Charge" | charge | |
| "HBondDonorCount" | hydrogen bond donor count | |
| "HBondAcceptorCount" | hydrogen bond acceptor count | |
| "RotatableBondCount" | rotatable bond count | |
| "HeavyAtomCount" | number of non-hydrogen atoms | |
| "IsotopeAtomCount" | number of atoms with enriched isotope(s) | |
| "AtomStereoCount" | total number of atoms with tetrahedral (sp3) stereo | |
| "DefinedAtomStereoCount" | defined atoms stereo count | |
| "UndefinedAtomStereoCount" | undefined atoms stereo count | |
| "BondStereoCount" | total number of bonds with planar (sp2) stereo | |
| "DefinedBondStereoCount" | defined bond stereo count | |
| "UndefinedBondStereoCount" | undefined bond stereo count | |
| "CovalentUnitCount" | covalent unit count | |
| "Volume3D" | volume 3D | |
| "XStericQuadrupole3D" | X steric quadrupole in 3D | |
| "YStericQuadrupole3D" | Y steric quadrupole in 3D | |
| "ZStericQuadrupole3D" | Z steric quadrupole in 3D | |
| "FeatureCount3D" | total number of 3D features | |
| "FeatureAcceptorCount3D" | number of acceptor 3D features | |
| "FeatureDonorCount3D" | number of donor 3D features | |
| "FeatureAnionCount3D" | number of anion 3D features | |
| "FeatureCationCount3D" | number of cation 3D features | |
| "FeatureRingCount3D" | number of ring 3D features | |
| "FeatureHydrophobeCount3D" | number of hydrophobe 3D features | |
| "ConformerModelRMSD3D" | RMSD of all conformers in the 3D model | |
| "EffectiveRotorCount3D" | number of effective rotors | |
| "ConformerCount3D" | number of conformers in the 3D model | |
| "Fingerprint2D" | 2D fingerprint bits (base64 encoded) |
| "RegistryID" | external registry identifier | |
| "RN" | registry number | |
| "PubMedID" | NCBI PubMed identifier | |
| "MMDBID" | NCBI MMDB identifier | |
| "DBURL" | external database home page URL | |
| "SBURL" | external database substance URL | |
| "ProteinGI" | NCBI protein GI | |
| "NucleotideGI" | NCBI nucleotide GI | |
| "TaxonomyID" | NCBI taxonomy identifier | |
| "MIMID" | NCBI MIM identifier | |
| "GeneID" | NCBI gene identifier | |
| "ProbeID" | NCBI probe identifier | |
| "PatentID" | patent identifier | |
| "SourceName" | external depositor name | |
| "SourceCategory" | depositor category or categories |
| All | all | |
| "Standardized" | standardized | |
| "Component" | component |
| All | all | |
| "Active" | active | |
| "Inactive" | inactive |
| "Original" | original | |
| "SameExact" | exact | |
| "SameStereo" | same stereo | |
| "SameIsotopes" | same isotopes | |
| "SameConnectivity" | same connectivity | |
| "SameTautomer" | same tautomer | |
| "SameParent" | same parent | |
| "SameParentStereo" | same parent stereo | |
| "SameParentIsotopes" | same parent isotopes | |
| "SameParentConnectivity" | same parent connectivity | |
| "SameParentTautomer" | same parent tautomer |