aromaticity-core

The core of aromaticity.

Use that library to compute Molecule Properties and query PubChem.

For more information visit: https://aromaticity.io/core.

Docs

• Compute Molecule Properties
  • Constructor
  • Molecule Properties
  • Molfile
• Query PubChem
  • Query
  • Fetched Properties
• Examples

Compute Molecule Properties

Constructor

new Molecule(SMILES: string)

Molecule Properties

|Properties|Description| |---|---| |acceptor: number|Returns the Acceptor Number.| |averageBondLength(nonHydrogenBondsOnly: boolean = false): number|Returns the Average Bond Length.| |bonds: number|Returns the Bonds Number.| |donor: number|Returns the Donor Number.| |formula(isHTML: boolean = false): string|Returns the Molecular Formula.| |IUPACName(cb: Function): void|Get the IUPAC Name and pass it to a callback function.| |logP: number|Returns the LogP.| |logS: number|Returns the LogS.| |polarSurfaceArea: number|Returns the Polar Surface Area.| |rotatableBonds: number|Return the Rotatable Bonds Number.| |stereoCenters: number|Returns the Stereo Centers Number.| |SVG(width: number = 400, height: number = 400): string|Returns the SVG.| |weight: number|Returns the Molecular Weight.| |toMolfile(isV2000: boolean = false): string|Return the MolFile.| |toSMILES(): string|Returns the SMILES.|

Molfile

|Function|Description| |---|---| |molFileToMol(Molfile: string): Molecule|Returns Molecule from Molfile.| |molFileToSmiles(Molfile: string): string|Returns SMILES from Molfile.|

Query PubChem

Query

PubChem(smiles: string, PropertiesToFetch: Property[]|Property, cb: Function)

Fetched Properties

From PubChem you can fetch the following properties:

|Property|Description| |---|---| |MolecularFormula|Molecular formula.| |MolecularWeight|The molecular weight is the sum of all atomic weights of the constituent atoms in a compound, measured in g/mol. In the absence of explicit isotope labelling, averaged natural abundance is assumed. If an atom bears an explicit isotope label, 100% isotopic purity is assumed at this location.| |CanonicalSMILES|Canonical SMILES (Simplified Molecular Input Line Entry System) string. It is a unique SMILES string of a compound, generated by a “canonicalization” algorithm.| |IsomericSMILES|Isomeric SMILES string. It is a SMILES string with stereochemical and isotopic specifications.| |InChl|Standard IUPAC International Chemical Identifier (InChI). It does not allow for user selectable options in dealing with the stereochemistry and tautomer layers of the InChI string.| |InChIKey|Hashed version of the full standard InChI, consisting of 27 characters.| |IUPACName|Chemical name systematically determined according to the IUPAC nomenclatures.| |XLogP|Computationally generated octanol-water partition coefficient or distribution coefficient. XLogP is used as a measure of hydrophilicity or hydrophobicity of a molecule.| |ExactMass|The mass of the most likely isotopic composition for a single molecule, corresponding to the most intense ion/molecule peak in a mass spectrum.| |MonoisotopicMass|The mass of a molecule, calculated using the mass of the most abundant isotope of each element.| |TPSA|Topological polar surface area, computed by the algorithm described in the paper by Ertl et al.| |Complexity|The molecular complexity rating of a compound, computed using the Bertz/Hendrickson/Ihlenfeldt formula.| |Charge|The total (or net) charge of a molecule.| |HBondDonorCount|Number of hydrogen-bond donors in the structure.| |HBondAcceptorCount|Number of hydrogen-bond acceptors in the structure.| |rotatableBondCount|Number of rotatable bonds.| |HeavyAtomCount|Number of non-hydrogen atoms.| |IsotopeAtomCount|Number of atoms with enriched isotope(s)| |AtomStereoCount|Total number of atoms with tetrahedral (sp3) stereo [e.g., (R)- or (S)-configuration]| |DefinedAtomStereoCount|Number of atoms with defined tetrahedral (sp3) stereo.| |UndefinedAtomStereoCount|Number of atoms with undefined tetrahedral (sp3) stereo.| |BondStereoCount|Total number of bonds with planar (sp2) stereo [e.g., (E)- or (Z)-configuration].| |DefinedBondStereoCount|Number of atoms with defined planar (sp2) stereo.| |UndefinedBondStereoCount|Number of atoms with undefined planar (sp2) stereo.| |CovalentUnitCount|Number of covalently bound units.| |Volume3D|Analytic volume of the first diverse conformer (default conformer) for a compound.| |XStericQuadrupole3D|The x component of the quadrupole moment (Qx) of the first diverse conformer (default conformer) for a compound.| |YStericQuadrupole3D|The y component of the quadrupole moment (Qy) of the first diverse conformer (default conformer) for a compound.| |ZStericQuadrupole3D|The z component of the quadrupole moment (Qz) of the first diverse conformer (default conformer) for a compound.| |FeatureCount3D|Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)| |FeatureAcceptorCount3D|Number of hydrogen-bond acceptors of a conformer.| |FeatureDonorCount3D|Number of hydrogen-bond donors of a conformer.| |FeatureAnionCount3D|Number of anionic centers (at pH 7) of a conformer.| |FeatureCationCount3D|Number of cationic centers (at pH 7) of a conformer. | |FeatureRingCount3D|Number of rings of a conformer.| |FeatureHydrophobeCount3D|Number of hydrophobes of a conformer.| |ConformerModelRMSD3D|Conformer sampling RMSD in Å.| |EffectiveRotorCount3D|Total number of 3D features (the sum of FeatureAcceptorCount3D, FeatureDonorCount3D, FeatureAnionCount3D, FeatureCationCount3D, FeatureRingCount3D and FeatureHydrophobeCount3D)| |ConformerCount3D|The number of conformers in the conformer model for a compound.| |Fingerprint2D|Base64-encoded PubChem Substructure Fingerprint of a molecule.|

Examples

import { Molecule } from 'aromaticity-core';

let mol = new Molecule('CCCO');

mol.IUPACName((name) => {
    console.log(name);  // propan-1-ol
})

console.log(mol.weight);    // 60

console.log(mol.formula())  // C3H8O

import { PubChem, Property } from 'aromaticity-core';

PubChem('CCC', [Property.MolecularFormula, Property.Complexity], (res) => {
    console.log(res);   // { CID: 6334, MolecularFormula: 'C3H8', Complexity: 0 }
})

PubChem('[Ca++]', Property.Charge, (res) => {
    console.log(res);   // 2
})