aromaticity-core

The core of aromaticity. All the functions for existing and future applications.

Usage no npm install needed!

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README

aromaticity-core

npm version

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

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
})