1.6.5 • Published 4 years ago
aromaticity-core v1.6.5
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()) // C3H8Oimport { 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
})