# aromaticity-core

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

Latest version **1.6.5** (published 2020-10-25) · GPL-3.0 license · 0 weekly downloads

## Install

```sh
npm install aromaticity-core
pnpm add aromaticity-core
yarn add aromaticity-core
bun add aromaticity-core
```

## Health

**Score 25/100 (F)** — status: abandoned.

Positive: has types; no vulnerabilities; high quality score.

Warnings: low downloads; no esm support.

Negative: abandoned; low maintenance score.

## Facts

| | |
|---|---|
| Version | 1.6.5 |
| Published | 2020-10-25 |
| First published | 2020-09-15 |
| Weekly downloads | 0 |
| License | GPL-3.0 |
| TypeScript types | bundled |
| Module format | CommonJS |
| Dependencies | 3 |
| Unpacked size | 68 KB |
| Known vulnerabilities | 0 (+25 in 1 direct dependencies) |
| Install scripts | no |
| GitHub stars | 2 |
| Author | Giulio De Matteis |
| Maintainers | themagiulio |

## Links

- npm: https://www.npmjs.com/package/aromaticity-core
- Repository: https://github.com/aromaticity/aromaticity-core
- Homepage: https://aromaticity.io
- Issues: https://github.com/aromaticity/aromaticity-core/issues
- npm.io page: https://npm.io/package/aromaticity-core

## Dependencies (3)

- [axios](https://npm.io/package/axios.md) ^0.20.0
- [openchemlib](https://npm.io/package/openchemlib.md) ^7.2.3
- [@types/fs-extra](https://npm.io/package/@types/fs-extra.md) ^9.0.2

## Recent versions

- 1.6.5 (latest) — 2020-10-25
- 1.6.4 — 2020-10-25
- 1.6.3 — 2020-10-25
- 1.6.2 — 2020-10-25
- 1.6.1 — 2020-10-25
- 1.6.0 — 2020-10-16
- 1.5.0 — 2020-10-06
- 1.0.8 — 2020-10-04
- 1.0.7 — 2020-10-04
- 1.0.6 — 2020-09-23
- 1.0.5 — 2020-09-16
- 1.0.4 — 2020-09-16
- 1.0.3 — 2020-09-16
- 1.0.2 — 2020-09-15
- 1.0.0 — 2020-09-15

## README

# aromaticity-core

[![npm version](https://badge.fury.io/js/aromaticity-core.svg)](https://badge.fury.io/js/aromaticity-core)

The core of aromaticity.

Use that library to compute Molecule Properties and query PubChem.

For more information visit: <a href="https://aromaticity.io/core">https://aromaticity.io/core</a>.


## Docs
- <a href="#compute-molecule-properties">Compute Molecule Properties</a>
    - <a href="#constructor">Constructor</a>
    - <a href="#molecule-properties">Molecule Properties</a>
    - <a href="#molfile">Molfile</a>
- <a href="#query-pubchem">Query PubChem</a>
    - <a href="#query">Query</a>
    - <a href="#fetched-properties">Fetched Properties</a>
- <a href="#examples">Examples</a>


## 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
})
```

---
_Source: https://npm.io/package/aromaticity-core · Machine-readable twin of the npm.io package page. Health data is recomputed on every publish._