chemical-groups

Chemical groups used in organic chemistry, like Ph, Tips or Ala.

Installation

$ npm install --save chemical-groups

Usage

import { groups, groupsObject, groupsToSequence } from 'chemical-groups';

groups.length;
// 299

groupsObject.Ala;
// {
//   symbol: 'Ala',
//   name: 'Alanine diradical',
//   mf: 'C3H5NO',
//   kind: 'aa',
//   oneLetter: 'A',
//   alternativeOneLetter: 'α',
//   ocl: { value: 'gNyDBaxmqR[fZjZ@', coordinates: '…' },
//   mass: 71.07801959624871,
//   monoisotopicMass: 71.03711378515,
//   unsaturation: 2,
//   elements: [{ symbol: 'C', number: 3 }, …],
// }

groupsToSequence('HOAlaGlyOH');
// 'AG'

The Group, GroupElement, GroupOcl and Kind types are exported as well.

What a group carries

• symbol and name, like Ala and Alanine diradical.
• mf, the molecular formula of the group without its R atoms.
• mass, monoisotopicMass, unsaturation and elements, all computed from mf by mf-parser.
• ocl, the structure as an openchemlib idcode with its 2D coordinates, R attachment points included.
• oneLetter and alternativeOneLetter on the amino acids and the nucleotides, like A and α for Ala.
• kind, the family the group belongs to. See below.
• toVerify, on a group whose structure was generated instead of drawn and still has to be checked by a human.

R, R1, R2 and R3 are the attachment points. They are ordinary openchemlib atoms with their own atomic numbers (154, 142, 143, 144), so they appear in the structure but are excluded from mf. A monoradical uses R, a diradical R1 on the amine side and R2 on the carbonyl side, a triradical adds R3 for the side chain.

The data file

src/groups.ts holds the whole list on a single line of compact JSON, so that editing one group produces a one-group diff instead of a whole-file one. It is listed in the repository .prettierignore and in the eslint globalIgnores for that reason. Never edit it by hand, and never reformat it.

Kinds

kind says which family a group belongs to. The vocabulary is closed — the Kind type and the test suite both hold the list — and a group that is part of no biopolymer, such as a protecting group or a substituent, carries no kind. 50 of the 299 groups carry none.

| Kind | What it is | Groups | | ---------- | ----------------------------------------------- | ------ | | aa | Amino acid residue | 63 | | DNA | Deoxyribonucleoside, no phosphate | 5 | | DNAp | Deoxyribonucleotide monophosphate | 6 | | DNApp | Deoxyribonucleotide diphosphate | 5 | | DNAppp | Deoxyribonucleotide triphosphate | 5 | | RNA | Ribonucleoside, no phosphate | 5 | | RNAp | Ribonucleotide monophosphate | 7 | | RNApp | Ribonucleotide diphosphate | 5 | | RNAppp | Ribonucleotide triphosphate | 5 | | RNApMod | Modified ribonucleotide monophosphate, Modomics | 135 | | RNAppMod | The same as diphosphate: the 5′ caps | 4 | | RNAEnd | A 5′ end that terminates the chain | 4 |

A group of one of the chain kinds carries the R1 and R2 that let it extend a chain, and an RNAEnd carries a single attachment point, so it can only close one. Furp is the exception: it is an RNAp with a single R.

Editing the groups

The groups are edited with the chemical-groups-editor repository, checked out next to the mass-tools one, at ../chemical-groups-editor:

git clone https://github.com/cheminfo/chemical-groups-editor.git
cd chemical-groups-editor
npm install
npm run dev

The editor finds this package as a sibling checkout and reads and writes src/groups.ts directly, keeping the layout of the file untouched. It lists the groups with their structures, offers a structure editor, and reports every group whose structure and formula disagree. It also removes toVerify when you mark a group as checked.

License

MIT