README

Cheminformatics for PHP, powered by RDKit

Installation

Run:

composer require ankane/rdkit

Add scripts to composer.json to download the shared library:

    "scripts": {
        "post-install-cmd": "RDKit\\Vendor::check",
        "post-update-cmd": "RDKit\\Vendor::check"
    }

And run:

composer install

Getting Started

Create a molecule

use RDKit\Molecule;

$mol = Molecule::fromSmiles('c1ccccc1O');

Get the number of atoms

$mol->numAtoms();

Get substructure matches

$mol->match(Molecule::fromSmarts('ccO'));

Get fragments

$mol->fragments();

Generate an SVG

$mol->toSvg();

Fingerprints

A number of fingerprints are supported.

RDKit

$mol->rdkitFingerprint();

Morgan

$mol->morganFingerprint();

Pattern

$mol->patternFingerprint();

Atom pair

$mol->atomPairFingerprint();

Topological torsion

$mol->topologicalTorsionFingerprint();

MACCS

$mol->maccsFingerprint();

You can use a library like pgvector-php to find similar molecules. See an example.

Updates

Add or remove hydrogen atoms

$mol->addHs();
$mol->removeHs();

Standardize

$mol->cleanup();
$mol->normalize();
$mol->neutralize();
$mol->reionize();
$mol->canonicalTautomer();
$mol->chargeParent();
$mol->fragmentParent();

Conversion

SMILES

$mol->toSmiles();

SMARTS

$mol->toSmarts();

CXSMILES

$mol->toCXSmiles();

CXSMARTS

$mol->toCXSmarts();

JSON

$mol->toJson();

Reactions

Create a reaction

use RDKit\Reaction;

$rxn = Reaction::fromSmarts('[CH3:1][OH:2]>>[CH2:1]=[OH0:2]');

Generate an SVG

$rxn->toSvg();

History

View the changelog

Contributing

Everyone is encouraged to help improve this project. Here are a few ways you can help:

• Report bugs
• Fix bugs and submit pull requests
• Write, clarify, or fix documentation
• Suggest or add new features

To get started with development:

git clone https://github.com/ankane/rdkit-php.git
cd rdkit-php
composer install
composer test