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License: BSD 3-Clause "New" or "Revised" License

CMake 1.65% JavaScript 31.49% C++ 8.77% HTML 41.44% Shell 0.13% Makefile 1.23% Python 0.41% CSS 3.00% TeX 11.87%

rdkitjs-legacy's Introduction

RDKit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

BSD license - a business friendly license for open source
Core data structures and algorithms in C++
Python 3.x wrapper generated using Boost.Python
Java and C# wrappers generated with SWIG
2D and 3D molecular operations
Descriptor and Fingerprint generation for machine learning
Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
Cheminformatics nodes for KNIME
Contrib folder with useful community-contributed software harnessing the power of the RDKit

Community

Code

GitHub code and bug tracker

Web presence

Materials from user group meetings

Documentation

Available on the RDKit page and in the Docs folder on GitHub

Installation

Installation instructions are available in Docs/Book/Install.md.

Binary distributions, anaconda, homebrew

binaries for conda python or, if you are using the conda-forge stack, the RDKit is also available from conda-forge.
RPMs for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
debs for Ubuntu and other Debian-derived Linux distros. Contributed by the Debichem team.
homebrew formula for building on the Mac. Contributed by Eddie Cao.
recipes for building using the excellent conda package manager. Contributed by Riccardo Vianello.
APKs for Alpine Linux. Contributed by da Verona
Wheels at PyPi for all major platforms and python versions. Contributed by Christopher Kuenneth

Projects using RDKit

ROBERT - Automated Machine Learning Protocols
AQME - Automated Quantum Mechanical Environment
chemprop - message passing neural networks for molecular property prediction
RMG - Reaction Mechanism Generator
RDMC - Reaction Data and Molecular Conformers - package for dealing with reactions, molecules, conformers, mainly in 3D
pychemprojections - python library for visualizing various 2D projections of molecules.
pychemovality - python library for estimating the ovality of molecules.
ChEMBL Structure Pipeline - ChEMBL protocols used to standardise and salt strip molecules.
FPSim2 - Simple package for fast molecular similarity searches.
Datamol (docs, repo) - A Python library to intuitively manipulate molecules.
Scopy (docs, paper) - an integrated negative design Python library for desirable HTS/VS database design
stk (docs, paper) - a Python library for building, manipulating, analyzing and automatic design of molecules.
gpusimilarity - A Cuda/Thrust implementation of fingerprint similarity searching
Samson Connect - Software for adaptive modeling and simulation of nanosystems
mol_frame - Chemical Structure Handling for Dask and Pandas DataFrames
RDKit.js - The official JavaScript release of RDKit
DeepChem - python library for deep learning for chemistry
mmpdb - Matched molecular pair database generation and analysis
CheTo (paper)- Chemical topic modeling
OCEAN (paper)- Optimized cross reactivity estimation
ChEMBL Beaker - standalone web server wrapper for RDKit and OSRA
ZINC - Free database of commercially-available compounds for virtual screening
sdf_viewer.py - an interactive SDF viewer
sdf2ppt - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation.
MolGears - A cheminformatics tool for bioactive molecules
PYPL - Simple cartridge that lets you call Python scripts from Oracle PL/SQL.
shape-it-rdkit - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend
WONKA - Tool for analysis and interrogation of protein-ligand crystal structures
OOMMPPAA - Tool for directed synthesis and data analysis based on protein-ligand crystal structures
OCEAN - web-tool for target-prediction of chemical structures which uses ChEMBL as datasource
chemfp - very fast fingerprint searching
rdkit_ipynb_tools - RDKit Tools for the IPython Notebook
Vernalis KNIME nodes
Erlwood KNIME nodes
AZOrange

License

Code released under the BSD license.

rdkitjs-legacy's People

Contributors

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Forkers

gmrandazzo ptosco yccai pgrinaway mengwuxiao ruska612 harryjubb bmiles greglandrum lakshmananan prakashrathi dot23

rdkitjs-legacy's Issues

Compilation test pickle failed with RDKit 2018.09.1

after adding in compiler.js
'libRDKitDepictor.so',
'libRDKitcoordgenlib.so',
'libRDKitmaeparser.so',

and changing deps to 2018.09.1 there is an issue with pickle testcase:

FAIL tests/rdchem/pickle.js
● Console

console.log __tests__/rdchem/pickle.js:10
  mol from Smiles
console.log __tests__/rdchem/pickle.js:12
  toPickle
console.log __tests__/rdchem/pickle.js:15
  type of toPickle
console.log lib/Mol.js:52
  fromPickle
console.log lib/Mol.js:53

● from and to pickle

Error
  6070248 thrown

Cannot import the module with require('rdkit')

I wanted to test the library (would be really cool to have RDKit in the browser!), but unfortunately was unable to get it to work. I am using what I assume is the latest version (0.5.1) from npm.

When I execute the following code:

const RDKit = require('rdkit'); // using 'rdkit' because 'RDKit' from the README did not work for me

I am getting the following error:

TypeError: rdkit.wast is not a valid URL.

Callstack:

locateFile rdkit.js:21
    integrateWasmJS rdkit.js:63
    rdk rdkit.js:63
    js rdkit.js:77
    __WEBPACK_AMD_DEFINE_RESULT__ rdkit.js:52
    js rdkit.js:53
    js rdkit.js:59
    js 1.chunk.js:289967
    Webpack 28

Relevant code bit:

  18 | var path = getCurrentPathBrowser();
  19 | var Module = {
  20 |   locateFile(url) {
> 21 |     return new URL(url, path).href;
     | ^  22 |   },
  23 |   onRuntimeInitialized() {
  24 |     resolve();

Any idea? Thanks!

Smiles can be converted to mol files

Proposed API

var molecule=RDK.Molecule.fromSmiles();
var molecule=RDK.Molecule.fromMolfile();
var smiles=molecule.toSmiles();
var molfile=molecule.toMolfile(v3000);

by default: v2000, v3000 true / false

var logP=RDK.Descriptors.logP(molecule);

Fingerprints ?
Minimisation ?

TypeError: bindings.SmilesToMol is not a function

Error below when executing script in command line:

/Users/ben/node_modules/RDKit/lib/Mol.js:183
        bindings.SmilesToMol(
                 ^

TypeError: bindings.SmilesToMol is not a function
    at Function.fromSmiles (/Users/ben/node_modules/RDKit/lib/Mol.js:183:18)
    at atoms (/Users/ben/Documents/dev/comp_chem/rdkitjs/application.js:6:23)
    at Object.<anonymous> (/Users/ben/Documents/dev/comp_chem/rdkitjs/application.js:13:1)
    at Module._compile (internal/modules/cjs/loader.js:689:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:700:10)
    at Module.load (internal/modules/cjs/loader.js:599:32)
    at tryModuleLoad (internal/modules/cjs/loader.js:538:12)
    at Function.Module._load (internal/modules/cjs/loader.js:530:3)
    at Function.Module.runMain (internal/modules/cjs/loader.js:742:12)
    at startup (internal/bootstrap/node.js:283:19)

Script below launched in the terminal with node js node application.js

// applications.js
const RDKit = require('RDKit');
var my_mol = "COc1ccc(CCN(C(=O)CCCBr)C2c3cc(NC(C)=O)c([N+](=O)[O-])cc3OC(C)(C)C2O)cc1";

function atoms(smi) {
  var mol = RDKit.Mol.fromSmiles(smi);
  var num_atoms = mol.getNumAtoms();
  console.log( num_atoms );
}

atoms(my_mol)

If I open up a node js REPL and copy and paste in the script it works just fine. Any idea where this bindings.SmilesToMol( issue is arising?

cannot create molecule from pickle

implementation of molfrompickle done but issue to convert the moltobinary back to molecule using this function. 4879a12

we try to reproduce this python code

The RDKit pickle format is fairly compact and it is much, much faster to build a molecule from a pickle than from a Mol file or SMILES string, so storing molecules you will be working with repeatedly as pickles can be a good idea.

The raw binary data that is encapsulated in a pickle can also be directly obtained from a molecule:

binStr = m.ToBinary()
This can be used to reconstruct molecules using the Chem.Mol constructor:

m2 = Chem.Mol(binStr)
Chem.MolToSmiles(m2)
'c1ccncc1'
len(binStr)
123
len(pkl)
475