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

Need to add them

I might be missing something, but the substructure and similarity functionality does not seem to be exposed in the current version of RDKitjs (it was accessible in the old version). Do you have plans to add this in the near future?

how to do this python command ?

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?

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

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 ?

The port of the python part is always more difficult ... we need to find a process for pure python code.

Undefined result from MolToBinary

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

We cannot use this version to bind RDKit for the moment.

Mol2BlockToMol