CDK Python wrapper

Python wrapper to ease the calculation of CDK molecular descriptors and fingerprints.

Installation

From source:

git clone https://github.com/OlivierBeq/CDK_pywrapper.git
pip install ./CDK_pywrapper

with pip:

pip install CDK-pywrapper

Get started

from CDK_pywrapper import CDK
from rdkit import Chem

smiles_list = [
  # erlotinib
  "n1cnc(c2cc(c(cc12)OCCOC)OCCOC)Nc1cc(ccc1)C#C",
  # midecamycin
  "CCC(=O)O[C@@H]1CC(=O)O[C@@H](C/C=C/C=C/[C@@H]([C@@H](C[C@@H]([C@@H]([C@H]1OC)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C)O[C@H]3C[C@@]([C@H]([C@@H](O3)C)OC(=O)CC)(C)O)N(C)C)O)CC=O)C)O)C",
  # selenofolate
  "C1=CC(=CC=C1C(=O)NC(CCC(=O)OCC[Se]C#N)C(=O)O)NCC2=CN=C3C(=N2)C(=O)NC(=N3)N",
  # cisplatin
  "N.N.Cl[Pt]Cl"
]
mols = [Chem.AddHs(Chem.MolFromSmiles(smiles)) for smiles in smiles_list]

cdk = CDK()
print(cdk.calculate(mols))

The above calculates 222 molecular descriptors (23 1D and 200 2D).

The additional 65 three-dimensional (3D) descriptors may be obtained with the following: :warning: Molecules are required to have conformers for 3D descriptors to be calculated.

from rdkit.Chem import AllChem

for mol in mols:
    _ = AllChem.EmbedMolecule(mol)

cdk = CDK(ignore_3D=False)
print(cdk.calculate(mols))

To obtain molecular fingerprint, one can used the following:

from CDK_pywrapper import CDK, FPType
cdk = CDK(fingerprint=.PubchemFP)
print(cdk.calculate(mols))

The following fingerprints can be calculated:

Documentation

class CDK(ignore_3D=True, fingerprint=None, nbits=1024, depth=6):

Constructor of a CDK calculator for molecular descriptors or fingerprints

Parameters:

• ignore_3D : bool Should 3D molecular descriptors be calculated (default: False). Ignored if a fingerprint is set.
• fingerprint : FPType
  Type of fingerprint to calculate (default: None). If None, calculate descriptors.
• nbits : int
  Number of bits in the fingerprint.
• depth : int
  Depth of the fingerprint.

Default method to calculate CDK molecular descriptors and fingerprints.

Parameters:

• mols : Iterable[Chem.Mol]
  RDKit molecule objects for which to obtain CDK descriptors.
• show_banner : bool
  Displays default notice about CDK.
• njobs : int
  Maximum number of simultaneous processes.
• chunksize : int
  Maximum number of molecules each process is charged of.