Python wrapper for jCompoundMapper molecular fingerprints

Python wrapper to ease the calculation of jCompoundMApper molecular fingerprints.

Installation

From source:

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

with pip:

pip install jcompoundmapper-pywrapper

Get started

from jcompoundmapper_pywrapper import JCompoundMapper
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.MolFromSmiles(smiles) for smiles in smiles_list]

jcm = JCompoundMapper()
print(jcm.calculate(mols))

One can use any of the following fingerprints: DFS, ASP, AP2D, AT2D, AP3D, AT3D, CATS2D, CATS3D, PHAP2POINT2D, PHAP3POINT2D, PHAP2POINT3D, PHAP3POINT3D, ECFP, ECFPVariant, LSTAR, SHED, RAD2D, RAD3D or MACCS.

By default, 1024 bits fingerprints are generated, except for the 166 bits MACCS.

jcm = JCompoundMapper('ECFP')
print(jcm.calculate(mols, 2048))

# or

from jCompoundMapper_pywrapper import Fingerprint

jcm = JCompoundMapper(Fingerprint.DFS)
print(jcm.calculate(mols, 2048))

⚠️ Molecules with 3D conformers must be provided to calculate 3D fingerprints (i.e. CATS3D, PHAP2POINT3D, PHAP3POINT3D and RAD3D).

One can specify advanced parameters to the fingerprinter:

from jCompoundMapper_pywrapper import DEFAULT_FP_PARAMETERS

custom_ecfp_params = DEFAULT_FP_PARAMETERS['ECFP']
custom_ecfp_params.depth = 6

jcm = JCompoundMapper('ECFP', custom_ecfp_params)
print(jcm.calculate(mols))

Documentation

def calculate(mols, nbits=1024, show_banner=True, njobs=1, chunksize=1000):

Default method to calculate jCompoundMapper fingerprints.

Parameters:

• mols : Iterable[Chem.Mol]
  RDKit molecule objects for which to obtain jCompoundMapper fingerprints.
• nbits : Union[int, List[int]]
  Size of the fingerprints.
• show_banner : bool
  Displays default notice about jCompoundMapper.
• njobs : int
  Maximum number of simultaneous processes.
• chunksize : int
  Maximum number of molecules each process is in charge of.