BlueDesc-pywrapper 0.0.4

Python wrapper for BlueDesc molecular descriptors

Python wrapper for BlueDesc molecular descriptors

Installation

From source:

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

with pip:

pip install BlueDesc-pywrapper

Get started

from BlueDesc_pywrapper import BlueDesc
from rdkit import Chem
from rdkit.Chem import AllChem

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",
]
mols = [Chem.AddHs(Chem.MolFromSmiles(smiles)) for smiles in smiles_list]
for mol in mols:
    _ = AllChem.EmbedMolecule(mol)

bluedesc = BlueDesc()
print(bluedesc.calculate(mols))

The above calculates 118 molecular descriptors (33 1D and 85 2D).
:warning: BlueDesc skips molecules it cannot parse internally, a warning is given when that is the case. The following command is recommended, should this occur, to prevent the unalignment of input and output indices.

bluedesc.calculate(mols, chunksize=1, njobs=-1)

The additional 56 three-dimensional (3D) descriptors may be computed like so: :warning: Molecules are required to have conformers for 3D descriptors to be calculated.

bluedesc = BlueDesc(ignore_3D=False)
print(bluedesc.calculate(mols))

Documentation

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

Default method to calculate BlueDesc fingerprints.

Parameters:

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