From source:
git clone https://github.com/OlivierBeq/bluedesc_pywrapper.git
pip install ./bluedesc_pywrapper
with pip:
pip install BlueDesc-pywrapperfrom 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).
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))def calculate(mols, show_banner=True, njobs=1, chunksize=1000):Default method to calculate BlueDesc descriptors.
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.
