Signature-pywrapper 0.0.2

Python wrapper for signature molecular descriptors

Python wrapper for Molecular Signature Descriptors

Python wrapper to ease the calculation of Signature molecular descriptors.

Notice

This work relies on Gilleain Torrance's re-write of Jean-Loup Faulon's signature code for molecules (https://github.com/gilleain/signatures/).

The Signature Molecular Descriptor. 2. Enumerating Molecules from Their Extended Valence Sequences Jean-Loup Faulon, Carla J. Churchwell, and Donald P. Visco Journal of Chemical Information and Computer Sciences 2003 43 (3), 721-734 DOI: 10.1021/ci020346o

Installation

From source:

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

with pip:

pip install Signature-pywrapper

Get started

from Signature_pywrapper import Signature

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]

sig = Signature()
print(sig.calculate(mols, depth=1))

One can also calculate signatures for multiple depths:

print(sig.calculate(mols, depth=[1, 2, 3]))

Documentation

def calculate(mols, show_banner=True, njobs=1, chunksize=100):

Default method to calculate counts of signatures for each vertex of the molecule.

Parameters:

• mols : Iterable[Chem.Mol]
  RDKit molecule objects for which to obtain Signature descriptors.
• depth : Union[int, List[int]]
  Depth of the signatures of vertices.
• show_banner : bool
  Displays default notice about Signature descriptors.
• njobs : int
  Maximum number of simultaneous processes.
• chunksize : int
  Maximum number of molecules each process is charged of.
• return_type : pd.DataFrame
  Pandas DataFrame containing Signature molecular descriptors. If executables have not previously been downloaded, attempts to download and install them.