Mold2-pywrapper 0.0.4

Python wrapper for Mold2 descriptors

Mold² Python wrapper

Python wrapper to ease the calculation of Mold2 molecular descriptors.

Copyright notice

Mold2 is a product designed and produced by the National Center for Toxicological Research (NCTR).
FDA and NCTR retain ownership of this product.

Olivier J. M. Béquignon is neither the copyright holder of Mold2 nor responsible for it.

Only the Python wrapper is the work of Olivier J. M. Béquignon.

Installation

From source:

git clone https://github.com/OlivierBeq/Mold2_pywrapper.git
pip install ./Mold2_pywrapper

with pip:

pip install mold2-pywrapper

Get started

from Mold2_pywrapper import Mold2

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]

mold2 = Mold2()
print(mold2.calculate(mols))

Instantiating a Mold2 object ensures that the executables for your platform are accessible. If this is not the case, an attempt to download them from the website of the FDA is made.

Should one have downloaded the original ZIP file available from the website of the FDA, the executables can be installed using the following:

path_to_zipfile = '...'  # Replace by the path to the ZIP file on your machine
mold2 = Mold2.from_executable(path_to_zipfile)
print(mold2.calculate(mols))

Executables will be installed for future use. From then on, default instanciation may be carried out:

mold2 = Mold2()
print(mold2.calculate(mols))

Details about descriptors

Any detail about the 777 Mold2 descriptors can be obtained either for a single descriptor, by providing its index:

print(mold2.descriptor_detail(15))
# rotatable bond fraction

Or for all at once:

print(mold2.descriptor_details())
# {"D001": "number of 6-membered aromatic rings (only carbon atoms)",
#  "D002": "number of 03-membered rings",
#  ...
#  }

Documentation

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

Default method to calculate #### Parameters

• mols : Iterable[Chem.Mol]
  RDKit molecule objects for which to obtain Mold2 descriptors.
• show_banner : bool
  Displays default notice about Mold2 descriptors.
• njobs : int
  Maximum number of simultaneous processes.
• chunksize : int
  Maximum number of molecules each process is charged of.
• return_type : pd.DataFramce
  Pandas DataFrame containing Mold2 molecular descriptors.Mold2 descriptors. If executables have not previously been downloaded, attempts to download and install them.

---

def descriptor_detail(index):

Obtain detils about one descriptor.

Parameters

• index : int
  Index of the descriptor.
• return_type : str
  Description of the descriptor.

---

def descriptor_details():

Obtain details about all descriptors.

Parameters

• return_type : dict
  Mapping of molecular descriptors with their details.

---

def from_executable(zipfile_path):

Install executables and instantiate a Mold2 calculator.

Parameters

• zipfile_path : str
  Path to the user-downloaded ZIP file containing Mold2 executables.