mordred-ojmb 1.2.2

molecular descriptor calculator

molecular descriptor calculator.

number of descriptors

>>> from mordred import Calculator, descriptors
>>> n_all = len(Calculator(descriptors, ignore_3D=False).descriptors)
>>> n_2D = len(Calculator(descriptors, ignore_3D=True).descriptors)
>>> print("2D:    {:5}\n3D:    {:5}\n------------\ntotal: {:5}".format(n_2D, n_all - n_2D, n_all))
2D:     1613
3D:      213
------------
total:  1826

Installation

pip

1. install mordred

pip install https://github.com/OlivierBeq/mordred/tarball/master

Testing the installation

python -m mordred.tests

Python examples

>>> from rdkit import Chem
>>> from mordred import Calculator, descriptors

# create descriptor calculator with all descriptors
>>> calc = Calculator(descriptors, ignore_3D=True)

>>> len(calc.descriptors)
1613

>>> len(Calculator(descriptors, ignore_3D=True, version="1.0.0"))
1612

# calculate single molecule
>>> mol = Chem.MolFromSmiles('c1ccccc1')
>>> calc(mol)[:3]
[4.242640687119286, 3.9999999999999996, 0]

# calculate multiple molecule
>>> mols = [Chem.MolFromSmiles(smi) for smi in ['c1ccccc1Cl', 'c1ccccc1O', 'c1ccccc1N']]

# as pandas
>>> df = calc.pandas(mols)
>>> df['SLogP']
0    2.3400
1    1.3922
2    1.2688
Name: SLogP, dtype: float64

see examples

Citation

Moriwaki H, Tian Y-S, Kawashita N, Takagi T (2018) Mordred: a molecular descriptor calculator. Journal of Cheminformatics 10:4 . doi: 10.1186/s13321-018-0258-y

Documentation

• master

• develop

• v1.1.0

• v1.0.0