Introduction¶
mordred¶
molecular descriptor calculator.
Installation¶
conda(recommended)¶
install conda
install mordred
$ conda install -c rdkit -c mordred-descriptor mordred
examples¶
as command¶
usage: python -m mordred [-h] [--version] [-t {auto,sdf,mol,smi}] [-o OUTPUT]
[-p PROCESSES] [-q] [-s] [-d DESC] [-3] [-v]
INPUT [INPUT ...]
positional arguments:
INPUT
optional arguments:
-h, --help show this help message and exit
--version input molecular file
-t {auto,sdf,mol,smi}, --type {auto,sdf,mol,smi}
input filetype (default: auto)
-o OUTPUT, --output OUTPUT
output file path (default: stdout)
-p PROCESSES, --processes PROCESSES
number of processes (default: number of logical
processors)
-q, --quiet hide progress bar
-s, --stream stream read
-d DESC, --descriptor DESC
descriptors to calculate (default: all)
-3, --3D use 3D descriptors (require sdf or mol file)
-v, --verbosity verbosity
descriptors: ABCIndex AcidBase AdjacencyMatrix Aromatic AtomCount
Autocorrelation Autocorrelation3D BalabanJ BaryszMatrix BCUT BertzCT BondCount
CarbonTypes Chi Constitutional CPSA DetourMatrix DistanceMatrix
EccentricConnectivityIndex EState ExtendedTopochemicalAtom FragmentComplexity
Framework GeometricalIndex GravitationalIndex HydrogenBond InformationContent
KappaShapeIndex Lipinski McGowanVolume MoeType MolecularDistanceEdge
MolecularId MomentOfInertia MoRSE PathCount Polarizability RingCount
RotatableBond SLogP TopologicalCharge TopologicalIndex TopoPSA VdwVolumeABC
as library¶
>>> from rdkit import Chem
>>> from mordred import Calculator, all_descriptors
# create descriptor calculator with all descriptors
>>> calc = Calculator(all_descriptors(), exclude3D=True)
>>> len(calc.descriptors)
1824
# 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