[](https://opensource.org/licenses/MIT)
# PaDEL Python wrapper
Python wrapper to ease the calculation of [PaDEL molecular descriptors](https://doi.org/10.1002/jcc.21707) and fingerprints.
## Copyright notice
Olivier J. M. Béquignon is **neither** the copyright holder of PaDEL **nor** responsible for it.
The work carried out here concerns
- the Python wrapper,
- the ePaDEL executable,
- the extendedlibpadeldescriptor library.
## Installation
From source:
git clone https://github.com/OlivierBeq/PaDEL_pywrapper.git
pip install ./PaDEL_pywrapper
with pip:
```bash
pip install padel-pywrapper
```
### Get started
#### 1D and 2D descriptors
Descriptors of the module `PaDEL_pywrapper.descriptors` can be computed as follows:
```python
from PaDEL_pywrapper import PaDEL
from PaDEL_pywrapper.descriptor import ALOGP, Crippen, FMF
from rdkit import Chem
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.MolFromSmiles(smiles) for smiles in smiles_list]
descriptors = [ALOGP, Crippen, FMF]
padel = PaDEL(descriptors)
print(padel.calculate(mols))
```
Instances of descriptors can be supplied as well.
```python
descriptors = [ALOGP(), Crippen(), FMF()]
padel = PaDEL(descriptors)
print(padel.calculate(mols))
```
To calculate all possible descriptors, import the `descriptors` list from the module `PaDEL_pywrapper` directly:
```python
from PaDEL_pywrapper import descriptors
padel = PaDEL(descriptors)
print(padel.calculate(mols))
```
#### 3D descriptors
By default, the `ignore_3D` parameter is set to `True`, preventing any provided 3D descriptor to be calculated.
Should molecules with 3D coordinates be provided, one can turn on 3D descriptor calculation.
```python
from rdkit.Chem import AllChem
mols = [Chem.AddHs(mol) for mol in mols]
_ = [AllChem.EmbedMolecule(mol) for mol in mols]
padel = PaDEL(descriptors, ignore_3D=False)
print(padel.calculate(mols))
```
:warning: A warning is raised if molecules lack hydrogens.<br/>
:warning: An exception is raised if molecules do not have 3D coordinates.
```python
mol = Chem.MolFromSmiles('CCC')
padel = PaDEL(descriptors, ignore_3D=False)
print(padel.calculate([mol]))
# ValueError: Cannot calculate descriptors for a conformer-less molecule
```
#### Fingerprints
Fingerprints of the module `PaDEL_pywrapper.descriptors can be computed as follows:
```python
from PaDEL_pywrapper.descriptor import GraphOnlyFP
fp = GraphOnlyFP
padel = PaDEL([fp], ignore_3D=False)
print(padel.calculate(mols))
```
Custom parameter sets can be provided for some fingerprints:
```python
fp = GraphOnlyFP(size=2048, searchDepth=8)
padel = PaDEL([fp], ignore_3D=False)
print(padel.calculate(mols))
```
### Other parameters
```python
class PaDEL:
...
def calculate(self, mols: Iterable[Chem.Mol], show_banner: bool = True, njobs: int = 1, chunksize: int = 100):
```
#### Parameters
- ***mols : Iterable[Chem.Mol]***
RDKit molecule objects for which to obtain PaDEL descriptors.
- ***show_banner : bool***
Displays default notice about PaDEL descriptors.
- ***njobs : int***
Maximum number of simultaneous processes. Ignored if `self.descriptors` are instances and not class names.
- ***chunksize : int***
Maximum number of molecules each process is charged of. Ignored if `self.descriptors` are instances and not class names.
### Details about descriptors
Details about each descriptor and fingerprint can be obtained as follows:
```python
print(ALOGP.description)
print(GraphOnlyFP.description)
```
For full details about all descriptors, one can obtain the path to the original Excel file of the PaDEL descriptors with:
```python
print(padel.details)
```
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"description": "[](https://opensource.org/licenses/MIT)\r\n\r\n# PaDEL Python wrapper\r\n\r\nPython wrapper to ease the calculation of [PaDEL molecular descriptors](https://doi.org/10.1002/jcc.21707) and fingerprints.\r\n\r\n## Copyright notice\r\n\r\nOlivier J. M. B\u00e9quignon is **neither** the copyright holder of PaDEL **nor** responsible for it.\r\n\r\nThe work carried out here concerns\r\n- the Python wrapper, \r\n- the ePaDEL executable,\r\n- the extendedlibpadeldescriptor library. \r\n\r\n## Installation\r\n\r\nFrom source:\r\n\r\n git clone https://github.com/OlivierBeq/PaDEL_pywrapper.git\r\n pip install ./PaDEL_pywrapper\r\n\r\nwith pip:\r\n\r\n```bash\r\npip install padel-pywrapper\r\n```\r\n\r\n### Get started\r\n\r\n#### 1D and 2D descriptors\r\n\r\nDescriptors of the module `PaDEL_pywrapper.descriptors` can be computed as follows:\r\n\r\n```python\r\nfrom PaDEL_pywrapper import PaDEL\r\nfrom PaDEL_pywrapper.descriptor import ALOGP, Crippen, FMF\r\nfrom rdkit import Chem\r\n\r\nsmiles_list = [\r\n # erlotinib\r\n \"n1cnc(c2cc(c(cc12)OCCOC)OCCOC)Nc1cc(ccc1)C#C\",\r\n # midecamycin\r\n \"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\",\r\n # selenofolate\r\n \"C1=CC(=CC=C1C(=O)NC(CCC(=O)OCC[Se]C#N)C(=O)O)NCC2=CN=C3C(=N2)C(=O)NC(=N3)N\",\r\n]\r\nmols = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]\r\n\r\ndescriptors = [ALOGP, Crippen, FMF]\r\n\r\npadel = PaDEL(descriptors)\r\nprint(padel.calculate(mols))\r\n```\r\n\r\nInstances of descriptors can be supplied as well.\r\n\r\n```python\r\ndescriptors = [ALOGP(), Crippen(), FMF()]\r\n\r\npadel = PaDEL(descriptors)\r\nprint(padel.calculate(mols))\r\n```\r\n\r\nTo calculate all possible descriptors, import the `descriptors` list from the module `PaDEL_pywrapper` directly:\r\n\r\n\r\n```python\r\nfrom PaDEL_pywrapper import descriptors\r\n\r\npadel = PaDEL(descriptors)\r\nprint(padel.calculate(mols))\r\n```\r\n\r\n#### 3D descriptors\r\n\r\nBy default, the `ignore_3D` parameter is set to `True`, preventing any provided 3D descriptor to be calculated.\r\n\r\nShould molecules with 3D coordinates be provided, one can turn on 3D descriptor calculation.\r\n\r\n```python\r\nfrom rdkit.Chem import AllChem\r\n\r\nmols = [Chem.AddHs(mol) for mol in mols]\r\n_ = [AllChem.EmbedMolecule(mol) for mol in mols]\r\n\r\npadel = PaDEL(descriptors, ignore_3D=False)\r\nprint(padel.calculate(mols))\r\n```\r\n\r\n:warning: A warning is raised if molecules lack hydrogens.<br/>\r\n:warning: An exception is raised if molecules do not have 3D coordinates.\r\n\r\n```python\r\nmol = Chem.MolFromSmiles('CCC')\r\n\r\npadel = PaDEL(descriptors, ignore_3D=False)\r\nprint(padel.calculate([mol]))\r\n# ValueError: Cannot calculate descriptors for a conformer-less molecule\r\n```\r\n\r\n#### Fingerprints\r\n\r\n\r\nFingerprints of the module `PaDEL_pywrapper.descriptors can be computed as follows:\r\n\r\n```python\r\nfrom PaDEL_pywrapper.descriptor import GraphOnlyFP\r\n\r\nfp = GraphOnlyFP\r\n\r\npadel = PaDEL([fp], ignore_3D=False)\r\nprint(padel.calculate(mols))\r\n```\r\n\r\nCustom parameter sets can be provided for some fingerprints:\r\n\r\n```python\r\nfp = GraphOnlyFP(size=2048, searchDepth=8)\r\n\r\npadel = PaDEL([fp], ignore_3D=False)\r\nprint(padel.calculate(mols))\r\n```\r\n\r\n### Other parameters\r\n\r\n```python\r\nclass PaDEL:\r\n ...\r\n def calculate(self, mols: Iterable[Chem.Mol], show_banner: bool = True, njobs: int = 1, chunksize: int = 100):\r\n```\r\n\r\n#### Parameters\r\n\r\n- ***mols : Iterable[Chem.Mol]*** \r\n RDKit molecule objects for which to obtain PaDEL descriptors.\r\n- ***show_banner : bool*** \r\n Displays default notice about PaDEL descriptors.\r\n- ***njobs : int*** \r\n Maximum number of simultaneous processes. Ignored if `self.descriptors` are instances and not class names.\r\n- ***chunksize : int*** \r\n Maximum number of molecules each process is charged of. Ignored if `self.descriptors` are instances and not class names.\r\n\r\n### Details about descriptors\r\n\r\n\r\nDetails about each descriptor and fingerprint can be obtained as follows:\r\n\r\n```python\r\nprint(ALOGP.description)\r\n\r\nprint(GraphOnlyFP.description)\r\n```\r\n\r\nFor full details about all descriptors, one can obtain the path to the original Excel file of the PaDEL descriptors with:\r\n\r\n```python\r\nprint(padel.details)\r\n```\r\n",
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