[](https://opensource.org/licenses/MIT)
# Python wrapper for jCompoundMapper molecular fingerprints
Python wrapper to ease the calculation of jCompoundMApper molecular fingerprints.
## Installation
From source:
git clone https://github.com/OlivierBeq/jcompoundmapper_pywrapper.git
pip install ./jcompoundmapper_pywrapper
with pip:
```bash
pip install jcompoundmapper-pywrapper
```
### Get started
```python
from jcompoundmapper_pywrapper import JCompoundMapper
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",
# cisplatin
"N.N.Cl[Pt]Cl"
]
mols = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
jcm = JCompoundMapper()
print(jcm.calculate(mols))
```
One can use any of the following fingerprints: DFS, ASP, AP2D, AT2D, AP3D, AT3D, CATS2D, CATS3D, PHAP2POINT2D, PHAP3POINT2D, PHAP2POINT3D, PHAP3POINT3D,
ECFP, ECFPVariant, LSTAR, SHED, RAD2D, RAD3D or MACCS.
By default, 1024 bits fingerprints are generated, except for the 166 bits MACCS.
```python
jcm = JCompoundMapper('ECFP')
print(jcm.calculate(mols, 2048))
# or
from jCompoundMapper_pywrapper import Fingerprint
jcm = JCompoundMapper(Fingerprint.DFS)
print(jcm.calculate(mols, 2048))
```
:warning: Molecules with 3D conformers must be provided to calculate 3D fingerprints (i.e. CATS3D, PHAP2POINT3D, PHAP3POINT3D and RAD3D).
One can specify advanced parameters to the fingerprinter:
```python
from jCompoundMapper_pywrapper import DEFAULT_FP_PARAMETERS
custom_ecfp_params = DEFAULT_FP_PARAMETERS['ECFP']
custom_ecfp_params.depth = 6
jcm = JCompoundMapper('ECFP', custom_ecfp_params)
print(jcm.calculate(mols))
```
## Documentation
```python
def calculate(mols, nbits=1024, show_banner=True, njobs=1, chunksize=1000):
```
Default method to calculate jCompoundMapper fingerprints.
Parameters:
- ***mols : Iterable[Chem.Mol]***
RDKit molecule objects for which to obtain jCompoundMapper fingerprints.
- ***nbits : Union[int, List[int]]***
Size of the fingerprints.
- ***show_banner : bool***
Displays default notice about jCompoundMapper.
- ***njobs : int***
Maximum number of simultaneous processes.
- ***chunksize : int***
Maximum number of molecules each process is in charge of.
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"description": "[](https://opensource.org/licenses/MIT)\r\n\r\n# Python wrapper for jCompoundMapper molecular fingerprints\r\n\r\nPython wrapper to ease the calculation of jCompoundMApper molecular fingerprints.\r\n\r\n## Installation\r\n\r\nFrom source:\r\n\r\n git clone https://github.com/OlivierBeq/jcompoundmapper_pywrapper.git\r\n pip install ./jcompoundmapper_pywrapper\r\n\r\nwith pip:\r\n\r\n```bash\r\npip install jcompoundmapper-pywrapper\r\n```\r\n\r\n### Get started\r\n\r\n```python\r\nfrom jcompoundmapper_pywrapper import JCompoundMapper\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 # cisplatin\r\n \"N.N.Cl[Pt]Cl\"\r\n]\r\nmols = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]\r\n\r\njcm = JCompoundMapper()\r\nprint(jcm.calculate(mols))\r\n```\r\n\r\nOne can use any of the following fingerprints: DFS, ASP, AP2D, AT2D, AP3D, AT3D, CATS2D, CATS3D, PHAP2POINT2D, PHAP3POINT2D, PHAP2POINT3D, PHAP3POINT3D,\r\nECFP, ECFPVariant, LSTAR, SHED, RAD2D, RAD3D or MACCS.\r\n\r\nBy default, 1024 bits fingerprints are generated, except for the 166 bits MACCS.\r\n\r\n```python\r\njcm = JCompoundMapper('ECFP')\r\nprint(jcm.calculate(mols, 2048))\r\n\r\n# or\r\n\r\nfrom jCompoundMapper_pywrapper import Fingerprint\r\n\r\njcm = JCompoundMapper(Fingerprint.DFS)\r\nprint(jcm.calculate(mols, 2048))\r\n```\r\n\r\n:warning: Molecules with 3D conformers must be provided to calculate 3D fingerprints (i.e. CATS3D, PHAP2POINT3D, PHAP3POINT3D and RAD3D).\r\n\r\nOne can specify advanced parameters to the fingerprinter:\r\n\r\n```python\r\nfrom jCompoundMapper_pywrapper import DEFAULT_FP_PARAMETERS\r\n\r\ncustom_ecfp_params = DEFAULT_FP_PARAMETERS['ECFP']\r\ncustom_ecfp_params.depth = 6\r\n\r\njcm = JCompoundMapper('ECFP', custom_ecfp_params)\r\nprint(jcm.calculate(mols))\r\n```\r\n## Documentation\r\n\r\n```python\r\ndef calculate(mols, nbits=1024, show_banner=True, njobs=1, chunksize=1000):\r\n```\r\n\r\nDefault method to calculate jCompoundMapper fingerprints.\r\n\r\nParameters:\r\n\r\n- ***mols : Iterable[Chem.Mol]*** \r\n RDKit molecule objects for which to obtain jCompoundMapper fingerprints.\r\n- ***nbits : Union[int, List[int]]*** \r\n Size of the fingerprints.\r\n- ***show_banner : bool*** \r\n Displays default notice about jCompoundMapper.\r\n- ***njobs : int*** \r\n Maximum number of simultaneous processes.\r\n- ***chunksize : int*** \r\n Maximum number of molecules each process is in charge of.\r\n",
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