chem-templates 0.0.7

A python library for controlling chemical space

chem_templates

chem_templates provides an expressive and flexible way of defining desired chemical spaces

See the documentation for documentation and tutorials

Install

pip install chem_templates

Basic Usage

For more detail on the API, see the basic tutorial

from rdkit.Chem import rdMolDescriptors, Descriptors
from chem_templates.filter import RangeFunctionFilter, Template
from chem_templates.chem import Molecule

def hbd(molecule):
    return rdMolDescriptors.CalcNumHBD(molecule.mol)

def hba(molecule):
    return rdMolDescriptors.CalcNumHBA(molecule.mol)

def molwt(molecule):
    return rdMolDescriptors.CalcExactMolWt(molecule.mol)

def logp(molecule):
    return Descriptors.MolLogP(molecule.mol)

hbd_filter = RangeFunctionFilter(hbd, 'hydrogen_bond_donor', None, 5)
hba_filter = RangeFunctionFilter(hba, 'hydrogen_bond_acceptor', None, 10)
molwt_filter = RangeFunctionFilter(molwt, 'mol_weight', None, 500)
logp_filter = RangeFunctionFilter(logp, 'logp', None, 5)

filters = [
    hbd_filter,
    hba_filter,
    molwt_filter,
    logp_filter
]

ro5_template = Template(filters)

smiles = ['C=CCNC(=O)N1CCN(C(=O)[C@H]2C[C@@H]2c2cccc(F)c2F)CC1',
 'C[C@@H]1CCCC[C@@H]1OCC(=O)OCc1nnc(-c2cccc(Br)c2)o1',
 'CCC[C@@H](OC)C(=O)N[C@@H](CNc1cnc(F)cn1)C(C)C',
 'CC(C)/C=C\\C(=O)N1CCC[C@@](CO)(NC(=O)OC(C)(C)C)C1',
 'C(c1ccccc1)CCC[C@@H](C)c1nnc(N2CCN(C(=O)OC(C)(C)C)[C@@H](C)C2)n1Cc1csc(C(C)(C)C)n1',
 'O=C(c1cccc(F)c1)N1CC[C@]2(CN(CC3=CCCCC3)CCO2)C1']

molecules = [Molecule(i) for i in smiles]
results = [ro5_template(i).result for i in molecules]
>[True, True, True, True, False, True]