PubChemFingerprints module

This file provides internal functions to calculate pubchem fingerprints If you have any questions, please feel free to contact us. E-mail: biomed@csu.edu.cn

@File name: PubChemFingerprints @author: Jie Dong and Zhijiang Yao

PubChemFingerprints.InitKeys(keyList, keyDict)

Internal Use Only

generates SMARTS patterns for the keys, run once

PubChemFingerprints.calcPubChemFingerAll(mol)

Internal Use Only

Calculate PubChem Fingerprints

PubChemFingerprints.calcPubChemFingerPart1(mol, **kwargs)

Calculate PubChem Fingerprints （1-115; 263-881)

Arguments

• mol: the molecule to be fingerprinted
• any extra keyword arguments are ignored

Returns

a _DataStructs.SparseBitVect_ containing the fingerprint.

>>> m = Chem.MolFromSmiles('CNO')
>>> bv = PubChemFingerPart1(m)
>>> tuple(bv.GetOnBits())
(24, 68, 69, 71, 93, 94, 102, 124, 131, 139, 151, 158, 160, 161, 164)
>>> bv = PubChemFingerPart1(Chem.MolFromSmiles('CCC'))
>>> tuple(bv.GetOnBits())
(74, 114, 149, 155, 160)

PubChemFingerprints.calcPubChemFingerPart2(mol)

Internal Use Only

Calculate PubChem Fingerprints （116-263)

PubChemFingerprints.func_1(mol, bits)

Internal Use Only

Calculate PubChem Fingerprints （116-263)

PubChemFingerprints.func_2(mol, bits)

Internal Use Only

saturated or aromatic carbon-only ring

PubChemFingerprints.func_3(mol, bits)

Internal Use Only

saturated or aromatic nitrogen-containing

PubChemFingerprints.func_4(mol, bits)

Internal Use Only

saturated or aromatic heteroatom-containing

PubChemFingerprints.func_5(mol, bits)

Internal Use Only

unsaturated non-aromatic carbon-only

PubChemFingerprints.func_6(mol, bits)

Internal Use Only

unsaturated non-aromatic nitrogen-containing

PubChemFingerprints.func_7(mol, bits)

Internal Use Only

unsaturated non-aromatic heteroatom-containing

PubChemFingerprints.func_8(mol, bits)

Internal Use Only

aromatic rings or hetero-aromatic rings