rdkit
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60 lines
2.2 KiB
60 lines
2.2 KiB
# Copyright 2021 Zilliz. All rights reserved.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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import logging
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from towhee import register
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from towhee.operator import Operator
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from rdkit import DataStructs, Chem
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log = logging.getLogger()
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@register(output_schema=['fingerprint'])
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class Rdkit(Operator):
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"""
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Generate molecular fingerprint with RDKit.
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Args:
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algorithm (`str`):
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Which algorithm to use for fingerprinting, including morgan, daylight, ap, maccs, and defaluts to 'morgan'.
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size (`int`):
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The bit vector size, defaults to 2048.
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"""
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def __init__(self, algorithm: str = 'morgan', size: int = 2048):
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self.algorithm = algorithm
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self.size = size
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def __call__(self, smiles: str):
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mols = Chem.MolFromSmiles(smiles)
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try:
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if self.algorithm == 'daylight':
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fp = Chem.RDKFingerprint(mols, fpSize=self.size)
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elif self.algorithm == 'morgan':
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from rdkit.Chem import AllChem
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AllChem.GetMorganFingerprint
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fp = AllChem.GetMorganFingerprintAsBitVect(mols, 2, self.size)
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elif self.algorithm == 'ap':
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from rdkit.Chem.AtomPairs import Pairs
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fp = Pairs.GetAtomPairFingerprintAsBitVect(mols)
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elif self.algorithm == 'maccs':
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from rdkit.Chem import MACCSkeys
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fp = MACCSkeys.GenMACCSKeys(mols)
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except Exception as e:
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log.error(f'{e}, cannot generate fingerprint of {smiles}.')
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raise KeyError(e)
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hex_fp = DataStructs.BitVectToFPSText(fp)
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fingerprint = bytes.fromhex(hex_fp)
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return fingerprint
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