计算atom pair指纹:GetAtomPairFingerprint(mol, minLength, maxLength, …) 同GetAtomPairFingerprintAsIntVect() 这个方法生成的指纹非常庞大稀疏。 >>> from rdkit.Chem.AtomPairs import Pairs >>> fps = [Pairs.GetAtomPairFingerprint(x) for x in ms] 可以通过该方法获取atom pairs算法产生的非空元素:Get...
1回答 rdkit.Chem.rdMolDescriptors.GetAtomPairFingerprint(str)中的ArgumentError参数类型与C++签名不匹配: 、、、 我目前正在处理肽数据,并试图从肽数据集中提取原子对指纹,用于机器学习分类器中。import rdkit from rdkit</ 浏览4提问于2021-11-07得票数 0 回答已采纳 1回答 无法使用rdkit将分子转换为指纹 ...
计算atom pair指纹:GetAtomPairFingerprint(mol, minLength, maxLength, ...) 同GetAtomPairFingerprintAsIntVect() 这个方法生成的指纹非常庞大稀疏。 >>>fromrdkit.Chem.AtomPairsimportPairs>>>fps=[Pairs.GetAtomPairFingerprint(x)forxinms] 可以通过该方法获取atom pairs算法产生的非空元素:GetNonzeroElements()...
Atom Pairs and Topological Torsions 代码语言:javascript 复制 #原子对指纹,Atom Pairs from rdkit.Chem.AtomPairsimportPairs ms=[Chem.MolFromSmiles('C1CCC1OCC'),Chem.MolFromSmiles('CC(COCC'),Chem.MolFromSmiles('CCOCC')]pairFps=[Pairs.GetAtomPairFingerprint(x)forxinms] Morgan Fingerprints (Circ...
>>> fp1 = AllChem.GetAtomPairFingerprint(mol) >>> print(fp == fp1) True >>> fp = SimilarityMaps.GetTTFingerprint(mol, fpType='normal') >>> fp1 = AllChem.GetTopologicalTorsionFingerprint(mol) >>> print(fp == fp1) True >>> fp = SimilarityMaps.GetMorganFingerprint(mol, fpType='bv...
from rdkit.Chem.AtomPairs import Pairs # 提取分子指纹MACCS ms = [Chem.MolFromSmiles('CCOC'), Chem.MolFromSmiles('CCO'), ... Chem.MolFromSmiles('COC')] pairFps = [Pairs.GetAtomPairFingerprint(x) for x in ms] #pairFps = [Pairs.GetAtomPairFingerprintAsBitVect(x) for x in ms]...
atompairbv_fp(mol):atompair的bfp指纹 atompair_fp(mol):atompair的sfp指纹 rdkit_fp(mol):rdkit的拓扑指纹 maccs_fp(mol):预定义的MACCS指纹 接下来在postgresql中计算分子指纹 根据rdk.mols中的m列(存放分子的mol对象),计算torsion、morgan ECFP、morgan FCFP指纹,分别命名为torsionbv、mfp2、ffp2,并放入到...
Chem.rdMolDescriptors import (GetAtomPairFingerprint, GetTopologicalTorsionFingerprint) from rdkit.Chem import rdFingerprintGenerator numPathBits = rdMolDescriptors.AtomPairsParameters.numPathBits _maxPathLen = (1 << numPathBits) - 1 # Unused variable @@ -72,8 +71,25 @@ def AssignPattyTypes(...
Describe the bug GetBPFingerprint and GetBTFingerprint generate deprecation warnings: DEPRECATION WARNING: please use AtomPairGenerator and DEPRECATION WARNING: please use TopologicalTorsionGenerator, respectively. I have found no way to...
Include a graph distance fingerprint showing the graph distance between each attachment point in the fragmentation 'value'. The fingeprint is the number of bonds between each pair of attachment points, so '[*:1]-[*:2]' is {1}, '[*:1]c1c([*:2])cc([*:3])cc1' is {3,5,4} e...