# 使用特征工厂再来构建指纹工厂signature，factory用于设置指纹参数
# 构建指纹工厂 ：
SigFactory(
featFactory, # 特征工厂
useCounts=False, # 默认False。False不考虑指纹频数，并生成SparseBitVect
minPointCount=2, # 默认为2.生成指纹时包括的最少的药效团数量。
maxPointCount=3, # 默认为3。生成指纹时包括的最多的药效团数量。
...)
sigFactory = SigFactory(featFactory, minPointCount=2, maxPointCount=3)
# 对拓扑距离进行分段
sigFactory.SetBins([(0, 2), (2, 5), (5, 8)])
# 每次修改参数后，都要初始化一下
sigFactory.Init()
# 计算指纹的长度
print('指纹长度=', sigFactory.GetSigSize()) # 指纹长度= 2988
# # 4.2 生成2D药效团指纹
# 指纹工厂中的参数设置完毕，接下来就可以生成2D指纹了。
# 计算2D药效团指纹 ：
Gen2DFingerprint(
mol, # 要计算指纹的mol对象
sigFactory, # 设置了参数的指纹工厂
bitinfo # 获取指纹id及对应的原子
)
mol = Chem.MolFromSmiles('OCC(=O)CCCN')
fp = Generate.Gen2DFingerprint(mol, sigFactory)
print(len(fp)) # 2988
print(fp.GetNumOnBits()) # 23
import search2d
from time import time
import sys
fdefName = 'data/minimalFeatures.fdef'
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefName)
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
sigFactory = SigFactory(featFactory,
minPointCount=2,
maxPointCount=3,
trianglePruneBins=False)
sigFactory.SetBins([(0, 2), (2, 5), (5, 8)])
sigFactory.Init()
sigFactory.GetSigSize()
def similarityMeasure(fps, neg, mol2):
fps2 = Generate.Gen2DFingerprint(mol2, sigFactory)
similarityPos = DataStructs.FingerprintSimilarity(
fps, fps2, metric=DataStructs.TanimotoSimilarity)
similarityNeg = DataStructs.FingerprintSimilarity(
neg, fps2, metric=DataStructs.TanimotoSimilarity)
# if similarityPos>=0.75:
print Chem.MolToSmiles(mol2), similarityPos, similarityNeg
return similarityPos, similarityPos - similarityNeg