RDKit | 基于RDKit(≥2020.09.1)的相似图绘制新方法

导入库

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import SimilarityMaps
from IPython.display import SVG
import numpy as np
import rdkit
print(rdkit.__version__)

2020.09.1

基于Morgan指纹的相似图绘制

atorvastatin = Chem.MolFromSmiles('O=C(O)C[C@H](O)C[C@H](O)CCn2c(c(c(c2c1ccc(F)cc1)c3ccccc3)C(=O)Nc4ccccc4)C(C)C')
rosuvastatin = Chem.MolFromSmiles('OC(=O)C[C@H](O)C[C@H](O)\C=C\c1c(C(C)C)nc(N(C)S(=O)(=O)C)nc1c2ccc(F)cc2')
Draw.MolsToGridImage((atorvastatin,rosuvastatin))

d = Draw.MolDraw2DSVG(400, 400)
_, maxWeight = SimilarityMaps.GetSimilarityMapForFingerprint(atorvastatin, rosuvastatin, 
                                        lambda m, i: SimilarityMaps.GetMorganFingerprint(m, i, radius=2, fpType='bv'), 
                                        draw2d=d)
d.FinishDrawing()
SVG(d.GetDrawingText())

d = Draw.MolDraw2DSVG(400, 400)
_, maxWeight = SimilarityMaps.GetSimilarityMapForFingerprint(atorvastatin, rosuvastatin, 
                                        lambda m, i: SimilarityMaps.GetMorganFingerprint(m, i, radius=2, fpType='count'), 
                                        draw2d=d)
d.FinishDrawing()
SVG(d.GetDrawingText())

from rdkit.Chem import rdMolDescriptors
ator_contribs = rdMolDescriptors._CalcCrippenContribs(atorvastatin)
d = Draw.MolDraw2DSVG(400, 400)
SimilarityMaps.GetSimilarityMapFromWeights(atorvastatin,[x[0] for x in ator_contribs],draw2d=d)
d.FinishDrawing()
SVG(d.GetDrawingText())

from rdkit.Chem import rdEHTTools
from rdkit.Chem import rdDistGeom
mh = Chem.AddHs(atorvastatin)
rdDistGeom.EmbedMolecule(mh)
_,res = rdEHTTools.RunMol(mh)
static_chgs = res.GetAtomicCharges()[:atorvastatin.GetNumAtoms()]
d = Draw.MolDraw2DSVG(400, 400)
SimilarityMaps.GetSimilarityMapFromWeights(atorvastatin,list(static_chgs),draw2d=d)
d.FinishDrawing()
SVG(d.GetDrawingText())

mh = Chem.AddHs(atorvastatin)
ps = rdDistGeom.ETKDGv2()
ps.pruneRmsThresh = 0.5
ps.randomSeed = 0xf00d
rdDistGeom.EmbedMultipleConfs(mh,10,ps)
print(f'Found {mh.GetNumConformers()} conformers')
chgs = []
for conf in mh.GetConformers():
    _,res = rdEHTTools.RunMol(mh,confId=conf.GetId())
    chgs.append(res.GetAtomicCharges()[:atorvastatin.GetNumAtoms()])
chgs = np.array(chgs)
mean_chgs = np.mean(chgs,axis=0)
std_chgs = np.std(chgs,axis=0)
d = Draw.MolDraw2DSVG(400, 400)
SimilarityMaps.GetSimilarityMapFromWeights(atorvastatin,list(mean_chgs),draw2d=d)
d.FinishDrawing()
SVG(d.GetDrawingText())

print(std_chgs)
print(max(std_chgs),min(std_chgs))
d = Draw.MolDraw2DSVG(400, 400)
SimilarityMaps.GetSimilarityMapFromWeights(atorvastatin,list(std_chgs),draw2d=d)
d.FinishDrawing()
SVG(d.GetDrawingText())