柔性二面角

分子原子编号以及柔性二面角扫面方法(供参考，有问题请指出，谢谢）

from rdkit import Chem
from rdkit.Chem import AllChem, rdMolTransforms
from rdkit import ForceField
from rdkit.Chem import  Draw
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions 
from rdkit.Chem.Draw import IPythonConsole,rdMolDraw2D
from PIL import Image, ImageOps
from io import BytesIO
import matplotlib.pyplot as plt
import numpy as np

s = 'CN1C=C(C(=O)N2CCC(CC2)C2=CC(=NN2)C2=CC=C(Cl)C=C2)C(C)=N1'
m = Chem.MolFromSmiles(s)
m = Chem.AddHs(m)

#给原子编号
for atom in m.GetAtoms():
    atom.SetProp('atomLabel',str(atom.GetIdx()))
m

柔性二面角识别
def enumerateTorsions(mol):
    torsionSmarts = '[A;!$(*#*)&!D1]~[A;!$(*#*)&!D1]'
    torsionQuery = Chem.MolFromSmarts(torsionSmarts)
    matches = mol.GetSubstructMatches(torsionQuery)
    torsionList = []
    for match in matches:
        idx2 = match[0]
        idx3 = match[1]
        bond = mol.GetBondBetweenAtoms(idx2, idx3)
        jAtom = mol.GetAtomWithIdx(idx2)
        kAtom = mol.GetAtomWithIdx(idx3)
        if (((jAtom.GetHybridization() != Chem.HybridizationType.SP2)
             and (jAtom.GetHybridization() != Chem.HybridizationType.SP3))
            or ((kAtom.GetHybridization() != Chem.HybridizationType.SP2)
                and (kAtom.GetHybridization() != Chem.HybridizationType.SP3))):
            continue 

        for b1 in jAtom.GetBonds():
            if (b1.GetIdx() == bond.GetIdx()):
                continue
                
            idx1 = b1.GetOtherAtomIdx(idx2)
            
        for b2 in kAtom.GetBonds():
            if ((b2.GetIdx() == bond.GetIdx())
                or (b2.GetIdx() == b1.GetIdx())):
                continue
            
            idx4 = b2.GetOtherAtomIdx(idx3)
         # skip 3-membered rings
            if (idx4 == idx1):
                continue
        torsionList.append((idx1, idx2, idx3, idx4))
    return torsionList

生成结构图片，高亮柔性二面角区域

def _drawerToImage(d2d):
    sio = BytesIO(d2d.GetDrawingText())
    return Image.open(sio)

def clourMol(mol,highlightAtoms_p=None,highlightAtomColors_p=None,highlightBonds_p=None,highlightBondColors_p=None,sz=[400,400]):
    '''

    '''
    d2d = rdMolDraw2D.MolDraw2DCairo(sz[0], sz[1])
    op = d2d.drawOptions()
    op.dotsPerAngstrom = 20
    op.useBWAtomPalette()
    mc = rdMolDraw2D.PrepareMolForDrawing(mol)
    d2d.DrawMolecule(mc, legend='', highlightAtoms=highlightAtoms_p,highlightAtomColors=highlightAtomColors_p, highlightBonds= highlightBonds_p,highlightBondColors=highlightBondColors_p)
    d2d.FinishDrawing()
    product_img=_drawerToImage(d2d)
    return product_img

二面角识别

for i in range(len(torsionList)):
    atom_list=torsionList[i]
    img1 = clourMol(m,highlightAtoms_p=atom_list)
    display(img1)