#!/usr/bin/env python
# coding: utf-8

# In[1]:


from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdFMCS
from rdkit.Chem.Draw import IPythonConsole


# In[2]:


mol1 = Chem.MolFromSmiles('CCc1ccccc1')
mol2 = Chem.MolFromSmiles('CCc1nnccc1')


# In[3]:


AllChem.EmbedMolecule(mol1)


# In[4]:


IPythonConsole.drawMol3D(mol1, size=(200,200))


# In[5]:


mcs = rdFMCS.FindMCS([mol1, mol2])
mcs_mol = Chem.MolFromSmarts(mcs.smartsString)


# In[6]:


ref_match = mol1.GetSubstructMatch(mcs_mol)
target_match = mol2.GetSubstructMatch(mcs_mol)


# In[7]:


print(ref_match, target_match)


# In[8]:


rwmol = Chem.RWMol(mcs_mol)


# In[9]:


rwconf = Chem.Conformer(rwmol.GetNumAtoms())
matches = rwmol.GetSubstructMatch(mcs_mol)


# In[10]:


ref_conf = mol1.GetConformer()
for i, match in enumerate(matches):
    print(ref_conf.GetAtomPosition(ref_match[i]).x)
    rwconf.SetAtomPosition(match, ref_conf.GetAtomPosition(ref_match[i]))

    


# In[18]:


for i in matches:
    pos=rwconf.GetAtomPosition(i)
    print(pos.x, pos.y, pos.z)


# In[12]:


rwmol.AddConformer(rwconf)


# In[13]:


IPythonConsole.drawMol3D(rwmol)


# In[14]:


AllChem.ConstrainedEmbed(mol2, rwmol)


# In[15]:


IPythonConsole.drawMol3D(mol2)


# In[ ]:


print(Chem.MolToMolBlock(mol1))
print(Chem.MolToMolBlock(mol1))