Hi Per
Just by looking at your code I would assume you have a sanitization issue. You
create your pentane molecule and then add H’s. This will saturate each single
carbon. When you then add a bond between the two fragments your atom 3 will
have a valence of 5 and this causes issues.
Maybe do the fragment combination first and then add the H’s? Or do an explicit
handling of the correct carbon you link to upfront.
Hope this helps
Nik
From: "Per Jr. Greisen" <pgrei...@gmail.com>
Date: Sunday 6 August 2017 at 19:55
To: RDKit <rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] adding fragment to existing molecule
Hi all,
I am trying to add a fragment to an existing molecule using RDkit - I start by
generating the desired molecules I would like to combine:
oh = '[OH-]'
ohh = Chem.MolFromSmiles(oh)
oh = Chem.AddHs(ohh)
oh.SetProp("_Name","OH-")
AllChem.EmbedMolecule(oh, AllChem.ETKDG())
smiles_ = 'CCCCC'
m = Chem.MolFromSmiles(smiles_)
m_h = Chem.AddHs(vxm)
m_h.SetProp("_Name","XP")
AllChem.EmbedMolecule(m_h, AllChem.ETKDG())
I combine them which works fine:
combo = Chem.CombineMols(m_h,oh)
and I can add the bond between the desired atoms:
edcombo = Chem.EditableMol(combo)
edcombo.AddBond(3,1,order=Chem.rdchem.BondType.SINGLE)
back = edcombo.GetMol()
The problems arises when I want to edit the geometry between the two :
from rdkit.Chem import rdMolTransforms as rdmt
conf = back.GetConformer(0)
rdmt.SetBondLength(conf,3,43,10)
writer3 = Chem.SDWriter('out_long.sdf')
writer3.write(back,confId=0)
RuntimeError Traceback (most recent call last)
<ipython-input-193-36d3c0480a45> in <module>()
2 conf = back.GetConformer(0)
3
----> 4 rdmt.SetBondLength(conf,3,43,10)
5
6 writer3 = Chem.SDWriter('out_long.sdf')
RuntimeError: Pre-condition Violation
RingInfo not initialized
Violation occurred on line 66 in file Code/GraphMol/RingInfo.cpp
Failed Expression: df_init
RDKIT: 2017.03.3
BOOST: 1_56
So I am not sure how fix - thanks in advance
--
With kind regards
Per
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