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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