Hi Nikolaus and Ling,
Thanks for your help (the atom numbe shouldnt be 43 but it still gives the
error I will clarify)- yes Nikolaus you are right it is a sanitization
issue and in this case I am trying to use it as a molecular editor to build
a model molecule (a transition state model to be exact) - I would normally
do this calling some other script but it would be very nice to do all of it
in the framework of RDkit - can this be done? Thanks
On Mon, Aug 7, 2017 at 12:05 PM, Stiefl, Nikolaus <
nikolaus.sti...@novartis.com> wrote:
> 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
>
--
With kind regards
Per
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
