Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Greg Landrum
hen 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" >> *Date: *Sunday 6 August 2017 at 19:55 >>

Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Christos Kannas
t. >> >> Hope this helps >> >> Nik >> >> >> >> >> >> *From: *"Per Jr. Greisen" >> *Date: *Sunday 6 August 2017 at 19:55 >> *To: *RDKit >> *Subject: *[Rdkit-discuss] adding fragment to existing

Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Per Jr. Greisen
ination 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" > *Date: *Sunday 6 August 2017 at 19:55 > *To: *RDKit > *Subject: *[Rdkit

Re: [Rdkit-discuss] adding fragment to existing molecule

2017-08-07 Thread Stiefl, Nikolaus
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" Date: Sunday 6 August 2017 at 19:55 To: RDKit Subject: [Rdkit-discuss] adding fragment to existing molecule Hi all, I

[Rdkit-discuss] adding fragment to existing molecule

2017-08-06 Thread Per Jr. Greisen
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_ = 'C' m