Re: [Rdkit-discuss] generate conformes with a restrained core

Hi Chris yesterday I realize about this and using the following command appears to do the job: for cid in cids: AllChem.ConstrainedEmbed(newMol3D,coreMol,useTethers=True) ... but then I cannot save the conformers because something is different: for cid in cids:

Re: [Rdkit-discuss] generate conformes with a restrained core

Hi Felipe You're doing something similar to the problem Paolo addressed. ConstrainedEmbed (see http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#ConstrainedEmbed) requires a mol object as the first parameter, but you are passing it an integer cid value, not a molecule. Your code

Re: [Rdkit-discuss] generate conformes with a restrained core

I understand, but I want the constrained core to be fixed How would you optimize each conformers with the initial constraints? If i don’t include de UFFOptimizeMolecule I still have important differences at the level of the core...so they are not really constrained...? Thanks Felipe On Fri,

Re: [Rdkit-discuss] generate conformes with a restrained core

For the record, it would be nice to see an *EmbedMultipleConstrainedConfs* function in rdkit. Atenciosamente, Luan Carvalho Martins luancarvalhomart...@gmail.com On Fri, Mar 23, 2018 at 9:20 PM, Luan Carvalho Martins < luancarvalhomart...@gmail.com> wrote: > No, what I am suggesting is you to

Re: [Rdkit-discuss] generate conformes with a restrained core

No, what I am suggesting is you to use a scheme similar to that applied in ConstrainedEmbed, namely, to add restraints between atoms you know the position. If you call ConstrainedEmbed several times, you will obtain the same confirmation again and again. Sincerely, Luan Carvalho Atenciosamente,

Re: [Rdkit-discuss] generate conformes with a restrained core

Hi Luan! thanks! I was trying to use it but I am still struggling with very basic problems. What you are saying is that I can delete the UFFOptimizeMolecule and add a loop with ConstrainedEmbed to minimize with constraints? in my script, using: for cid in cids:

Re: [Rdkit-discuss] generate conformes with a restrained core

When you used AllChem.UFFOptimizeMolecule(newMol3D,confId=cid) the minimization proceeded without constraints, therefore, the core embedding was lost. Read the source of ConstrainedEmbed [ http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-pysrc.html#ConstrainedEmbed]. This function does a

Re: [Rdkit-discuss] generate conformes with a restrained core

Hi Paolo great! it was a very simple thing. Now the sdf file with the conformers is generated but the conformers were not constraints at the core of the ligand...as I was trying? can you tell me why? thanks a lot! felipet 2018-03-23 15:37 GMT-03:00 Paolo Tosco : > Dear

Re: [Rdkit-discuss] generate conformes with a restrained core

Dear Felipe, cids is a list of conformer ids, i.e. integer numbers. Therefore prbMol = cids[prbNum] sets prbMol to the integer value of the prbNum element of the cids list. The reason of the error message you are getting: Boost.Python.ArgumentError: Python argument types in    

[Rdkit-discuss] generate conformes with a restrained core

Dear all, sorry but I am really new at using RDkit. By looking at the scripts and tutorial available I wrote the following script. The idea is to generate a number of conformers for a big and flexible ligand, but with constraints. This script generate a set of conformers but I can't write a SDF