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 fi
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
SDWriter.write
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 Felipe,
>
> cids is a li
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 restric
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:
AllChem.ConstrainedEmbed(cid,c
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,
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 us
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, Ma
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 mus
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:
w.write(newMol
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