Does this AllChem.UFFOptimizeMolecule(mol_h) optimize all the
conformers present in mol_h ?
The documentation is vague:
http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#UFFOptimizeMolecule
Thanks
JP
--
Cre
Hi Greg - great news about the beta / new functionality!
> Greg wrote:
> This morning I tagged the beta for the Q1 2011 (2011.03 in the new
> numbering) release in svn:
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_201
> 1_03_1beta1/
>
> and uploaded a source distribution to the go
On Mon, Apr 4, 2011 at 3:17 PM, JP wrote:
> Does this AllChem.UFFOptimizeMolecule(mol_h) optimize all the
> conformers present in mol_h ?
It just optimizes a single conformer.
Since it might be interesting, here's how I answered that question:
[1]>>> from rdkit import Chem
[2]>>> from rdkit.Ch
Hi there,
I am doing a UFFOptimizeMolecule - to optimize a molecule - is it
possible to get the final energy value for this?
Details: I have a list of 50 conformers and I would like to sample
the conformational space (I do not want to have lots of similar
conformers).
I though I could find the 5
Sorry for the repeated emails/questions.
I am a bit confused about the RMS usage in RDKit.
When comparing two different structures you can easily get an RMSD
score (as the delta takes the difference between the coordinates from
one structure to the other -
http://en.wikipedia.org/wiki/Root_mean_s
Dear Greg,
we have started using RDKit today. We would like to use RDKit to
perceive bond types, even for topological molecules without 3D
coordinates. We tried to do this by creating an RWMol object for methane
consisting of one carbon and four hydrogen atoms, with four C-H bonds
all of type Bond
Can anyone explain why the conformer RMS values which are printed out
are all smaller than 1.0?
I am pruning using the pruneRmsThresh (=1.0) variable in
EmbedMultipleConfs method so I was expecting this would not happen.
I am expecting to see values > 1.0 since they should be at least this
distance
Dear Jacco,
On Mon, Apr 4, 2011 at 6:48 PM, Jacco van de Streek
wrote:
> Dear Greg,
>
> we have started using RDKit today. We would like to use RDKit to
> perceive bond types, even for topological molecules without 3D
> coordinates. We tried to do this by creating an RWMol object for methane
> co
On Mon, Apr 4, 2011 at 3:29 PM, James Davidson wrote:
>>
>> and uploaded a source distribution to the google code site:
>> http://code.google.com/p/rdkit/downloads/detail?name=RDKit_201
>> 1_03_1beta1.tgz
>> If there's demand for it, I will also put up a windows binary.
>
> As usual, "yes, please"
Dear JP,
On Mon, Apr 4, 2011 at 6:27 PM, JP wrote:
> Sorry for the repeated emails/questions.
No worries, that's what the list is for. :-)
> I am a bit confused about the RMS usage in RDKit.
>
> When comparing two different structures you can easily get an RMSD
> score (as the delta takes the d
Dear JP,
On Mon, Apr 4, 2011 at 5:28 PM, JP wrote:
> Hi there,
>
> I am doing a UFFOptimizeMolecule - to optimize a molecule - is it
> possible to get the final energy value for this?
You need to work directly with the force field if you want the energy:
>>> ff = AllChem.UFFGetMoleculeForceField
Dear JP,
On Mon, Apr 4, 2011 at 6:53 PM, JP wrote:
> Can anyone explain why the conformer RMS values which are printed out
> are all smaller than 1.0?
> I am pruning using the pruneRmsThresh (=1.0) variable in
> EmbedMultipleConfs method so I was expecting this would not happen.
> I am expecting
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