On 19/11/2019 03:34, Benjamin Datko wrote:
Hello all,
I am curious on how to fold a count vector fingerprint. I understand
when folding bit vectors the most common way is to split the vector in
half, and apply a bitwise OR operation. I think this is how the
function
On Nov 18, 2019, at 17:40, David Cosgrove wrote:
>
> Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
> strings out unless you tortured it pretty hard, however.
Did someone mention one of my favorite things to do? :) See:
Hello all,
I am curious on how to fold a count vector fingerprint. I understand when
folding bit vectors the most common way is to split the vector in half, and
apply a bitwise OR operation. I think this is how the function
rdkit.DataStructs.FoldFingerprint works in RDKit, correct me if I am
Hi Paolo,
Very clear explanation. Thank you!!
Best,
Leon
On Mon, Nov 18, 2019 at 12:27 PM Paolo Tosco
wrote:
> Hi Leon,
>
> MMFFOptimizeMoleculeConfs() by default will distribute minimization tasks
> across all available CPU cores as it is multi-threaded at the C++ level,
> while
Hi Leon,
MMFFOptimizeMoleculeConfs() by default will distribute minimization
tasks across all available CPU cores as it is multi-threaded at the C++
level, while ff.Minimize() will run single-threaded, unless you do the
distribution of individual minimization tasks yourself in the Python
On Mon, 18 Nov 2019 16:40:28 +
David Cosgrove wrote:
> Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
> strings out unless you tortured it pretty hard, however.
Export smiles with arbitrary given atom order is diffrent problem.
Normally working with mol object you
Hey guys,
Thanks for the responses!
So I now got the answer for my Q #2: No symmetry taken into account for
AlignMolConformers(). Thanks Paolo for the example link.
You guys are all very welcome to give me any suggestions on all three
questions I asked. I appreciate it.
Best,
Leon
On Mon,
Hi Rocco,
Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
strings out unless you tortured it pretty hard, however.
Dave
On Mon, 18 Nov 2019 at 16:36, Rocco Moretti wrote:
> Actually, it is possible to get arbitrary orders, if you (ab)use the '.'
> component ("zero
Actually, it is possible to get arbitrary orders, if you (ab)use the '.'
component ("zero order bond") directive and the numeric bonding ("ring
closure") directives:
>>> Chem.MolToSmiles( Chem.MolFromSmiles("O1.Cl2.C12" ) )
'OCCl'
Whether you want to do things that way is another question.
On
Hi Rafal,
It is not always possible to preserve the atom ordering in the SMILES
string because there is an implied bond between contiguous symbols in the
SMILES. I think, for example, that the molecule with the SMILES OCCl
couldn’t have the order in the molecule object O first, Cl second, C third,
Hi Omar,
you may have a look at this thread for an explanation and an example:
https://sourceforge.net/p/rdkit/mailman/message/36787480/
Cheers,
p.
On 18/11/2019 15:28, Omar H94 wrote:
What does it mean to take symmetry into account ?
On Mon, Nov 18, 2019 at 6:07 PM topgunhaides .
What does it mean to take symmetry into account ?
On Mon, Nov 18, 2019 at 6:07 PM topgunhaides . wrote:
> Hi Greg,
>
> Thanks a lot! This is very helpful. Further questions:
>
> 1. If I need RMSD matrix for clustering, I guess I will have to figure out
> a way to loop over all conformers to get
Hi Greg,
Thanks a lot! This is very helpful. Further questions:
1. If I need RMSD matrix for clustering, I guess I will have to figure out
a way to loop over all conformers to get the matrix first, if I choose to
use GetBestRMS()?
2. Does the AlignMolConformers() handle symmetry and align all
Hi all,
Is there any way to preserve atom order from Mol object during
exporting to smiles? I tried MolToSmiles with rootedAtAtom=0 and
canonical=False options but it not always prevent oryginal order.
I know I can use _smilesAtomOutputOrder to map old indices to new one
in canonical smiles but
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