Hi Greg,
I am trying to reproduce some machine learning scripts using
https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/solubility.test.sdf
https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/solubility.train.sdf
What is the source of these data? How are they organized? Any
On 21/02/2020 22:45, Paolo Tosco wrote:
Hi Jitender,
you could do that quite easily using reaction SMARTS; see for example
this thread:
https://sourceforge.net/p/rdkit/mailman/message/35730514/
You could selectively replace a specific R attachment point by
isotopically labeling it.
Cheers,
Thanks a lot!
I've learnt two messages:
1. I agree GetBestRMS() is the right tool to compare conformers of the same
structure
2. O3A is good for aligning different structures(or structures with
different topology). However not only the O3A.Align() rmsd value should be
check, the Score should be
Hi Zhenting,
if you compare different conformers of the same structure you won't need
O3A at all, as the atom-atom correspondences will be 1:1, as all
conformers share the same topology; GetBestRMS() is all you need.
O3A is useful when you need to align molecules which have different
Hi Zhenting,
O3A.Align() returns the RMSD between the atom pairs that the O3A
algorithm was able to match across the two molecules.
O3A.Score() returns the score for an alignment. The score is directly
proportional to:
* the number of atom pairs that could be matched across the two
Hi Greg,
I am learning Open3D ALIGN
example code:
pyO3A = rdMolAlign.GetO3A(mol2py, mol1)
pyO3A.Align()
Questions
- what is the meaning of the value from O3A.Align()
- is that similar to atom wise RMSD?
-
- what is the meaning of the value from O3A.Score()
Hmm, that’s a first: they actually subscribed to the list in order to post.
This isn’t exactly spam, but since the email is generic and from an
organization that’s never been active on the list I am going to block the
sender. If you disagree with this, please let me know off list and I will
Not yet, sorry.
Still on my list, but I'm not sure when it'll actually get done.
On Sun, Feb 23, 2020 at 8:56 PM Tim Dudgeon wrote:
> Hi Greg,
>
> Did you get a chance to add any more tests or docs here?
> I'm happy to help to improve the docs (see my recent message about RDKit
> from Java),
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