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
topologies, as it will find non-obvious matches between atoms.
Regarding open-sorce shape similarity tools you might have a look at
Shape-it:
http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html
Cheers,
p.
On 24/02/2020 14:16, Gao Zhenting wrote:
Hi Paolo,
Thanks for pointing that out. Currently, I am using Open3DAlign to
select diverse conformers of a single structure by measuring the rmsd.
According to your explanation, I will choose O3A.Align() to record the
rmsd between conformers. And my preliminary observation is O3A.Align()
gave me a more expected rmsd value comparing to
rdkit.Chem.rdMolAlign.GetBestRMS(probeMol, refMol). (python code
attached) What is your comment on this?
I do imagine to use Open3DAlign as a shape similarity tool. However
with your advice, I will think it over again.
Do you have any suggestions on an open source shape similarity tool?
Best regards
Zhenting
Paolo Tosco <paolo.tosco.m...@gmail.com
<mailto:paolo.tosco.m...@gmail.com>> 于2020年2月24日周一 下午9:21写道：
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
molecules
* the closeness of the match (i.e., how similar actually the atoms
in the matched pair are)
It is important to note that Open3DAlign was originally conceived
as a tool to generate good quality 3D overlays of molecules ahead
of a 3D-QSAR analysis. It was not designed, nor tested, as a tool
to assess 3D similarity between molecules and do virtual
screening. O3A.Score is used internally purely to pick the best
overlay between two molecules.
Cheers,
p
On 24/02/2020 12:45, Gao Zhenting wrote:
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()
o is that similar to atom wise RMSD?
o
* what is the meaning of the value from O3A.Score()
o only an online tutorial presented the Score
+ ~ open3dqsar.org > Downloads > Open3DTOOLS tutorial
20130812
<http://open3dqsar.org/downloads/Open3DTOOLS_tutorial_20130812.pdf>
*
* Best Regards
o
+
* Zhenting
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