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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