generating a vector to describe orientation of a pose

User b4f15198ac

02-09-2014 03:14:39


I am attempting to create a descriptor to measure the orientation of a molecule. I have PDB files of the same molecule, posed in different ways, and need to describe the different orientations. I thought dipole vectors would be perfect, but it seems the molecule is always rotated away from its original pose, to minimize the z-component.  Is there a way to do this with the geometry plugin (or other)? What is important is being able to compare different orientations of the same molecule with a numeric metric. Thank you! 



ChemAxon 044c6721bc

03-09-2014 12:04:05

The question was moved to the appropriate forum section.

The relevant experts will respond soon.


ChemAxon d51151248d

15-09-2014 12:47:56

Hi Aiden, 

currently we do not have any direct metric to measure the orientation/pose of the molecule. Can you give us any information on what representation of the orientation you want. What for do you want to use that? 

Thank you,