Overlay and RMS calculation of 3D structures

Hi,


is there a way create an overlay picture as seen in this ChemAxon PDF


"Figure 18. Another two structures" (discussing 3D structure generation) and calculate an RMS within MarvinView?





Actually to overlay conformers directly coming fom MarvinView (generate low energy conformers)? Hence for a list of 100 conformers to have the RMS for the top one next to each molecule. Or is this something for the API?





Thank you


Tobias

Hi Tobias,





at present, classes that are capable of overlaying two structures (either in rigid or flexible manner) are not part of the public API. We may consider putting them in the public API later, though at present we do not have such plans.


I reckon this could be relevant and interesting for a very small group of users, that's one main reason behind this decision.





I hope you understand it. Apologies.





Regards,


Miklos

Hi Miklos,


but in the ChemAxon forum post the QuatFit algorithm was provided.


http://www.chemaxon.com/forum/ftopic1889.html.


I just want to do that with the API (although I thought MSpace would be wonderful fur such a purpose. I will transfer this question to the API.





Cheers


Tobias

Hi Tobias,





I am afraid we cannot support contributed code, you can take it and use it 'as it is' - even if the code presented in the public contrib area serves as the basis for our rigid alignment.


We will provide the proper API documentation when the production code (similar to the one presented in the forum) is released.





I hope you understand this policy.





Regards,


Miklos

Hi Miklos,


no problem, I understand because it probably takes time away from other implementations.





Cheers


Tobias