ChemAxon Forum Archive » Structure based predictions: Calculator Plugins & Chemical Terms

Molecular Volume determination

User f564ccf382

04-06-2008 17:10:39

Hi All,





I was wondering is there a plug-in available to determine Molecular Volume. If not, does anybody know how I would calculate it?





Thanks,


Miriam

ChemAxon e08c317633

06-06-2008 08:33:17

Hi,
miriam.oriordan wrote:
I was wondering is there a plug-in available to determine Molecular Volume.
No, there isn't (yet).
Quote:
If not, does anybody know how I would calculate it?
The algorithm described here can be a good starting point. It is used for calculating surface area, but can be modified to calculate volume.





Zsolt

ChemAxon d76e6e95eb

06-06-2008 10:30:21

Thank you for the idea, Miriam! We will implement the molecular volume function in the Geometry plugin.

User f564ccf382

06-06-2008 15:04:42

Thanks Zsolt for your help. I'll read through the link that you've posted.





All the best,


Miriam

ChemAxon efa1591b5a

09-02-2010 12:50:32

Dear Miriam,


 


Is the prediction of the volume of molecules still relevant in your work? We have something that might be interesting for you.  Please get back and respond in this forum thread if you're still interested.


 


Kind regards


Miklos


 

User f564ccf382

09-02-2010 13:20:07

Hi Miklos,


Yes, it is still of interest to me.


Thanks,


Miriam

ChemAxon efa1591b5a

09-02-2010 15:09:24

Hi Miriam,


great!


I admit it took fairly long time... but I'm glad to inform you that the molecular volume calculation is available for online try-out.  


It will be released later in version Marvin 5.3.1 around the end of Q1 2010. Till then, the online version can be used for beta testing, validation and for discussion. 



 


There are two similar web based implementations provided, one of them using the AJAX technology and the other uses plain HTML. The AJAX is more trendy, though right now the HTML is somewhat more stable. 


 


Originally, these pages have been built to demonstrate Generate3D, our 2D->3D structure converter, but it appeared to be straightforward to add themolecular volume calculation to this try-out page. There is one limitation at present, which we will resolve within the next few days: the input is always a 2D structure and the tool generates one low energy conformer and calculates the volume of that particular conformer. Apparently, you may want to upload a particular 3D structure and calculate the volume specific to that conformation without altering the geometry at all. We will implement this option shortly.



The usage is quite simple: either type a SMILES string or a chemical name (traditional or IUPAC) in the edit field (like CCCCC or benzene etc.) and hit the "Generate" button (only in case if you see a green tick mark in front of the edit slot). Then a new window pops up showing the 3D structure and under the structure, at the bottom of this window the calculated volume is displayed.

If you hit OK in this window then you get back to the initial screen where a new molecule can be entered.

If smiles or chemical name input is not convenient, MarvinSketch can be launched by pressing the 'Edit' button.



I believe that this simple web based interface enables a quick test drive without the hassle of downloading and deployment etc. It is suitable to assess the accuracy of the volume calculation, though not directly applicable to test its performance (due to network lag).



Your feedback is warmly welcome.


regards,

Miklos

User ed092f316e

15-04-2010 23:03:51

Hi Miklos,


I'm looking for a method to compute molecular volume as well, and just came across this. You mentioned that this will be available in Marvin 5.3.1? However, it doesn't seem to be the case(I didn't find an option for molecular volume when I typed cxcalc on the prompt). Am I missing something, or will this be imcorporated to a later version?


 


Thanks,


Hetu


 











mvargyas wrote:

Hi Miriam,


great!


I admit it took fairly long time... but I'm glad to inform you that the molecular volume calculation is available for online try-out.


It will be released later in version Marvin 5.3.1 around the end of Q1 2010. Till then, the online version can be used for beta testing, validation and for discussion.


 


 


There are two similar web based implementations provided, one of them using the AJAX technology and the other uses plain HTML. The AJAX is more trendy, though right now the HTML is somewhat more stable.



Originally, these pages have been built to demonstrate Generate3D, our 2D->3D structure converter, but it appeared to be straightforward to add themolecular volume calculation to this try-out page. There is one limitation at present, which we will resolve within the next few days: the input is always a 2D structure and the tool generates one low energy conformer and calculates the volume of that particular conformer. Apparently, you may want to upload a particular 3D structure and calculate the volume specific to that conformation without altering the geometry at all. We will implement this option shortly.



The usage is quite simple: either type a SMILES string or a chemical name (traditional or IUPAC) in the edit field (like CCCCC or benzene etc.) and hit the "Generate" button (only in case if you see a green tick mark in front of the edit slot). Then a new window pops up showing the 3D structure and under the structure, at the bottom of this window the calculated volume is displayed.

If you hit OK in this window then you get back to the initial screen where a new molecule can be entered.

If smiles or chemical name input is not convenient, MarvinSketch can be launched by pressing the 'Edit' button.



I believe that this simple web based interface enables a quick test drive without the hassle of downloading and deployment etc. It is suitable to assess the accuracy of the volume calculation, though not directly applicable to test its performance (due to network lag).



Your feedback is warmly welcome.


regards,

Miklos

 

ChemAxon efa1591b5a

16-04-2010 09:15:17

Hi Hetu,


Apologies, I did not update this post when 5.3.1 had to be released sooner than expected because of some serious issues...


Anyway, Molecular Volume calculation will be released in 5.3.2 within days - I'll let you know in this topic.


In the meantime, you can test it online here: discoverygroup.chemaxon.com


regards


Miklos

ChemAxon efa1591b5a

15-11-2010 12:31:29

Hi Hetu,


did you have the time to test the molecular volume calculation? Just download any recent release if you have not yet done it. Or alternatively, if you do not want to download and install anything, either visit the discovery tools sandbox, or the chemicalize.org page. Both are web based and can do this calculation.


Regards


Miklos