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Calculation of compounds properties for rdf-files.
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Pavel

Joined: 16 Nov 2010
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Link to postPosted: Tue Nov 03, 2015 4:42 pmPost subject: Calculation of compounds properties for rdf-files. Reply with quote

I discovered that using cxcalc for a rdf-file with -S option retuned a valid rxn file.

cxcalc -S charge 1.rdf -o 1.rxn

But not all properties are supported. Some of them like refractivity and logp return warnings that for reactions it is not possible to calculate them. Other ones like acc and don simply return errors.

Of course. these is a workaround: convert rdf to sdf first and then calculate what you need, but it is not always convenient.

Do you plan to add support of rdf files for these plugins in near future?

Thank you in advance.

Pavel.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Mon Nov 09, 2015 11:49 amPost subject: Reply with quote

Hi, 

Thank you for sending us this issue. However, we would need some test files so that we can reproduce and investigate it further. Can you please send us something that we can use? You can attach test files to this forum post.

Best regards,

Daniel 

Pavel

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Link to postPosted: Mon Nov 09, 2015 12:23 pmPost subject: Reply with quote

Hello,

I attached input rdf-file and output rxn-file obtained with this command (logp plugin returns error in console output)

cxcalc -S -o test.rxn charge logp don acc 1.rdf

However such behavior is undocumented because cxcalc converts rdf input in rxn format and add sdf fileds to it. But rxn file may not contain additional sdf-like fields. See my related question in the other thread - https://www.chemaxon.com/forum/ftopic14534.html

So it seems not an issue but a feature.

 

Daniel
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Link to postPosted: Mon Nov 09, 2015 3:38 pmPost subject: Reply with quote

Hi, 

Regarding the calculations for reactions, currently only a few of them can be applied for reactions. We currently don't plan to extend this feature for other calculations. 

Regarding the rdf/rxn issue do you find it a problem? What solution would be good for you?

Thank you,

Daniel

Pavel

Joined: 16 Nov 2010
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Link to postPosted: Mon Nov 09, 2015 3:50 pmPost subject: Reply with quote

It is not a problem at all. It is a feature for me.

I implement calculation of descriptors for reactions based on atomic properties. I found it is convenient to parse cxcalc output as a reaction file format to avoid unnecessary conversion of rdf to sdf.

Daniel
ChemAxon personnel
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Link to postPosted: Tue Nov 10, 2015 10:22 amPost subject: Reply with quote

Hi, 

Ok, I just wanted to make it clear. Again, regarding running calculations for reactions, not every calculation is supported. Currently this is not a priority for us to extend this, so the best I can offer you is that we put it in our backlog and will get back to you when we can devote efforts to this issue.

Thank you for your understanding.

Daniel 

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