logD in batch mode

How can i load a text file with compound names and smiles string on one line and get the logD for all of them?

Hi Yash,

Please read the following page:

http://www.chemaxon.com/marvin/help/applications/calc.html

Although cxcalc accepts SMILES as input, if you want to convert your input file to another format you may also need this:

http://www.chemaxon.com/marvin/help/applications/molconvert.html

 

Best regards:

Akos

 

I have visited that site before. No where does it tell me where the input file is or what format it needs to be in. An example is given:

LogP calculation with both result types (atomic increments and overal molecule) and
user defined SDF tag name, piping the result to MarvinView:

cxcalc -S mols.sdf -t LOGP_BOTH logp -t increments,logP | mview -

But here is "mols.sdf" the output file, if so where in this code can you insert an input file. Also,
there is no place for this in Marvin view. There is no command line. I have found the command line
under Jchem manager.

Thanks

yashman84 wrote:

I have visited that site before. No where does it tell me where the input file is or what format it needs to be in. I does tell. If you go through the examples one by one, you will quickly understand how to use cxcalc. Actually, mols.sdf wants to represent the input file. The input file can be in any format that is understood by Marvin, which includes most of the popular file formats (http://www.chemaxon.com/marvin/help/formats/formats.html). SMILES is among them. An example is given: LogP calculation with both result types (atomic increments and overal molecule) and user defined SDF tag name, piping the result to MarvinView: cxcalc -S mols.sdf -t LOGP_BOTH logp -t increments,logP | mview - But here is "mols.sdf" the output file, if so where in this code can you insert an input file. No, mols.sdf is the input file. With the "-S" option the output is specified to be in SDFile and the calculated logp values are written into a separte field (in this example the field is titled LOGP_BOTH), but the output filename is not specified, therefore it is not saved to a file; instead, the output is directed to MarvinView (where it will be shown as a spreadsheet by default). Also, there is no place for this in Marvin view. There is no command line. ??? You have to start a command line (e.g. under Windows, click on the Start button, then select Run, and then type "cmd"), then browse to the "Program Files\Chemaxon\MarvinBeans\bin" directory. Best regards, Akos I have found the command line under Jchem manager. Thanks

 

thanks for your earlier comments. I can get it to run now with the following code

cxcalc marvintest.txt -o output.txt logd

and this gives me the logD from ph 0 to 14 for the compounds in the file marvintest.txt and saves them in the output file output.txt

BUt the problem is when i try to make any changes to the code, like change the step size from the default value of 1 to 0.5, by changing the code to

cxcalc marvintest.txt -s 0.5 -o output.txt logd

i get an error that says "The system cannot find the specified file". IM not sure if i need to download updates to the plugin for logD. I get the same error if I try to change the order of the text in my original code. IM not sure if the options for stepsize or other things have to go in a certain order

thank you very much

Hi,

Write the outputfile first and the step size at the end:

cxcalc -o output.txt marvintest.txt logd -s 0.5

Best regards,

Akos

 

thanks a lot

i appreciate it