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Smiles files with command line tools
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Peter

Joined: 19 Sep 2016
Posts: 1

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Link to postPosted: Mon Sep 19, 2016 10:19 amPost subject: Smiles files with command line tools Reply with quote

Dear Chemaxon Support,

I found very useful the command line tools (molconvert, cxcalc, evaluate, presently using version: 16.2.1.0), however I am constantly facing the problem that I cannot write a smiles file with multiple columns. With evaluate previously I could write an output with different columns with this command:

evaluate -g -e reos_rules.txt -x smiles:T:f1:f2:f3:f4 i.smi -o output.smi

In the input file these columns are separated with tab. In the output the tabs are put between the columns, however, no data is present. Can you please tell me, that how should be this problem properly solved?

With this command I want basically to remove those compounds which do not pass through the reos filter. These "rows" should be removed and the rest should be kept with all the properties which were generated before.

Best regards,

Peter Pogany

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Tue Dec 13, 2016 3:00 pmPost subject: Reply with quote

Hi Peter, 

Sorry for the late answer. To answer your question I think you used the wrong format for the SMILES property extraction. Instead of smiles:T:f1:f2:f3:f4 you should use smiles:Tf1:f2:f3:f4 for extraction. 

I prepared an example for you. I calculated a set of 3 properties (atom count, logP and TPSA) for a random set of 1000 NCI molecules with cxcalc. I saved the input molecules and the calculated results in a file (nci1000_props.smi).

Then screened these molecules based on molecular mass, so I used the following example command:

 evaluate -g -e "mass>=500" -x smiles:TlogP:atomcount:psa nci1000_props.smi 

This command filters out those molecules for which the mass is less than 500 and extracts the input and already calculated fields. 

I hope this helps and solves your problem. I'm looking for your feedback.

Daniel

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