calculating properties

Hello,


Does Marvin provide a command line utility to batch-calculate compound properties from an sdf file or a compound table? I am looking to calculate logP, MW etc for my compound collection to test Lipinski rule. What is the best approach?


Thanks!

We have the cxcalc command line tool in Marvin for batch processing plugin calculations (logP, logD, pKa, ...), here is a forum topic that describes this in detail:


http://www.chemaxon.com/forum/ftopic271.html





However, it is also possible to evaluate more complex chemical expressions by our chemical terms evaluator in JChem. You can download JChem from:


http://www.chemaxon.com/jchem/





Here are links to the chemical terms evaluator documentation:





description:


http://www.chemaxon.com/jchem/doc/user/Evaluator.html





list of available functions:


http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html





a set of working examples:


http://www.chemaxon.com/jchem/examples/evaluator/index.html#basic_examples


Here you can also find the Lipinski rule.


I also attach this to this post:

Code:

evaluate -e lipinski.txt test.sdf 0 1 1

In this example the 2nd and the 3rd molecule satisfy the Lipinski rule, while the first one does not: it has logP > 5. You can also write the expression directly on the command line:

Code:

evaluate -e  '(mass() <= 500) && (logP() <= 5) && (donorCount() <= 5) && (acceptorCount() <= 10)' test.sdf 0 1 1

Thanks, Nora. It's really nice to know that the evaluate() function handles most of structure based prediction parameters. I was wondering if there is a plug-in to detect the name(e.g IUPAC) from the structure. I didn't find any that describes this feature.


Thanks!


Renju

The naming module is under development and it is in an early stage. We are planning to add it as a molecule Import/Export module rather than a plugin but we do not yet have a release date for it.

Thanks for the update, Nora. I was browsing through the basic examples and was wondering if there is a way to group output multiple plugins (e.g logP, Hacc, Lipinski together) into one file. I want to upload them all in one go, since my compound library file is large.


So , I am looking for the equivalent of:


evaluate -e lipinski.txt logp.txt Hacc.txt test.sdf -S -o output.sdf

If you use evaluate then you can do this by piping:

Code:

evaluate -e lipinski.txt -S -t LIPINSKI test.sdf | evaluate -e "logp()" -S -t LOGP

In cxcalc there is a possibility to run multiple calculations (but you can also use piping in a similar way as well):

Code:

cxcalc -S logp pka test.sdf