Returning indexes of atoms matching SMARTS

Dear all,

I would like to return the index number of an atom matching a particular SMARTS query, so that I can compute a specific property on this atom. I cannot find the corresponding function for this.

Alternatively, if you know a way to directly compute the a property on an atom that matches a SMARTS query, this would be just as useful for me.

Best regards,

Sandro

Hi,

Check these Chemical Terms functions:

1. Match functions: http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html#match_functions

2. Filter function: http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html#filterdesc

Example:

$ evaluate -e "charge(filter(atoms(), \"match('[#8][C:1]=O', 1)\"))" "OC(=O)C1=CC=CC=C1"
0.08

It calculates the partial charge of the carboxylic carbon.

Evaluator manual: http://www.chemaxon.com/marvin/help/chemicalterms/Evaluator.html

Zsolt

 

Dera Zsolt,

Sorry for the late reply.

Unfortunately, there seems to be something wrong for me: even while copying the "evaluate " expression you provided me with, I cannot calculate values.

Instead, while using

 ./evaluate -e "charge(filter(atoms(), \"match('[#8][C:1]=O', 1)\"))" "OC(=O)C1=CC=CC=C1"

I get the following error message (this is only the start

Exception in thread "main" chemaxon.nfunk.jep.ParseException: Error while evaluating expression:
charge(filter(atoms(), "match('[#8][C:1]=O', 1)"))
    Error while evaluating expression:
match('[#8][C:1]=O', 1)
    Class not found: chemaxon.jep.function.Match
    chemaxon.jep.function.Match
 at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:502)
 at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)
 at chemaxon.jep.Evaluator.main(Evaluator.java:1203)
Caused by:
chemaxon.nfunk.jep.ParseException: Error while evaluating expression:
match('[#8][C:1]=O', 1)
    Class not found: chemaxon.jep.function.Match
    chemaxon.jep.function.Match

This is only the beginning, but I assume this means that there is a problem with the "match" expression.

I hope you can help!

Sandro

You have to install JChem if you want to use the "match" functions (installing MarvinBeans is not enough).

Zsolt