Error Calculating hbonddonoracceptor, molecularsurfacearea,

Hi,


I'm trying to calculate some chemical terms from already existing table and add the resulting column to the table.


I'm using the GUI, jcman.


When I issue this command:

Quote:

jcman -Xmx512m m str_table_name --add-ctcolcfg "HB_ACCEPTOR=hbonddonoracceptor"

I got this error:


java.lang.IllegalArgumentException: Error while testing Chemical Terms 'hbonddonoracceptor' for column 'HB_ACCEPTOR': Error while evaluating expression:


hbonddonoracceptor


Unrecognized symbol: "hbonddonoracceptor"


at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.java:889)


at chemaxon.jchem.Command.setChemTermColCfg(Command.java:1306)


at chemaxon.jchem.Command.addChemTermColCfg(Command.java:1300)


at chemaxon.jchem.Command.manageChemTermColsCfg(Command.java:1271)


at chemaxon.jchem.Command.manageTable(Command.java:1225)


at chemaxon.jchem.Command.run(Command.java:613)


at chemaxon.jchem.Command.main(Command.java:201)





I'm assuming my syntax is not correct.


I will appreciate if some one can provide the correct syntax to calculate hbonddonoracceptor, molecularsurfacearea, polarsurfacearea using the GUI as above.





Thank you in advance.





Saif

Hi,





Here you can find the list of Chemical Terms functions you can use: Chemical Terms Reference Tables





I think you are looking for the following functions:





acceptorCount() and donorCount() (note: these are two separate functions.)


topologicalPolarSurfaceArea()


vanDerWaalsSurfaceArea()


solventAccessibleSurfaceArea()





Regards,


Zsolt

Hi,


Thank you Zsolt for your replay. I'm aware of these links. The functions are well explained to be used from command line using the cxcalc. But I'm trying to use the functions using

Code:

jcman m  tableName --add-ctcolcfg "colName=function"

So my question is what is the correct systax to use this code to calculate molecularsurfacearea AND hbonddonoracceptor?








Thank you.





Saif

Hi sabayazid,





hbonddonoracceptor available only from cxcalc, you can use two different functions for this in chemical terms: acceptorCount(), donorCount()


For example:

Code:

jcman m  tableName --add-ctcolcfg "acceptors=acceptorCount();donors=donorCount()"

We have 3 molecular surface area calculation in chemical terms: topologicalPolarSurfaceArea(), vanDerWaalsSurfaceArea(), solventAccessibleSurfaceArea()


You can use the most appropriate of them.


For example:

Code:

jcman m  tableName --add-ctcolcfg "molSurfArea=topologicalPolarSurfaceArea()"

Edvard

Thank you Edvard.





Regards.








Saif