Problem with the action "Aromatize" on a pyrrol gr

Hello,


I have a little problem when I apply the command "standardize" on a molecule that contain a pyrrol group. I used a very simple XML config file:


<?xml version="1.0" encoding="UTF-8" ?>


- <StandardizerConfiguration schemaLocation="standardize.xsd">


- <Actions>


<Removal ID="keepOne" Method="keepLargest" Measure="atomCount" Optional="false" />


<Action ID="Aromatize" Act="aromatize" Optional="false" />


<Action ID="Dehydrogenize" Act="dehydrogenize" Optional="false" />


<Action ID="Aromatize2" Act="aromatize" Optional="false" />


<Clean ID="CleanIfNeeded" Always="false" Optional="false" />


</Actions>


</StandardizerConfiguration>


and the molecule on wich I apply the standardizer is the molecule attached in this post, named "molecule_test.sdf" and contain a pyrrol group. I used the command below with "standardize" in jchem3.0.14:


standardize molecule_test.sdf -c Standardize.xml -f sdf -o molecule_test_standardize.sdf


My problem is that when I open the resulting molecule "molecule_test_standardize.sdf" with mview (in MarvinBean4.0), the H on the N atom on the pyrrol group doesn't appears anymore, even if I apply "Add explicit H", and I couldnt' dearomatize my molecule too (the command "dearomatize" doesn't work on the viewer or on batch mode for this molecule "molecule_test_standardize.sdf".


I have also this problem when I use the molecule obtain before I apply calculator plugins majorms:


cxcalc -o molecule_test_mjms.sdf majorms -H 7.4 molecule_test.sdf -f sdf


Could you help me or explain me how I can correct y problem?


Thanks, regards


Samia ACI

The problem is that the SDF format cannot store aromatized molecules properly (cannot store the implicit H count). The solution is to dearomatize the molecule before saving. This can be done either in the Standardizer configuration XML or in the output format itself.





Type

Code:

standardize molecule_test.sdf -c Standardize.xml -f sdf:-a -o molecule_test_standardize.sdf

Note, that the format sdf:-a means dearomatization before saving into SDF.


Or else, you can use a different XML (attached) to perform the dearomatization:

Code:

standardize molecule_test.sdf -c StandardizeDearom.xml -f sdf -o molecule_test_standardize.sdf

Note, that the final Clean task is not needed in the latest JChem release: the changed atoms are cleaned automatically, while coordinates are preserved in the unchanged part.





The same sdf:-a format option should be used with cxcalc:

Code:

cxcalc -o molecule_test_mjms.sdf majorms -H 7.4 molecule_test.sdf -f sdf:-a

Note, that in this case the output is pure SDF (without the table header and the ID column) if you set the cxcalc parameter -N hi:

Code:

cxcalc -N hi -o molecule_test_mjms.sdf majorms -H 7.4 molecule_test.sdf -f sdf:-a

This is a bit uncomfortable and therefore these molecule outputs will be automatically written without the table header and the ID column from the next Marvin release.

Thanks a lot for your answer, I will used the parameter "sdf:-a" now! I also tried to use your parameter "-N:hi" in my calculation of the Major microspecies, but I have an other problem: I use a SDF file wich contain several molecules and, with the parameter "-N:hi" of course I don't anymore have neither the header nor the id but it appears an additionnal blank line between each molecules that prevent me to see my resulting SDF file with the Marvin viewer. Is ther an other option that could sort out this problem? Thanks again, regards,


Samia ACI

Hello,





The next version of JChem (3.1.2) will contain a molfile/SDfile extension which will allow us to store implicit hydrogens on aromatic nitrogens. However, this extension will only be read correctly by the latest Marvin and JChem versions.





For details, see the following forum topic:


http://www.chemaxon.com/forum/ftopic814.html





Best regards,





Szabolcs

samaci wrote:

Thanks a lot for your answer, I will used the parameter "sdf:-a" now! I also tried to use your parameter "-N:hi" in my calculation of the Major microspecies, but I have an other problem: I use a SDF file wich contain several molecules and, with the parameter "-N:hi" of course I don't anymore have neither the header nor the id but it appears an additionnal blank line between each molecules that prevent me to see my resulting SDF file with the Marvin viewer. Is ther an other option that could sort out this problem? Thanks again, regards, Samia ACI

I could not reproduce this: I tested with the latest JChem 3.1.1 and also with JChem 3.0.13 and both work fine. Could you send your input file (or a 3-4 molecule fragment of it if ti is too big) and the exact command line that you run?

I send you the files I used for the test. The command lines I runned was the ones below:





standardize molecules_test3.sdf -c Standardize.xml -f sdf:-a -o molecules_test3_standardize.sdf


cxcalc -N hi -o molecules_test3_standardize_mjms.sdf majorms -H 7.4 molecules_test3_standardize.sdf -f sdf:-a





and I use the Calculator version 4.0 (in Marvin4.0).


Thanks a lot for your answers, regards


Samia ACI

Sorry, I forgot the last commande line and the message error:


mview molecules_test3_standardize_mjms.sdf





Exception in thread "main" java.lang.NullPointerException


at chemaxon.marvin.modules.MolImport.readPropertiesBlockV2(Unknown Source)


at chemaxon.marvin.modules.MolImport.readCtab(Unknown Source)


at chemaxon.marvin.modules.MolImport.readMol0(Unknown Source)


at chemaxon.marvin.modules.MolImport.readMol(Unknown Source)


at chemaxon.formats.MolImporter.readDoc(Unknown Source)


at chemaxon.marvin.View.readStream(Unknown Source)


at chemaxon.marvin.View.main(Unknown Source)





and if I suppress a blank line between each molecule, the command line work and I see my molecules.


Thanks!

This is strange: I could reproduce the problem (the extra blank lines and the mview exception) with the Marvin 4.0.2pre-release but it is OK in the current CVS version as well as in the latest JChem 3.1.1 (including Marvin 4.0.1). I suggest that you should download this latest JChem from


www.chemaxon.com/jchem

You are totally right: it works perfectly when I use the last release of jchem (Jchem3.1.1). Thanks a lot for your answers and advice, regards,


Samia ACI