Possible to set timelimit for Standardizer?

I get the warning "Timelimit exceeded. Try to increase timelimit with option [timelimit]" for some structures of a large SD file. I tried to see which structures needed more time but neither the "-v" nor "--log" options were helpful (even with loglevel set to info).

I didn't find a way to set a time limit in the manual. The obvious "-l" or "--timelimit" command-line options weren't recognized. Is there some other way to pass this option to the function that needs it?

Thanks in advance,

Wes

Could you send us the relevant Standardizer configuration? 

Best Regards, 
Viktoria 

vpalfi wrote:

Could you send us the relevant Standardizer configuration?  Best Regards,  Viktoria



My Standardizer config is shown below. I tried leaving out the Clean command but get the same errors. Namely, timelimit violations with no way to reset the limit or see which entries cause the problem (without diving the file into small chunks, etc). This seems like a general situation.

---

<?xml version="1.0" encoding="UTF-8"?>
<!-- Standardizer configuration file -->

<StandardizerConfiguration Version ="0.1" schemaLocation="standardize.xsd">
    <Actions>
    <Action ID="keepone" Act="keepone"/>
    <Action ID="aliastogroup" Act="aliastogroup"/>
    <Action ID="aliastoatom" Act="aliastoatom"/>
    <Action ID="clearisotopes" Act="clearisotopes"/>
    <Action ID="removergroupdefinitions" Act="removergroupdefinitions"/>
    <Action ID="removeatomvalues" Act="removeatomvalues"/>
    <Action ID="removeattacheddata" Act="removeattacheddata"/>
    <Action ID="neutralize" Act="neutralize"/>
    <Action ID="aromatize" Act="aromatize"/>
    <Action ID="tautomerize" Act="tautomerize"/>
    <Action ID="dehydrogenize" Act="dehydrogenize"/>
    <Clean  ID="cleanIfNeeded"/>
    </Actions>
</StandardizerConfiguration>

We found a bug in Standardizer: "tautomerize" action cleans structures in 3D sometimes, the timelimit warning is displayed by 3D clean. The bug will be fixed in JChem 5.12, "tautomerize" will not clean the structures in 3D.

The format of the attached standardizer configuration is very old, and it is not supported by newer standardizer versions. Please update your configuration. Find the new configuration below.

 

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

<!--This file is created with ChemAxon's Configuration Builder-->
<!--This is a configuration file for ChemAxon's Standardizer-->
<StandardizerConfiguration>
  <Actions>
    <Removal ID="RemoveFragment" Method="keepLargest" Measure="atomCount"/>
    <AliasToGroup ID="AliasToGroup"/>
    <AliasToAtom ID="AliasToAtom"/>
    <ClearIsotopes ID="ClearIsotopes"/>
    <Removal ID="RemoveRGroups" Method="rgroups"/>
    <RemoveAtomValues ID="RemoveAtomValues"/>
    <RemoveAttachedData ID="RemoveAttachedData"/>
    <Neutralize ID="Neutralize"/>
    <Aromatize ID="Aromatize" Type="general"/>
    <Tautomerize ID="Tautomerize"/>
    <RemoveExplicitH ID="RemoveExplicitH"/>
    <Clean ID="Clean2D" Dim="2" Type="Partial"/>
  </Actions>
</StandardizerConfiguration>