Structure checker

 

Dear Chemaxon Team,

We are having some query in structure checker command line.

We have defined a structure checker option with mode as fix in
the structure checker configuration file.

In the command line we do not give the mode as fix.

What will happen if we process the sd file with the structure
checker config file in the command line for this case?

Will the structure checker consider the structure checker
optionin the config file and will it
apply the fix for
the sd file (mode given as fix in config file, but the mode is not mentioned in
the command line)?

Please find the sample config file option and command line as reference for the above query.

 

structure checker config file with an option:

<WedgeErrorChecker fixMode="fix" fixerClassName="chemaxon.fixers.WedgeCleanFixer"/>

 

command line(mode is not mentioned):

structurechecker –c checker_example_configuration.xml -f sdf -t separated -o out.sdf -l log.sdf -rf rpt.sdf input.sdf

 

 

 

Do we need to provide the -m fix in the command line to apply the fix, then only it will fix as per the config file option?

 

command line(mode as fix):

structurechecker –c checker_example_configuration.xml -m fix -f
sdf -t separated -o out.sdf -l log.sdf -rf rpt.sdf input.sdf

 

 

Please look into this and reply us the solution ASAP.

 

Thanks & Regards,

D. Senthil kumar vijai.

 

 

Dear Senthil ,

The table below summarizes the possible structurechecker command line behavior according to the set fixMode in configuration XML file and selected command line option (-m).

		fixMode setting of action in the Configuration XML
		fixMode="fix"	fixMode="ask"	fixMode="do_not_fix"
command- line option	-	check is performed	check is performed	check is performed
	-m check	check is performed	check is performed	check is performed
	-m fix	fix is performed	fix is performed	check is performed

If you have more questions, do not hesitate to contact us.

Best regards, 

Viktoria

Dear Viktoria,

Thanks for your reply, and for the presenting the below details of "possible structurechecker command line behavior".

		fixMode setting of action in the Configuration XML
		fixMode="fix"	fixMode="ask"	fixMode="do_not_fix"
command- line option	-	check is performed	check is performed	check is performed
	-m check	check is performed	check is performed	check is performed
	-m fix	fix is performed	fix is performed	check is performed

Still we have the below query on the behaviour of the command line structure checker.

We think the above highlighted combination (mentioned in the table) will not be possible in the Jchem Structuer checker. 

We have tried the below excercise in the structure checker with "fixMode setting of action in the Configuration XML = fixMode="ask", and command line option = -m fix", we are not getting the result as "fix is performed" as you mentioned in the table. Please clarify us on this.

-----------sample excersie-----------------------------

I have a molecule with bondlengtherror in it. The sd file is in the attachment (bondlength.sdf).

The structure checker settings configuration file has a checker option( as bondlength checker with mode as 'ask').

Our intention is, whenever a molecule has bondlength error, it should check for this error in the molecule and it should ask the user to fix the error, that means it should not fix the error in the molecule. The checker settings config file is bondlengthcheckerconfig.xml.

We are going to validate the structures using structure checker command line.

We defined the mode as fix (i.e., -m fix) in the command line. 

The Command line is:

structurechecker -c bondlengthcheckerconfig.xml -m fix -f sdf -t separated -o out_bl.sdf -l log_bl.sdf -rf rpt_bl.sdf bondlength.sdf

The structure checker setting config file option is:

<BondLengthChecker fixMode="ask" fixerClassName="chemaxon.fixers.CleanFixer" long="true" short="true"/>

Finally when we run the command line, It validated the structure and it found the bond length error in the structure. Then it has not fixed the bond length error, because the config setting file fix mode is "ask". It has not written any output to the output file.

---------------------------------------------------------------

So the highlighted behaviour(you mentioned in the table) is not possible in the structure checker.  if you are correct on this, please reply to us.

Thanks & Regards,

D. Senthil kumar vijai.

Dear Senthil, 

First of all, I need to make a quick amendment: I should have written "expected structurechecker command line behavior" instead of "possible structurechecker command line behavior".

I can verify that you are right; in version 5.10.x, it did not work as depicted in my table, your observation is correct. 

However, we fixed this issue in version 5.11.2.

Best regrads, 

Viktoria