Standardizer GUI - How to add own commands?

Hi,


how can I add my own XML commands (from the old commandline standardizer) to the Standardizer GUI with explanation and icon? Or are these hard-coded?


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Also I could not find the GUI XML editor for ChemAxon (I use the one of the free XML Notepads).


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For the GUI I also liked the example picture which are included in the DOC files, because this helps to understand whats going on, so they also could be very helpful in the Alchemist GUI.





Thank you.


Tobias

Hi,

TobiasKind wrote:

Hi, how can I add my own XML commands (from the old commandline standardizer) to the Standardizer GUI with explanation and icon? Or are these hard-coded?

You can use your existing Standardizer configuration XML-s with the GUI: open them in "Step 2 - Create configuration" step using "Open configuration" dialog.





Transform actions can be added, but the other actions in Standardizer are hard coded. To add a transform action add "Transform" to the configuration and create a transform using MarvinSketch, or just load an existing one. Transforms can be saved with name for later usage. Let me know if you need further help on this.

Quote:

Also I could not find the GUI XML editor for ChemAxon (I use the one of the free XML Notepads).

You do not need an XML editor if you use the Standardizer GUI. It is created to eliminate the need of editing the Standardizer configuration XML-s by hand. The created XML-s can be saved and used also with the command line Standardizer or with the API.

Quote:

For the GUI I also liked the example picture which are included in the DOC files, because this helps to understand whats going on, so they also could be very helpful in the Alchemist GUI.

All the documentation for Standardizer (GUI, command line tool, examples, flash animation, developer's guide) can be accessed from this page: http://www.chemaxon.com/jchem/doc/user/Standardizer.html?menu=af568df0





Best regards,


Zsolt

Hi Zsolt,


thanks alot. As I am not a command line guy and like the GUI because I dont want to know all the "secrets" about SMARTS programming (there are probably lots of people who know better) I just want to perform some click


and assign tasks.





If I want to repeat the remove solvent example, I come into serious trouble. I just wanted to import that file into the GUI.


The original XML file from your website says:





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


<StandardizerConfiguration Version="0.1">


<Actions>


<Aromatize ID="aromatize"/>


<Transformation ID="water" Structure="O>>" Exact="true"/>


<Transformation ID="methanol" Structure="CO>>" Exact="true"/>


<Transformation ID="ethanol" Structure="CCO>>" Exact="true"/>


<Transformation ID="dichloromethane" Structure="ClCCl>>" Exact="true"/>


<Transformation ID="chloroform" Structure="ClC(Cl)Cl>>" Exact="true"/>


<Transformation ID="diethylether" Structure="CCOCC>>" Exact="true"/>


<Transformation ID="diisopropylether" Structure="C(C)COC(C)C>>" Exact="true"/>


<Transformation ID="tetrahydrofuran" Structure="C1CCOC1>>" Exact="true"/>


<Transformation ID="acetone" Structure="CC(=O)C>>" Exact="true"/>


<Transformation ID="dimethylsulfoxyde" Structure="CS(=O)C>>" Exact="true"/>


<Transformation ID="ethylacetate" Structure="CC(=O)OCC>>" Exact="true"/>


<Transformation ID="dimethylformamide" Structure="CN(C)C=O>>" Exact="true"/>


<Transformation ID="acetonitrile" Structure="CC#N>>" Exact="true"/>


<Transformation ID="benzene" Structure="c1ccccc1>>" Exact="true"/>


</Actions>


</StandardizerConfiguration>





However, importing that gives me just errors after I pressed the finish button. Somehow I could not built an action string.





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





The other example is the Nitro cleaning.





"{query,target}aromatize..{target}removeexplicith..{g1,g2}[*+:1]-[*-:2]>>[*:1]=[*:2]..{g1}[*+:1]=[*-:2]>>[*:1]#[*:2]..[O:3][C:1]=[C:2]>>[C:2][C:1]=[O:3]"





The problem here is, that I can not built multiple actions in the marvin editor and my result file looks like that (exportet from the Standardizer GUI)





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


<!-- Standardizer configuration file -->


<!-- This configuration file is created with ChemAxon Config Builder -->





<StandardizerConfiguration Version ="0.1">


<Actions>


<RemoveExplicitH ID="removeexplicith" Lonely="true" Isotope="true" Charged="true" Radical="true" Mapped="true" Wedged="true"/>


<Aromatize ID="aromatize" Type="general"/>


<Transformation ID="Nitro-Transform" Structure="[*+:1]-[*-:2]>>[*:1]=[*:2] and [*+:1]=[*-:2]>>[*:1]#[*:2] and [O:3][C:1]=[C:2]>>[C:2][C:1]=[O:3]" Type="string"/>


</Actions>


</StandardizerConfiguration>





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


A third example, which I just want to use is from your website the complex standardization





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


<StandardizerConfiguration Version="0.1">


<Actions>


<Aromatize ID="aromatize"/>


<Dehydrogenize ID="dehydrogenize"/>


<Transformation ID="nitro" Structure="[O-:2][N+:1]=O>>[O:2]=[N:1]=O"/>


<Transformation ID="azide" Structure="N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]"/>


<Transformation ID="ammoniumhalide" Structure="C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1]"/>


<Transformation ID="enamine" Structure="[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]"/>


<Transformation ID="enol" Structure="[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]"/>


<Clean ID="cleanIfNeeded" />


</Actions>


</StandardizerConfiguration>





action string:





"aromatize..dehydrogenize..[O-:2][N+:1]=O>>[O:2]=[N:1]=O.. \


N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]..C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1].. \


[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]..[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]..clean"





which resulted in that XML file after exporting it into the GUI and


where you have to make sure because the dehydrogenize command is not available in the GUI (as is) that charged, radical, mapped, or isotope hydrogens are not removed:








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


<!-- Standardizer configuration file -->


<!-- This configuration file is created with ChemAxon Config Builder -->





<StandardizerConfiguration Version ="0.1">


<Actions>


<Aromatize ID="aromatize" Type="general"/>


<RemoveExplicitH ID="removeexplicith" Lonely="true" Wedged="true"/>


<Transformation ID="Complex Standardization (1)" Structure="[O-:2][N+:1]=O>>[O:2]=[N:1]=O and N=[N:1]#[N:2]>>N=[N+:1]=[N-:2] and C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1]..[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3] and [H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]" Type="string"/>


</Actions>


</StandardizerConfiguration>








The proble here is (clean is not included) that if I have ".." in the string the GUI parser does not accept that, it only accepts "and", but if you look into the GUI output there are some ".." and also some "and". So this is very confusing.





Tobias

Hi,

TobiasKind wrote:

If I want to repeat the remove solvent example, I come into serious trouble. I just wanted to import that file into the GUI. The original XML file from your website says: <?xml version="1.0" encoding="UTF-8" ?> <StandardizerConfiguration Version="0.1"> <Actions> <Aromatize ID="aromatize"/> <Transformation ID="water" Structure="O>>" Exact="true"/> <Transformation ID="methanol" Structure="CO>>" Exact="true"/> <Transformation ID="ethanol" Structure="CCO>>" Exact="true"/> <Transformation ID="dichloromethane" Structure="ClCCl>>" Exact="true"/> <Transformation ID="chloroform" Structure="ClC(Cl)Cl>>" Exact="true"/> <Transformation ID="diethylether" Structure="CCOCC>>" Exact="true"/> <Transformation ID="diisopropylether" Structure="C(C)COC(C)C>>" Exact="true"/> <Transformation ID="tetrahydrofuran" Structure="C1CCOC1>>" Exact="true"/> <Transformation ID="acetone" Structure="CC(=O)C>>" Exact="true"/> <Transformation ID="dimethylsulfoxyde" Structure="CS(=O)C>>" Exact="true"/> <Transformation ID="ethylacetate" Structure="CC(=O)OCC>>" Exact="true"/> <Transformation ID="dimethylformamide" Structure="CN(C)C=O>>" Exact="true"/> <Transformation ID="acetonitrile" Structure="CC#N>>" Exact="true"/> <Transformation ID="benzene" Structure="c1ccccc1>>" Exact="true"/> </Actions> </StandardizerConfiguration> However, importing that gives me just errors after I pressed the finish button. Somehow I could not built an action string.

It works for me. What is the error message you get? Does the standardizer actions appear on the right panel when you open the config file?

Quote:

The other example is the Nitro cleaning. "{query,target}aromatize..{target}removeexplicith..{g1,g2}[*+:1]-[*-:2]>>[*:1]=[*:2]..{g1}[*+:1]=[*-:2]>>[*:1]#[*:2]..[O:3][C:1]=[C:2]>>[C:2][C:1]=[O:3]" The problem here is, that I can not built multiple actions in the marvin editor and my result file looks like that (exportet from the Standardizer GUI) <?xml version="1.0" encoding="UTF-8"?> <!-- Standardizer configuration file --> <!-- This configuration file is created with ChemAxon Config Builder --> <StandardizerConfiguration Version ="0.1"> <Actions> <RemoveExplicitH ID="removeexplicith" Lonely="true" Isotope="true" Charged="true" Radical="true" Mapped="true" Wedged="true"/> <Aromatize ID="aromatize" Type="general"/> <Transformation ID="Nitro-Transform" Structure="[*+:1]-[*-:2]>>[*:1]=[*:2] and [*+:1]=[*-:2]>>[*:1]#[*:2] and [O:3][C:1]=[C:2]>>[C:2][C:1]=[O:3]" Type="string"/> </Actions> </StandardizerConfiguration>

Standardizer GUI does not support task groups. We recommend you to use separate configuration xml files for each group of molecule files you have (e.g. query, target).





Using Standardizer task groups is recommended only in special cases (e.g. Reactor uses task goups for separate standardization of the reactants).

Quote:

A third example, which I just want to use is from your website the complex standardization <?xml version="1.0" encoding="UTF-8" ?> <StandardizerConfiguration Version="0.1"> <Actions> <Aromatize ID="aromatize"/> <Dehydrogenize ID="dehydrogenize"/> <Transformation ID="nitro" Structure="[O-:2][N+:1]=O>>[O:2]=[N:1]=O"/> <Transformation ID="azide" Structure="N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]"/> <Transformation ID="ammoniumhalide" Structure="C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1]"/> <Transformation ID="enamine" Structure="[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]"/> <Transformation ID="enol" Structure="[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]"/> <Clean ID="cleanIfNeeded" /> </Actions> </StandardizerConfiguration> action string: "aromatize..dehydrogenize..[O-:2][N+:1]=O>>[O:2]=[N:1]=O.. \ N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]..C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1].. \ [H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]..[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]..clean" which resulted in that XML file after exporting it into the GUI and where you have to make sure because the dehydrogenize command is not available in the GUI (as is) that charged, radical, mapped, or isotope hydrogens are not removed: <?xml version="1.0" encoding="UTF-8"?> <!-- Standardizer configuration file --> <!-- This configuration file is created with ChemAxon Config Builder --> <StandardizerConfiguration Version ="0.1"> <Actions> <Aromatize ID="aromatize" Type="general"/> <RemoveExplicitH ID="removeexplicith" Lonely="true" Wedged="true"/> <Transformation ID="Complex Standardization (1)" Structure="[O-:2][N+:1]=O>>[O:2]=[N:1]=O and N=[N:1]#[N:2]>>N=[N+:1]=[N-:2] and C[N+:1][H:2].[F,Cl,Br,I;-:3]>>C[N:1]..[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3] and [H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]" Type="string"/> </Actions> </StandardizerConfiguration> The proble here is (clean is not included) that if I have ".." in the string the GUI parser does not accept that, it only accepts "and", but if you look into the GUI output there are some ".." and also some "and". So this is very confusing.

Code:

<Dehydrogenize ID="dehydrogenize"/>

was the old action for

Code:

<RemoveExplicitH ID="removeexplicith" Lonely="true" Isotope="true" Charged="true" Radical="true" Mapped="true" Wedged="true"/>

If you replace the old one with the new one it will work. You can use the GUI to specify which hydrogens you want to remove. We will update the documentation before we release the new version of JChem.





Best regards,


Zsolt

Zsolt wrote:

Quote: The other example is the Nitro cleaning. "{query,target}aromatize..{target}removeexplicith..{g1,g2}[*+:1]-[*-:2]>>[*:1]=[*:2]..{g1}[*+:1]=[*-:2]>>[*:1]#[*:2]..[O:3][C:1]=[C:2]>>[C:2][C:1]=[O:3]" The problem here is, that I can not built multiple actions in the marvin editor and my result file looks like that (exportet from the Standardizer GUI) <?xml version="1.0" encoding="UTF-8"?> <!-- Standardizer configuration file --> <!-- This configuration file is created with ChemAxon Config Builder --> <StandardizerConfiguration Version ="0.1"> <Actions> <RemoveExplicitH ID="removeexplicith" Lonely="true" Isotope="true" Charged="true" Radical="true" Mapped="true" Wedged="true"/> <Aromatize ID="aromatize" Type="general"/> <Transformation ID="Nitro-Transform" Structure="[*+:1]-[*-:2]>>[*:1]=[*:2] and [*+:1]=[*-:2]>>[*:1]#[*:2] and [O:3][C:1]=[C:2]>>[C:2][C:1]=[O:3]" Type="string"/> </Actions> </StandardizerConfiguration> Standardizer GUI does not support task groups. We recommend you to use separate configuration xml files for each group of molecule files you have (e.g. query, target). Using Standardizer task groups is recommended only in special cases (e.g. Reactor uses task goups for separate standardization of the reactants).

Sorry, I was wrong. Standardizer GUI already supports task groups. You can add an action to a group by right clicking the action and specifying the group(s) it belongs to. The actions have to be added to the configuration (have to be on the right panel) before setting their group.





Regards,


Zsolt