Standardizer Simple Examples

Version 5.3.1

Contents

The XML action examples of the following examples demonstrate the most important section of the Standardizer configuration, the action list within the <Actions>...</Actions> tags.
 

Built-in tasks

Aromatizing rings - default method
XML action: <Aromatize/>
action string: "aromatize"
Changes the type of alternating single-double bonds of aromatic rings to aromatic.

Aromatizing rings - basic method
XML action: <Aromatize Type="basic"/>
action string: "aromatize:b"
Aromatizes compounds according to the basic aromatization method.

Dearomatizing structures
XML action: <Deromatize/>
action string: "dearomatize"
Converts aromatic bonds to alternating single-double bonds.

Rearomatizing incorrectly aromatized rings
XML action: 
<Dearomatize/>
<Aromatize/>
action string: "dearomatize..aromatize"
Rearomatizes aromatic rings by an other aromatization method, or correcting wrong aromatizations (dearomatizes first).

Adding explicit hydrogen atoms
XML action: <AddExplicitH/>
action string: "addeexplicitH"
Converts implicit hydrogens to explicit (adds hydrogen atoms to the molecule graph).

Removing explicit hydrogen atoms
XML action: <RemoveExplicitH/>
action string: "removeexplicitH"
Converts explicit hydrogens to implicit (removes hydrogen atoms from the molecule graph).
Charged, radical, mapped, isotope or wedged hydrogens are not removed.

Removing special hydrogen atoms
XML action: <RemoveExplicitH Charged="true" Radical="true" Isotope="true" Mapped="true" Wedge="true"/>
Converts explicit hydrogens to implicit (removes hydrogen atoms from the molecule graph).
Customize how charged, radical, mapped, or isotope hydrogens are handled.

Recalculating atom coordinates
XML action: <Clean/>
action string: "clean:full"
Calculates two-dimensional coordinates for quality display with the clean function.

Calculating atom coordinates by given templates
XML action: <Clean Type="TemplateBased" TemplateFile="templates.mrv"/>
action string: "clean:<templates.mrv>"
Cleans structures according to scaffolds specified in a template file.

Removing counter ions and fragments
XML action: <Removal Method="keepLargest" Measure="molMass"/>
action string: "keepone:mass"
Removes separated components (fragments) of the molecules.
One available mthod is "keepLargest" to delete all fragments but the largest one. The fragment size is determined by molecular mass or the number of atoms (default).

Removing stereo features
XML action: <ClearStereo Type="doubleBond"/>
action string: "clearstereo:doublebond"
Stereo features of molecules can be removed by the ClearStereo action. In case of the "doubleBond" type the stereo configuration of the double bonds are removed. If the type is "chirality", then the tetrahedral stereo features are removed racemizing the compounds. if the Type attribute is omitted then both stereo types are removed.

Setting the "Chiral" flag
XML action: <AbsoluteStereo Act="set"/>
action string: "absolutestereo:set"
Sets the MDL "Chiral" flag if a structure has tetrahedral stereo center. Use Act="clear" ("absolutestereo:clear" in the action string) to remove the "Chiral" flag.

Ungrouping Sgroups
XML action: <Sgroups ID="ungroup" Act="ungroup"/>
action string: "sgroups:ungroup"
Ungroups abbreviated groups or multiple groups with the Sgroups action.

Neutralizing atoms
XML action: <Neutralize"/>
action string: "neutralize"
Neutralizes charged atoms. Mesomers like nitro or groups or quaternary nitrogens without hydrogen remain intact.

Clearing isotopes
XML action: <ClearIsotopes"/>
action string: "clearisotopes"
Converts isotopes to elemental atoms.

Adding atom maps
XML action: <MapReaction"/>
action string: "mapreaction"
Adds atom map numbers. The UnmapReactions action can remove atom maps.

 

Custom conversions

You can define custom transformations in the Structure attribute of the Transformation action. Simply type a reaction SMARTS/SMIRKS or specify the name of a reaction file. Do not forget mapping: by default, Standardizer assumes that changing atoms are mapped (ChemAxon mapping style). You can also specify an alternative mapping style in the MappingStyle attribute of the Actions element: set this to "matching" if matching atoms are mapped (Daylight style) or to "partial" for automatic mapping (experimental).


Converting nitro mesomers
XML action: <Transformation ID="nitro" Structure="[O-:2][N+:1]=O>>[O:2]=[N:1]=O"/>
action string: "[O-:2][N+:1]=O>>[O:2]=[N:1]=O"

Converting azide mesomers
XML action: <Transformation ID="azide" Structure="N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]"/>
action string: "N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]"

Converting oxo-enol tautomers
XML action: <Transformation ID="enol" Structure="[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]"/>
action string: "[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]"

Converting enamine-imine tautomers
XML action: <Transformation ID="enamine" Structure="[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]"/>
action string: "[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]"

Ynol-ketene conversion
XML action: <Transformation ID="ynol" Structure="[H:4][O:3][C:1]#[C:2]>>[H:4][C:2]=[C:1]=[O:3]"/>
action string: "[H:4][O:3][C:1]#[C:2]>>[H:4][C:2]=[C:1]=[O:3]"

Nitroso-oxime tautomerism
XML action: <Transformation ID="nitroso" Structure="[#6][CH1:3]([#6])[N:1]=[O:2]>>[#6][CH0:3]([#6])=[N:1][#8H1:2]"/>
action string: "[#6][CH1:3]([#6])[N:1]=[O:2]>>[#6][CH0:3]([#6])=[N:1][#8H1:2]"

Pyridone-pyridol type tautomerism
XML action: 
<Aromatize ID="aromatize"/>
<Transformation ID="pyridone" Structure="[H:4][n:3]:[c:1]=[O:2]>>[O:2]-[c:1]:[n:3]"/>
action string: "aromatize..[H:4][n:3]:[c:1]=[O:2]>>[O:2]-[c:1]:[n:3]"

Converting covalent form of alcoholates to ionic form
XML action: <Transformation ID="alcoholate" Structure="[#6][O:1][Na:2]>>[#6]-[#8-:1].[Na+:2]"/>
action string: "[#6][O:1][Na:2]>>[#6]-[#8-:1].[Na+:2]"

Hydrochloric acid removal from ammonium salts
XML action: <Transformation ID="ammoniumhalide" Structure="C[N+:1][H:2].[F,Cl,Br,I-:3]>>C[N:1]"/>
action string: "C[N+:1][H:2].[F,Cl,Br,I-:3]>>C[N:1]"

Replacing atoms with isotopes
XML action: <Transformation ID="replace isotopes" Structure="[H:2][O:1][#6:3]>>[2#1A:2][18O:1][14#6:3]"/>
action string: "[H:2][O:1][#6:3]>>[2#1A:2][18O:1][14#6:3]"

Removing large counterions
XML action: <Transformation ID="phenyletylammonium" Structure="[C:8][C:7]([N+:9])[c:6]1[c:1][c:2][c:3][c:4][c:5]1.[O-]C=O>>[O]C=O"/>
action string: "[C:8][C:7]([N+:9])[c:6]1[c:1][c:2][c:3][c:4][c:5]1.[O-]C=O>>[O]C=O"

Removing solvents
XML action: 
<?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>

Complex standardization
XML action: 
<?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"

 
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