Standardizer Actions

List of Available Standardizer Actions

• Add Explicit Hydrogens

• Alias to Atom

• Alias to Group

• Aromatize

• Clean 2D

• Clean 3D

• Clear Isotopes

• Clear Stereo

• Contract S-groups

• Convert Double Bonds

• Convert Pi-metal Bonds

• Convert to Enhanced Stereo

• Create Group

• Dearomatize

• Disconnect Metal Atoms

• Expand S-groups

• Expand Stoichiometry

• Map

• Map Reaction

• Mesomerize

• Neutralize

• Rearrange Reaction

• Remove Absolute Stereo

• Remove Atom Values

• Remove Attached Data

• Remove Explicit Hydrogens

• Remove Fragment

• Remove R-group Definitions

• Remove Solvents

• Remove Stereo Care Box

• Replace Atoms

• Set Absolute Stereo

• Set Hydrogen Isotope Symbol

• Strip Salts

• Tautomerize

• Transform

• Ungroup S-groups

• Unmap

• Wedge Clean

• Transform Standardizer

Besides the wide range of built-in Standardizer actions, custom Standardizer actions can also easily be defined and executed with Standardizer.

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General Comments

If an action has more than one options but none of them is specified by the user, the action with default option will be performed.

If the output format contains atom coordinates (e.g., mrv, sdf, mol, etc.), and the standardizer action changes any atom coordinate, a built-in clean action will be performed at the end of the standardization process according to the following:

• If the input format is in 0D (e.g., SMILES), the built-in clean action is "full clean".

• If the input format is in 2D (e.g., mrv), the built-in clean action is "partial clean".

• If the input format is in 3D (e.g., mrv), the built-in clean action is "clean3D".

The order of actions in a standardizer configuration is important since the output of the first transformation will become the input of the second one, and so on.

Keep in mind that numerous actions rely on substructure search , where the proper substructure definition has key importance.