Transform

You can add customized transformations to the standardization list using the Transform action. Two tabs are available in the options panel for this action:

  • Scheme tab: Edit transformations as reactions here.

    images/download/attachments/1803714/transform_example.png

    Do not forget mapping: by default, Standardizer assumes that changing atoms are mapped (ChemAxon mapping style).

    Double-click to edit structure: You can edit here the transformation and when you have finished drawing the transform, expand the drawing window and click the Accept button at bottom to return to the Standardizer window.

    images/download/attachments/1803714/Transform1.png

    images/download/attachments/1803714/Transform_Accept.png
  • Options tab: Set the Match Options to filter the input molecules.

    images/download/attachments/1803714/transform_options.png

    The transformation will only be executed if the input species meets the selected matching options. Find details on matching options here.

Using action strings in command line, you can define custom transformations as follows:

  • type a mapped reaction SMARTS/SMIRKS;
    Example:

    standardize -c "[O:3]=[N:1]=[O:2]>>[#8-:2]-[#7+:1]=[O:3]" "O=N(=O)C1CCCCC1"
    [O-][N+](=O)C1CCCCC1
    standardize -c "c1ccccc1>>" "O=N(=O)C1CCCCC1.c1ccccc1"
    O=N(=O)C1CCCCC1

Note :

  • Resetting default search options: remove "transform" from the standardizer list and add it again.

  • For a description of reaction mapping, see the Reaction mapping section of the Reactor Manual.