Structure Transformation Actions

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There are some structure transformation actions, which are not available in the JChem for Excel ribbon/context menu/menu/toolbar by default, but it is possible to make them available by customization of the ribbon/context menu/menu/toolbar. The Images folder contains images (AromatizeStructureAction.png, DearomatizeStructureAction.png, ThreeDCleanStructureAction.png, TwoDCleanStructureAction.png, HydrogenizeToStructureAction.png, DehydrogenizeStructureAction) which can be used as icons for these functions.

 

AromatizeStructureAction

Changes the type of alternating single-double bonds of aromatic rings to aromatic bonds.

 

       

 

DeromatizeStructureAction

Converts aromatic bonds to alternating single-double bonds.

 

 

         

 

ThreeDCleanStructureAction

Calculates new 3D coordinates for the molecule. Clean3D builds up conformers of fragments from which the best, i.e. the lowest energy conformer is given back. The quality of the structures is measured by a simple energy function (Dreiding type molecular mechanics).

 

       

 

TwoDCleanStructureAction

Calculates new 2D coordinates for the molecule.

 

         

 

HydrogenizeToStructureAction

Converts implicit hydrogens to explicit (adds hydrogen atoms to the molecule graph).

 

       

 

DehydrogenizeStructureAction

Converts explicit hydrogens to implicit (removes hydrogen atoms from the molecule graph). Charged, radical, mapped, isotope or wedged hydrogens are not removed.

 

         

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