Software Developer's Kit - ChemDraw

         

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Atom to Atom Mapping Overview
Project Overview
pVal
[in] Adds this atom to the collection of mapped atoms.

Description

You can create correspondences between atoms in different structures to use in creating queries to search reaction databases. The reactions mapped can be single or multi-step. You can assign atom-to-atom mapping creating records for a reaction database and for creating queries to search reaction databases.

The mapping algorithm perceives and assigns a reaction center for the reactants and products.

When a reaction map is established, you can point to an atom in one structure with the reaction atom-atom map tool selected to highlight the mapped atom in the other structure. Atom mapping can be assigned in two ways:

    
- Automatic mapping

Draw the reaction you want to map and select reactants and products. Click the map reaction atoms command on the structure menu. The symbol Rxn appears next to the bonds in the reactant and product that are perceived by the algorithm as being modified by the reaction. These symbols are bond properties that are automatically applied.

See diagram on the left, where the number 1 indicates the atoms that are mapped. 

    

 - Manual mapping

In situations that require manual mapping of atoms, you can use the reaction atom-atom map tool
A-->A on the main tool palette. This might be necessary when the automatic mapping is applied to complicated reactions, and gives incorrect results. In these cases you can manually readjust the reaction mapping.

                                       See diagram on the right, you must indicate which atoms you want to map.
 

Note:  Preferences.ShowReactionMap must be true, to make the symbols appear and print on the atoms when reaction mapping has been performed

Atom Properties to map atoms

Atom.AddMappedAtom     adds an atom to the collection of mapped atoms, for atom-atom mapping in reactions.
Atom.DeleteMapping        deletes all the atoms of the collection of mapped atoms, for atom-atom mapping in reactions.
Atom.MappedAtoms          returns the number of atoms mapped to a given atom. 

See Also

     Atom Object