Compute Selected Bonds


Adds bonds to specific atoms using a distance criteria. The module can add also coordination tetrahedra or sphere around the selected atoms.

Input Ports

structure_in MoleculeType Molecular structure data. Bonds are ignored.


Select atoms atom select Select the atom for which the bonds should be computed.
Bond marker type radio buttons Set the shape to be put around selected atoms. Possible values are:
Nothing is draw.
Coordination Polyhedra
The coordination polyhedra of the atom.
A sphere with radius equal to the bonding radius.
Max distance slider The maximum distance from selected atoms of other atoms to build a bond.
Opacity slider The polyhedra or sphere surface opacity value.
Borders toggle If selected, a line is draw along the borders of the polyhedras.
White borders toggle If selected, the border lines are draw white, otherwise black. Active only when Borders is selected.
Flat appearance toggle If selected, the polyhedras are rendered with flat shading. This can be useful to make them visually pop-out.
Force color toggle If selected, the polyhedra color is set by the user with the color chooser widget. Otherwise the color is set by the center atom type.

Output Ports

structure_out MoleculeType Molecular structure data with the computed bonds.
glyph DefaultObject The marker for the selected atoms.
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