This module inputs an Explorer Chemistry Pyramid and generates various ball and stick molecular geometries. Single double and triple bonds are supported, provided the incoming bond order information is correct.

The optional colormap can be used to color the atoms and bonds. If it is omitted, the values used are as follows:

ATOM NUMBER COLOR Hydrogen 1 pale white Carbon 6 pale green Nitrogen 7 blue Oxygen 8 red Fluorine 9 green Phosphorus 15 violet Sulfur 16 yellow Chlorine 17 green Bromine 35 gray


Port: Molecule
Type: Pyramid
Constraints: n-layer.
n-D compression.
n-compression type.
The source molecule.

Port: Colormap
Type: Lattice
Optional: This port is optional
Constraints: 1-D.
A colormap to color the atoms. The value from the colormap is the "color" data variable from the chemistry pyramid. Most chemistry reader modules fill this value with the atomic number of the atom.


Port: Atom Radius
Type: Dial
Sphere radius normalized to Van der Waals radius.

Port: Complexity
Type: Dial
The number of polygons for spheres and polytubes.

Port: model
Type: Radio Box
Menu Item: polytube
Menu Item: spacefill
Menu Item: lines
Menu Item: ball & stick
Selected geometry of spacefills, polytubes, ball and sticks, and lines.

Port: Bond Radius
Type: Dial
Polytube radius.


Port: Output
Type: Geometry
Sphere, Cylinder, and Line geometry.



The EyeChem readers ReadPDB AtomicSurf BallStick Render
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© The Numerical Algorithms Group Ltd, Oxford UK. 1996