Simple molecular graphics attributes for Feb 2015 Chimera 2

These are graphical molecular attributes that should be part of the C++ molecule classes or their base classes.

"*" indicates something we may change in Chimera 2.

Atom

BaseSphere (base class for Atom)

 drawMode (Dot, Sphere, EndCap, Ball)

Connectible (base class for BaseSphere)

 display (true/false)

 color

Connection (base class for Bond/PseudoBond)

 display (true/false)

 drawMode (wire, stick, spring)
 radius

 color
 halfbond (color each half of bond to match near atom)

Residue

 ribbonDisplay (true/False)
 ribbonDrawMode (2D, edged, round, custom)
 ribbonColor
 ribbonXSection (for custom cross-sections)
 ribbonStyle (width and thickness scale factors, e.g. for worms)

Chain

Molecule, also inherits from Model

 ballScale (float, scale ball size in ball and stick)
 stickScale (float, scale factor for bond radius)

 ribbonType (bspline, cardinal)
 ribbonStiffness (float, interpolation parameter)
 ribbonSmoothing (strand | coil mask, to smooth specific secondary structures)
 ribbonInsideColor (for inside/outside dual coloring)
 ribbonHidesMainChain (true/false)
 residueLabelPositionMode (centroid, backbone, primary-atom)

Model

 display (true/false)

 color

PseudoBondGroup (global bond settings like Molecule)

 stickScale (float, scale factor for bond radius)

Changes

7. Should color objects be immutable? Chimera 1 allows redefining a color and having all graphics objects using that color automatically update. Complex code.

8. How to handle different materials in addition to colors?

9. Keep color hierarchy (model->atom, model->ribbon)? What about surface colors?