Changes between Initial Version and Version 1 of Feb2015MolGraphics

Timestamp:

Jan 8, 2015, 4:59:19 PM (11 years ago)

Author:

Tom Goddard

Comment:

--

Feb2015MolGraphics

@@ +1 @@
+= 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?