Changes between Version 1 and Version 2 of MolGraphics

Timestamp:

Jan 6, 2015, 6:28:51 PM (11 years ago)

Author:

Tom Goddard

Comment:

--

MolGraphics

@@ -1 +1 @@
 = Molecule graphics attributes for Chimera 2, based on Chimera 1 =
+
+These are graphical molecular attributes that should be part of the C++ molecule classes.  This list is based on Chimera 1 and is meant as a starting point for discussing possible changes in Chimera 2.
+
 "*" indicates something we may change in Chimera 2.
 
 == Atom ==
-
+{{{
  display (true/false)
-
  hide (true/false, is atom shown when ribbon style shown)
 
@@ -12 +14 @@
  color
 
-
  label (text string for 3d label)
-
  labelOffset (xyz position relative to atom)
-
  labelColor
-
- minimumLabelRadius
-
+ minimumLabelRadius (float)
 
  *surfaceDisplay (drop this, visibility of surface per-atom)
-
  *surfaceColor (drop this, used for color by atom, instead have surface remember this mapping)
-
  *surfaceOpacity (drop this, used for color by atom)
-
  *surfaceCategory (drop this? categories will be like other named selectors?)
 
-
  *vdwPoints (drop this)
-
  *vdwColor (drop this)
 
  *Thermal ellipsoids for atoms -- in Python in Chimera 1
-
  scaleFactor (float, scales size)
-
  probabilityLevelForScaling (percentage)
-
  smoothingLevel (level of detail for ellipsoid)
-
  displayEllipsoid (true/false)
-
  displayPrincipalAxes (true/false, show lines for ellipsoid axes)
-
- axesLengthFactor (flaot)
-
+ axesLengthFactor (float)
  axesThickness (float)
-
  displayPrincipalEllipses (true/false, show orthogonal planes of ellipsoid)
-
  ellipsesSizeFactor (float)
-
  ellipsesThickness (float)
+}}}
 
 == Bond ==
+{{{
  display (true/false)
 
@@ -69 +53 @@
  labelColor
  labelOffset (xyz position relative to bond center)
+}}}
 
-== PseudoBond (same attributes as Bond) ==
+== !PseudoBond (same attributes as Bond) ==
+{{{
  display (true/false)
 
@@ -82 +68 @@
  labelColor
  labelOffset (xyz position relative to bond center)
+}}}
 
 == Residue ==
+{{{
  ribbonDisplay (true/False)
  ribbonDrawMode (2D, edged, round, custom)
@@ -97 +85 @@
  labelColor
  labelOffset (xyz position relative to residue CA?)
+}}}
 
 == Nucleotides - nucleic acid slab depictions in Python/VRML in Chimera 1 ==
+{{{
   *These attributes should probably be moved to Residue C++ object in Chimera 2
 
@@ -118 +108 @@
  ladderRelaxHBondConstraints (true/false)
  ladderHBondConstraints(angstroms and degrees, if relax enabled)
+}}}
 
 == Chain ==
+{{{
   No graphical attributes, Chain class does not exist in Chimera 1
 
@@ -147 +139 @@
   coilWidth (float)
   coilThickness (float)
+}}}
   
 == Molecule, also inherits from Model ==
+{{{
  ballScale (float, scale ball size in ball and stick)
  pointSize (pixels for dot display)
@@ -173 +167 @@
  *surfaceOpacity (drop this, for molecular surface, use surface attribute)
  *vdwDensity (drop this, density of surface vertices)
+}}}
 
 == Model ==
+{{{
  display (true/false)
 
@@ -185 +181 @@
 
  silhouette (true/false, silhouettes enabled for this model)
+}}}
 
-== PseudoBondGroup (global bond settings like Molecule) ==
+== !PseudoBondGroup (global bond settings like Molecule) ==
+{{{
  stickScale (float, scale factor for bond radius)
  lineWidth (pixels, for wire display)
@@ -192 +190 @@
  wireStipple (stipple pattern for wire bonds)
  showStubBonds (true/false, show a bond if atom not shown?)
+}}}
 
 == Other changes ==
 
-1. Make color objects immutable.  Chimera 1 allows redefining a color and having all graphics objects
-using that color automatically update.  Complexity of that is not worth it.
+1. Make color objects immutable.  Chimera 1 allows redefining a color and having all graphics objects using that color automatically update.  Complexity of that is not worth it.
 
 2. Integrating Nucleotides, Thermal ellipsoid, and Pipes and Plank styles into core is a lot of work.