Merge origin/main into wip/win-merge

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PFPK14wBcLD1s4dYUowpP4

Author: andy

CMakeLists.txt

@@ -1863,6 +1863,14 @@ if(PYTHON3_EXECUTABLE)
                    ${CMAKE_BINARY_DIR}/viewer-scenes)
   set_tests_properties(look_offscreen_shading PROPERTIES SKIP_RETURN_CODE 77 TIMEOUT 300)
 
+  # Sticks are thinner while normal-mode arrows are shown, normal again
+  # when they are hidden (#227).  Needs `ninja viewer-scenes` and Xvfb.
+  add_test(NAME look_nm_sticks
+           COMMAND ${PYTHON3_EXECUTABLE}
+                   ${CMAKE_CURRENT_SOURCE_DIR}/tests/look/nm_sticks.py
+                   ${CMAKE_BINARY_DIR}/viewer-scenes)
+  set_tests_properties(look_nm_sticks PROPERTIES SKIP_RETURN_CODE 77 TIMEOUT 300)
+
   # tests/guivalues -- memory sizes saved before the GB-everywhere change
   # (Megawords, Megabytes) are converted by GUIValues::load() before a
   # dialog or a generator reads them.  Needs g++ and libecceutil.a.

docs/claude/wx-viewer/ball-and-stick-is-the-default-and-sticks-thin-under-arrows.md

@@ -0,0 +1,23 @@
+---
+type: rule
+title: "Ball And Stick is the default style; sticks are drawn at 0.25 radius while normal-mode arrows are shown (#227)"
+area: wx-viewer
+paths: [src/tdat/chemistry/DisplayDescriptor.C, src/tdat/chemistry/TAtm.C, src/tdat/chemistry/Fragment.C, src/tdat/chemistry/Residue.C, include/tdat/DisplayStyle.H, src/viz/sgcommands/SGContainer.C, src/wxviz/viztools/ViewerEvtHandler.C, src/wxviz/viewer/VizRender.C, tests/look/nm_sticks.py]
+issues: [227]
+---
+The default comes from several places that must agree: `DisplayDescriptor::DISPLAY`,
+the `TAtm`/`Fragment`/`Residue` constructors, `DisplayStyle`'s default argument,
+`SGContainer`'s initial style and fragment style, and the two `DefaultStyle`
+fallbacks in `ViewerEvtHandler` and `VizRender`. A style a user saved
+(`DefaultStyle` in the viewer's ini, written on exit) still wins; there is no
+way to tell a saved Ball And Wireframe from the old default, so existing users
+keep it.
+
+An arrow along a bond lies inside the stick. While the normal-mode arrow switch
+(`getNMVecRoot()`) is not NONE and holds arrows, `SGContainer::applyNMStickScale`
+multiplies every `bondCylinderRadius` by `NM_STICK_FACTOR` (0.25) and divides it
+back when they are hidden; a field sensor on the switch's `whichChild` triggers
+it, so it runs from the event loop's delay queue (a scene script must call
+`processDelayQueue`, as `nmhide` does). At 0.15 the bond disappears, at 0.4 the
+shaft (0.035 A) is still half inside the stick. The normal-mode animation
+(`getNMRoot()`) shows no arrows and keeps normal sticks.

docs/claude/wx-viewer/wireframe-bonds-are-3-px-smoothed-and-scaled-by-the-canvas.md

@@ -5,7 +5,7 @@ area: wx-viewer
 paths: [src/tdat/chemistry/DisplayDescriptor.C, src/viz/sgcommands/SGContainer.C, src/inv/moiv/ChemDisplayWireframe.C, src/inv/wxinv/SoWxRenderArea.C, include/inv/ChemKit/ChemDisplayParam.H]
 issues: [227]
 ---
-At 1 px the default Ball And Wireframe bonds were unreadable on white.
+At 1 px the (then default) Ball And Wireframe bonds were unreadable on white; the default style is now Ball And Stick, see the entry on thin sticks.
 `DisplayDescriptor::LINEWDTH` is 3 and `SGContainer::applyStyle` sets
 `bondWireframeAntiAlias` to WITH_DEPTH_COMPARISON. GL line width is in device
 pixels, so `SoWxRenderArea::OnSize` publishes `GetContentScaleFactor()` through

include/tdat/DisplayStyle.H

@@ -17,7 +17,7 @@ class DisplayStyle
       enum Style { STICK, BALLSTICK, BALLWIRE, WIRE, DNONE, CPK,
          CAWIRE, CYLINDER, LINE, FLAT, SOLID, CARTOON, INVALIDSTYLE };
 
-      DisplayStyle(DisplayStyle::Style style = DisplayStyle::BALLWIRE);
+      DisplayStyle(DisplayStyle::Style style = DisplayStyle::BALLSTICK);
       virtual ~DisplayStyle();
 
       void setName(const string& name);

include/viz/SGContainer.H

@@ -4,6 +4,7 @@
 class ChemColor;
 class ChemRadii;
 class SoSeparator;
+class SoFieldSensor;
 class SoSwitch;
 class ChemDisplay;
 class ChemDisplayParam;
@@ -86,6 +87,8 @@ public:
     double displayedSphereRadius(int idx);
     // Re-seat the normal-mode arrows on the spheres now drawn.
     void updateNMVecStarts();
+    // Bond cylinders are drawn thinner while normal-mode arrows are shown.
+    void applyNMStickScale();
 
     DisplayStyle::Style toOurStyle(ChemDisplayParam::DisplayBinding style);
     ChemDisplayParam::DisplayBinding toChemkitStyle(DisplayStyle::Style style);
@@ -278,6 +281,8 @@ SoINTERNAL public:
    // ---------------------- Property Stuff ----------------------------
    SoSwitch*                 p_MOSwitch;
    SoSwitch*                 p_NMVecSwitch;
+   float                     p_nmStickScale;
+   SoFieldSensor*            p_nmSwitchSensor;
    SoSwitch*                 p_NMSwitch;
 
    // ---------------------- Grid Property Stuff ----------------------------

src/tdat/chemistry/DisplayDescriptor.C

@@ -17,7 +17,7 @@
 #include "tdat/DisplayDescriptor.H"
 
 //Default values
-const string DisplayDescriptor::DISPLAY = "Ball And Wireframe";
+const string DisplayDescriptor::DISPLAY = "Ball And Stick";
 const string DisplayDescriptor::COLORSCHEME = "Element";
 const int DisplayDescriptor::LINEWDTH = 3;
 const bool DisplayDescriptor::ANTIALIAS = false;

src/tdat/chemistry/DisplayStyle.C

@@ -7,7 +7,7 @@ DisplayStyle::DisplayStyle(DisplayStyle::Style style )
    p_displayFlag = true;
    if (style == DisplayStyle::DNONE) {
       p_displayFlag = false;
-      p_style = DisplayStyle::BALLWIRE;
+      p_style = DisplayStyle::BALLSTICK;
    }
    p_style = style;
 }

src/tdat/chemistry/Fragment.C

@@ -72,7 +72,7 @@
  * This fragment has no name, atoms, residues, or constraints.
  *
  */
-Fragment::Fragment() : p_mainDisplayStyle(DisplayStyle::BALLWIRE)
+Fragment::Fragment() : p_mainDisplayStyle(DisplayStyle::BALLSTICK)
 {
    p_name = "";
    p_charge = 0;
@@ -99,7 +99,7 @@ Fragment::Fragment(const string& name,
                    const double* coordinates,
                    const int numBonds,
                    const int *bonds) 
-                   : p_mainDisplayStyle(DisplayStyle::BALLWIRE)
+                   : p_mainDisplayStyle(DisplayStyle::BALLSTICK)
 {
    p_name = name;
    p_charge = 0;
@@ -138,7 +138,7 @@ Fragment::Fragment(const string& name,
                    const double* coordinates,
                    const int numBonds,
                    const int *bonds)
-                   : p_mainDisplayStyle(DisplayStyle::BALLWIRE)
+                   : p_mainDisplayStyle(DisplayStyle::BALLSTICK)
 {
    p_name = name;
    p_charge = 0;
@@ -164,7 +164,7 @@ Fragment::Fragment(const string& name,
 
 
 Fragment::Fragment( const string& name ) 
-                   : p_mainDisplayStyle(DisplayStyle::BALLWIRE)
+                   : p_mainDisplayStyle(DisplayStyle::BALLSTICK)
 {
    p_name = name;
    p_charge = 0;
@@ -188,7 +188,7 @@ Fragment::Fragment( const string& name )
  * Copy Constructor.
  */
 Fragment::Fragment(const Fragment& frag) 
-        : p_mainDisplayStyle(DisplayStyle::BALLWIRE)
+        : p_mainDisplayStyle(DisplayStyle::BALLSTICK)
 { 
    p_constraints = 0;
    p_potentials = 0;

src/tdat/chemistry/Residue.C

@@ -37,7 +37,7 @@ static int vnumStatus = sizeof(vstatusMap)/sizeof(char*);
 //
 ///////////////////////////////////////////////////////////////////////////////
 Residue::Residue(const char *cname, const int& number)
-      : p_displayStyle(DisplayStyle::BALLWIRE)
+      : p_displayStyle(DisplayStyle::BALLSTICK)
 {
 
   name(cname);

src/tdat/chemistry/TAtm.C

@@ -52,7 +52,7 @@ using std::find;
 //
 ///////////////////////////////////////////////////////////////////////////////
 TAtm::TAtm() 
-      : p_displayStyle(DisplayStyle::BALLWIRE)
+      : p_displayStyle(DisplayStyle::BALLSTICK)
 {
   TPerTab tpt;
   strcpy(p_atomName,"");
@@ -97,7 +97,7 @@ TAtm::TAtm()
 //
 ///////////////////////////////////////////////////////////////////////////////
 TAtm::TAtm(const char *tagString, const double* coord, const string& suffix)
-          : p_displayStyle(DisplayStyle::BALLWIRE)
+          : p_displayStyle(DisplayStyle::BALLSTICK)
 {
   TPerTab tpt;
   p_atomicNumber = tpt.atomicNumber(tagString);
@@ -142,7 +142,7 @@ TAtm::TAtm(const char *tagString, const double* coord, const string& suffix)
 //
 ///////////////////////////////////////////////////////////////////////////////
 TAtm::TAtm(short atomicNumber, const double* coord, const string& suffix) 
-      : p_displayStyle(DisplayStyle::BALLWIRE)
+      : p_displayStyle(DisplayStyle::BALLSTICK)
 {
   TPerTab tpt;
   string tagString = tpt.atomicSymbol(atomicNumber);
@@ -182,7 +182,7 @@ TAtm::TAtm(short atomicNumber, const double* coord, const string& suffix)
  * Copy constructor.
  */
    TAtm::TAtm(const TAtm& atom)
-: p_displayStyle(DisplayStyle::BALLWIRE)
+: p_displayStyle(DisplayStyle::BALLSTICK)
 { 
    *this = atom; 
 }