fixed bug in converting from gridless 3D positions to square grid pos…

…itions
UC-Davis-molecular-computing · Nov 1, 2020 · cc44388 · cc44388
1 parent 4c50667
commit cc44388
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Showing 5 changed files with 13 additions and 13 deletions.
diff --git a/lib/src/middleware/helix_grid_change.dart b/lib/src/middleware/helix_grid_change.dart
@@ -18,7 +18,7 @@ helix_grid_offsets_middleware(Store<AppState> store, dynamic action, NextDispatc
     Geometry geometry = store.state.design.geometry;
     Map<int, GridPosition> new_grid_positions_map = {
       for (var helix in store.state.design.helices_in_group(action.group_name).values)
-        helix.idx: util.position3d_to_grid(helix.position, action.grid, geometry)
+        helix.idx: util.position3d_to_grid_position(helix.position, action.grid, geometry)
     };
     Set<GridPosition> new_grid_positions_set = Set<GridPosition>.from(new_grid_positions_map.values);
     // if lengths don't match, there's a duplicate grid position

diff --git a/lib/src/reducers/helices_reducer.dart b/lib/src/reducers/helices_reducer.dart
@@ -461,15 +461,15 @@ BuiltMap<int, Helix> helix_grid_change_reducer(
     helix_builder.grid = action.grid;
     if (!action.grid.is_none() && helix.grid_position == null) {
       helix_builder.grid_position =
-          util.position3d_to_grid(helix.position, action.grid, geometry).toBuilder();
+          util.position3d_to_grid_position(helix.position, action.grid, geometry).toBuilder();
       helix_builder.position_ = null;
     }
     if (action.grid.is_none() && helix.position_ == null) {
       helix_builder.grid_position = null;
       //NOTE: it's important to use helix.grid (i.e., the OLD grid, since util.grid_to_position3d will crash
       // if given the none grid)
       helix_builder.position_ =
-          util.grid_to_position3d(helix.grid_position, helix.grid, geometry).toBuilder();
+          util.grid_position_to_position3d(helix.grid_position, helix.grid, geometry).toBuilder();
     }
     new_helices[idx] = helix_builder.build();
   }

diff --git a/lib/src/state/helix.dart b/lib/src/state/helix.dart
@@ -135,7 +135,7 @@ abstract class Helix with BuiltJsonSerializable, UnusedFields implements Built<H
   @nullable
   Position3D get position_;
 
-  Position3D get position => position_ ?? util.grid_to_position3d(grid_position, grid, geometry);
+  Position3D get position => position_ ?? util.grid_position_to_position3d(grid_position, grid, geometry);
 
   /// Helix rotation of the backbone of the forward strand at the helix's minimum base offset. (y-z)
   double get roll;

diff --git a/lib/src/util.dart b/lib/src/util.dart
@@ -746,13 +746,11 @@ GridPosition position_2d_to_grid_position_diameter_1_circles(Grid grid, num z, n
     if (h % 2 == 0) {
       int remainder_by_3 = y.floor() % 3;
       if (remainder_by_3 == 2) {
-        //        y += 0.5;
         y -= 0.5;
       }
     } else if (h % 2 == 1) {
       int remainder_by_3 = (y - cos(2 * pi / 6)).floor() % 3;
       if (remainder_by_3 == 1) {
-        //        y += cos(2 * pi / 6);
         y -= cos(2 * pi / 6);
       }
     }
@@ -784,12 +782,14 @@ GridPosition position_2d_to_grid_position_diameter_1_circles(Grid grid, num z, n
   return gp;
 }
 
-GridPosition position3d_to_grid(Position3D position, Grid grid, Geometry geometry) {
-  var gp = position_2d_to_grid_position_diameter_1_circles(grid, position.z, position.y);
+GridPosition position3d_to_grid_position(Position3D position, Grid grid, Geometry geometry) {
+  var position_normalized_diameter_1 = position * (1.0 / geometry.distance_between_helices_nm);
+  var gp = position_2d_to_grid_position_diameter_1_circles(grid,
+      position_normalized_diameter_1.z, position_normalized_diameter_1.y);
   return gp;
 }
 
-Position3D grid_to_position3d(GridPosition grid_position, Grid grid, Geometry geometry) {
+Position3D grid_position_to_position3d(GridPosition grid_position, Grid grid, Geometry geometry) {
   num y, z;
   if (grid == Grid.square) {
     z = grid_position.h * geometry.distance_between_helices_nm;

diff --git a/test/reducer_test.dart b/test/reducer_test.dart
@@ -5534,9 +5534,9 @@ main() {
       Grid grid = Grid.none;
       state = app_state_reducer(state, GridChange(grid: grid, group_name: constants.default_group_name));
 
-      var expected_position_h0 = util.grid_to_position3d(
+      var expected_position_h0 = util.grid_position_to_position3d(
           two_helices_design.helices[0].grid_position, Grid.square, two_helices_design.geometry);
-      var expected_position_h1 = util.grid_to_position3d(
+      var expected_position_h1 = util.grid_position_to_position3d(
           two_helices_design.helices[1].grid_position, Grid.square, two_helices_design.geometry);
 
       expect(state.design.default_group().grid, Grid.none);
@@ -5568,9 +5568,9 @@ main() {
           expected_position1.rebuild((b) => b.x = original_helix1.min_offset * geometry.base_width_svg);
 
       GridPosition expected_grid_position0 =
-          util.position3d_to_grid(expected_position0, grid, no_grid_two_helices_design.geometry);
+          util.position3d_to_grid_position(expected_position0, grid, no_grid_two_helices_design.geometry);
       GridPosition expected_grid_position1 =
-          util.position3d_to_grid(expected_position1, grid, no_grid_two_helices_design.geometry);
+          util.position3d_to_grid_position(expected_position1, grid, no_grid_two_helices_design.geometry);
 
       Helix new_helix0 = no_grid_two_helices_design.helices.values.first.rebuild((b) => b
         ..grid = grid