Merge pull request #995 from UC-Davis-molecular-computing/993-allow-p…

…er-helixhelix-group-geometry

993 allow per helixhelix group geometry

lib/src/actions/actions.dart

@@ -1450,6 +1450,25 @@ abstract class GeometrySet
   String short_description() => "set geometric parameters";
 }
 
+abstract class GeometryHelixGroupSet
+    with BuiltJsonSerializable, UndoableAction
+    implements Action, Built<GeometryHelixGroupSet, GeometryHelixGroupSetBuilder> {
+  String get group_name;
+
+  Geometry get geometry;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory GeometryHelixGroupSet({required String group_name, required Geometry geometry}) =
+      _$GeometryHelixGroupSet._;
+
+  GeometryHelixGroupSet._();
+
+  static Serializer<GeometryHelixGroupSet> get serializer => _$geometryHelixGroupSetSerializer;
+
+  @override
+  String short_description() => "set helix group geometric parameters ";
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // Selectables
 
@@ -2953,12 +2972,16 @@ abstract class DNAEndsMoveSetSelectedEnds
 
   BuiltSet<Strand> get strands_affected;
 
+  Geometry get geometry;
+
   /************************ begin BuiltValue boilerplate ************************/
-  factory DNAEndsMoveSetSelectedEnds(
-      {required BuiltList<DNAEndMove> moves,
-      required int original_offset,
-      required Helix helix,
-      required BuiltSet<Strand> strands_affected}) = _$DNAEndsMoveSetSelectedEnds._;
+  factory DNAEndsMoveSetSelectedEnds({
+    required BuiltList<DNAEndMove> moves,
+    required int original_offset,
+    required Helix helix,
+    required BuiltSet<Strand> strands_affected,
+    required Geometry geometry,
+  }) = _$DNAEndsMoveSetSelectedEnds._;
 
   DNAEndsMoveSetSelectedEnds._();
 

lib/src/middleware/dna_ends_move_start.dart

@@ -36,14 +36,17 @@ dna_ends_move_start_middleware(Store<AppState> store, action, NextDispatcher nex
       strands_affected.add(strand);
     }
     next(action);
+    var group = design.groups[action.helix.group]!;
+    var geometry = group.geometry ?? design.geometry;
 
     // important that we dispatch to app, not to store, because the app dispatch will know to route this
     // to the appropriate optimized store for moving DNAEnds
     app.dispatch(actions.DNAEndsMoveSetSelectedEnds(
         original_offset: action.offset,
         moves: moves.toBuiltList(),
         helix: action.helix,
-        strands_affected: strands_affected.toBuiltSet()));
+        strands_affected: strands_affected.toBuiltSet(),
+        geometry: geometry));
   } else {
     next(action);
   }

lib/src/middleware/dna_extensions_move_start.dart

@@ -28,18 +28,23 @@ dna_extensions_move_start_middleware(Store<AppState> store, action, NextDispatch
     for (var end in selected_ends) {
       var extension = design.end_to_extension[end]!;
       var helix = design.helices[extension.adjacent_domain.helix]!;
+      var group = design.groups[helix.group]!;
+      var geometry = group.geometry ?? design.geometry;
+
       var extension_start_point = util.compute_extension_attached_end_svg(
-          extension,
-          extension.adjacent_domain,
-          helix,
-          store.state.helix_idx_to_svg_position_map[extension.adjacent_domain.helix]!.y);
+        extension,
+        extension.adjacent_domain,
+        helix,
+        store.state.helix_idx_to_svg_position_map[extension.adjacent_domain.helix]!.y,
+        geometry,
+      );
 
       // extension_start_point is in helix group coordinate space, so add it with helix group position
       // to get canvas coordinate space
-      extension_start_point += design.groups[helix.group]!.translation(design.geometry);
+      extension_start_point += group.translation(geometry);
 
       var extension_end_point = util.compute_extension_free_end_svg(
-          extension_start_point, extension, extension.adjacent_domain, design.geometry);
+          extension_start_point, extension, extension.adjacent_domain, geometry);
       var color = design.extension_end_to_strand(end).color;
       var move = DNAExtensionMove(
           dna_end: end,

lib/src/middleware/helices_positions_set_based_on_crossovers.dart

@@ -53,15 +53,16 @@ List<actions.UndoableAction> get_helix_position_and_roll_actions(AppState state)
   for (var group_name in state.design.groups.keys) {
     if (group_names_to_skip.contains(group_name)) continue;
     var group = state.design.groups[group_name]!;
+    var geometry = group.geometry ?? state.design.geometry;
     List<Helix> helices = _get_helices_to_process(state, group);
     List<Tuple2<Address, Address>>? addresses = _get_addresses_to_process(state, helices);
     if (addresses == null) {
       continue;
     }
     double first_roll = helices[0].roll;
     List<RollXY> rolls_and_positions =
-        _calculate_rolls_and_positions(state.design, helices, addresses, first_roll);
-    var all_actions_this_group = set_rolls_and_positions(helices, rolls_and_positions);
+        _calculate_rolls_and_positions(state.design, geometry, helices, addresses, first_roll);
+    var all_actions_this_group = set_rolls_and_positions(helices, rolls_and_positions, geometry);
     all_actions.addAll(all_actions_this_group);
   }
 
@@ -277,14 +278,12 @@ class RollXY {
 /// Return list of rolls, same length as [helices], giving the roll that each should be to point
 /// each pair of helix backbones at each other through the given [addresses].
 /// The first roll is [first_roll].
-List<RollXY> _calculate_rolls_and_positions(
-    Design design, List<Helix> helices, List<Tuple2<Address, Address>> addresses, double first_roll) {
+List<RollXY> _calculate_rolls_and_positions(Design design, Geometry geometry, List<Helix> helices,
+    List<Tuple2<Address, Address>> addresses, double first_roll) {
   assert(helices.length == addresses.length + 1);
 
-  Geometry geometry = design.geometry;
-
-  double x = helices[0].position3d.z;
-  double y = helices[0].position3d.y;
+  double x = helices[0].position3d(geometry).z;
+  double y = helices[0].position3d(geometry).y;
   List<RollXY> rollxys = [RollXY(roll: first_roll, x: x, y: y)];
 
   for (int i = 0; i < addresses.length; i++) {
@@ -323,13 +322,14 @@ List<RollXY> _calculate_rolls_and_positions(
   return rollxys;
 }
 
-List<actions.UndoableAction> set_rolls_and_positions(List<Helix> helices, List<RollXY> rolls_and_positions) {
+List<actions.UndoableAction> set_rolls_and_positions(
+    List<Helix> helices, List<RollXY> rolls_and_positions, Geometry geometry) {
   List<actions.UndoableAction> all_actions = [];
   for (int i = 0; i < helices.length; i++) {
     var helix = helices[i];
     var rollxy = rolls_and_positions[i];
     var roll_action = actions.HelixRollSet(helix_idx: helix.idx, roll: rollxy.roll);
-    var position = Position3D(x: rollxy.x, y: rollxy.y, z: helix.position3d.z);
+    var position = Position3D(x: rollxy.x, y: rollxy.y, z: helix.position3d(geometry).z);
     var pos_action = actions.HelixPositionSet(helix_idx: helix.idx, position: position);
     all_actions.add(roll_action);
     all_actions.add(pos_action);

lib/src/middleware/helix_grid_change.dart

@@ -15,10 +15,11 @@ helix_grid_offsets_middleware(Store<AppState> store, dynamic action, NextDispatc
   if (action is actions.GridChange &&
       !action.grid.is_none &&
       store.state.design.groups[action.group_name]!.grid.is_none) {
-    Geometry geometry = store.state.design.geometry;
+    var group = store.state.design.groups[action.group_name]!;
+    Geometry geometry = group.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_position(helix.position, action.grid, geometry)
+        helix.idx: util.position3d_to_grid_position(helix.position(geometry), 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
@@ -32,8 +33,8 @@ helix_grid_offsets_middleware(Store<AppState> store, dynamic action, NextDispatc
           var gp2 = new_grid_positions_map[h2idx]!;
           if (gp1 == gp2) {
             var helices = store.state.design.helices;
-            var pos1 = helices[h1idx]!.position3d;
-            var pos2 = helices[h2idx]!.position3d;
+            var pos1 = helices[h1idx]!.position3d(geometry);
+            var pos2 = helices[h2idx]!.position3d(geometry);
             var msg = '''\
 This design cannot be automatically converted to the ${action.grid.name} grid.
 Two helices, with idx values ${h1idx} and ${h2idx}, have positions that are

lib/src/middleware/helix_group_move_start.dart

@@ -25,11 +25,13 @@ helix_group_move_start_middleware(Store<AppState> store, action, NextDispatcher
 
     if (helices_in_group.isNotEmpty) {
       next(action); // this lets the boolean be set that we are moving a helix group
+      var geometry = group.geometry ?? state.design.geometry;
       var helix_group_move = HelixGroupMove(
         group_name: group_name,
         group: group,
         helices: helices_in_group,
         original_mouse_point: action.mouse_point,
+        geometry: geometry,
       );
       // important that we dispatch to app, not to store, because the app dispatch will know to route this
       // to the appropriate optimized store for moving HelixGroup

lib/src/middleware/oxdna_export.dart

@@ -425,7 +425,7 @@ Tuple3<OxdnaVector, OxdnaVector, OxdnaVector> oxdna_get_helix_vectors(Design des
   */
   var group = design.groups[helix.group]!;
   var grid = group.grid;
-  var geometry = design.geometry;
+  var geometry = group.geometry ?? design.geometry;
 
   // var forward = OxdnaVector(0, 0, 1);
   // var normal = OxdnaVector(0, -1, 0);
@@ -465,7 +465,7 @@ Tuple3<OxdnaVector, OxdnaVector, OxdnaVector> oxdna_get_helix_vectors(Design des
   if (grid == Grid.none) {
     // unnecessary since this check is done in the position getter, but this way the code exactly mirrors
     // the Python package equivalent
-    position = helix.position;
+    position = helix.position(geometry);
   } else {
     position = util.grid_position_to_position3d(helix.grid_position!, grid, geometry);
   }
@@ -482,8 +482,6 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
   }
 
   var system = OxdnaSystem();
-  var geometry = design.geometry;
-  var step_rot = -360 / geometry.bases_per_turn;
 
   // each entry is the number of insertions - deletions since the start of a given helix
   Map<int, List<int>> mod_map = {};
@@ -533,6 +531,9 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
       // handle normal domains
       if (domain is Domain) {
         var helix = design.helices[domain.helix]!;
+        var group = design.groups[helix.group]!;
+        var geometry = group.geometry ?? design.geometry;
+        var step_rot = -360 / geometry.bases_per_turn;
         var origin_forward_normal = helix_vectors[helix.idx]!;
         var origin = origin_forward_normal.item1;
         var forward = origin_forward_normal.item2;
@@ -554,7 +555,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
           insertions[insertion.offset] = insertion.length;
         }
 
-        // use Design.geometry field to figure out various distances
+        // use Design.geometry or HelixGroup.geometry field to figure out various distances
         // https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/lib/src/state/geometry.dart
 
         // index is used for finding the base in our sequence
@@ -608,8 +609,16 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
         strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, true));
       } else if (domain is Extension) {
         bool is_5p = ss_idx == 0;
+        var helix = design.helices[domain.adjacent_domain.helix]!;
+        var group = design.groups[helix.group]!;
+        var geometry = group.geometry ?? design.geometry;
         var nucleotides = _compute_extension_nucleotides(
-            design: design, strand: strand, is_5p: is_5p, helix_vectors: helix_vectors, mod_map: mod_map);
+            design: design,
+            geometry: geometry,
+            strand: strand,
+            is_5p: is_5p,
+            helix_vectors: helix_vectors,
+            mod_map: mod_map);
         ox_strand.nucleotides.addAll(nucleotides);
         strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, false));
       } else {
@@ -651,11 +660,11 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
 
 List<OxdnaNucleotide> _compute_extension_nucleotides(
     {required Design design,
+    required Geometry geometry,
     required Strand strand,
     required bool is_5p,
     required Map<int, Tuple3<OxdnaVector, OxdnaVector, OxdnaVector>> helix_vectors,
     required Map<int, List<int>> mod_map}) {
-  var geometry = design.geometry;
   var step_rot = -360 / geometry.bases_per_turn;
 
   var adj_dom = is_5p ? strand.domains.first : strand.domains.last;

lib/src/reducers/design_reducer.dart

@@ -76,9 +76,6 @@ Design? design_geometry_set_reducer(Design? design, AppState state, actions.Geom
     return null;
   }
   var new_helices = design.helices.toMap();
-  for (var key in new_helices.keys) {
-    new_helices[key] = new_helices[key]!.rebuild((b) => b..geometry.replace(action.geometry));
-  }
 
   return design.rebuild((b) => b
     ..helices.replace(new_helices)

lib/src/reducers/dna_ends_move_reducer.dart

@@ -19,7 +19,8 @@ DNAEndsMove? dna_ends_move_set_selected_ends_reducer(
         moves: action.moves,
         original_offset: action.original_offset,
         current_offset: action.original_offset,
-        helix: action.helix);
+        helix: action.helix,
+        geometry: action.geometry);
 
 DNAEndsMove? dna_ends_move_adjust_reducer(DNAEndsMove? move, actions.DNAEndsMoveAdjustOffset action) =>
     move?.rebuild((b) => b..current_offset = action.offset);

lib/src/reducers/groups_reducer.dart

@@ -13,6 +13,7 @@ Reducer<BuiltMap<String, HelixGroup>> groups_local_reducer = combineReducers([
   TypedReducer<BuiltMap<String, HelixGroup>, actions.GroupRemove>(group_remove_reducer),
   TypedReducer<BuiltMap<String, HelixGroup>, actions.GroupChange>(group_change_reducer),
   TypedReducer<BuiltMap<String, HelixGroup>, actions.GridChange>(grid_change_reducer),
+  TypedReducer<BuiltMap<String, HelixGroup>, actions.GeometryHelixGroupSet>(geometry_helix_group_set_reducer),
 ]);
 
 GlobalReducer<BuiltMap<String, HelixGroup>, AppState> groups_global_reducer = combineGlobalReducers([
@@ -29,6 +30,15 @@ BuiltMap<String, HelixGroup> grid_change_reducer(
       return group;
     });
 
+BuiltMap<String, HelixGroup> geometry_helix_group_set_reducer(
+        BuiltMap<String, HelixGroup> groups, actions.GeometryHelixGroupSet action) =>
+    groups.map_values((name, group) {
+      if (name == action.group_name) {
+        group = group.rebuild((b) => b..geometry.replace(action.geometry));
+      }
+      return group;
+    });
+
 BuiltMap<String, HelixGroup> group_add_reducer(
         BuiltMap<String, HelixGroup> groups, actions.GroupAdd action) =>
     groups.rebuild((b) {

lib/src/reducers/helices_reducer.dart

@@ -63,7 +63,7 @@ GlobalReducer<BuiltMap<int, Helix>, AppState> helices_global_reducer = combineGl
       helix_offset_change_all_while_creating_strand_reducer),
   TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.ReplaceStrands>(first_replace_strands_reducer),
   TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.SelectionsClear>(
-      reset_helices_offsets_after_selections_clear)
+      reset_helices_offsets_after_selections_clear),
 ]);
 
 BuiltMap<int, Helix> helix_individual_reducer(
@@ -473,8 +473,9 @@ BuiltMap<int, Helix> helix_roll_set_at_other_reducer(
     BuiltMap<int, Helix> helices, AppState state, actions.HelixRollSetAtOther action) {
   Helix helix = helices[action.helix_idx]!;
   Helix helix_other = helices[action.helix_other_idx]!;
+  var group = state.design.groups[helix.group]!;
 
-  var geometry = state.design.geometry;
+  var geometry = group.geometry ?? state.design.geometry;
   num rotation = util.rotation_between_helices(helix, helix_other, action.forward, geometry);
   double old_rotation_at_anchor = state.design.helix_rotation_forward(helix.idx, action.anchor);
   double delta_roll = rotation - old_rotation_at_anchor;
@@ -526,7 +527,6 @@ Design? helix_add_design_reducer(Design? design, AppState state, actions.HelixAd
     idx: new_idx,
     grid: group.grid,
     group: state.ui_state.displayed_group_name,
-    geometry: design.geometry,
     grid_position: action.grid_position,
     position: action.position,
     min_offset: min_offset,
@@ -631,7 +631,8 @@ BuiltMap<int, Helix> helix_grid_change_reducer(
     BuiltMap<int, Helix> helices, AppState state, actions.GridChange action) {
   // make builder of all helices
   Map<int, Helix> new_helices = helices.toMap();
-  Geometry geometry = state.design.geometry;
+  var group = state.design.groups[action.group_name]!;
+  Geometry geometry = group.geometry ?? state.design.geometry;
 
   // process only those in this group
   var helix_idxs_in_group = state.design.helix_idxs_in_group[action.group_name]!;
@@ -641,7 +642,7 @@ 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_position(helix.position, action.grid, geometry).toBuilder();
+          util.position3d_to_grid_position(helix.position(geometry), action.grid, geometry).toBuilder();
       helix_builder.position_ = null;
     }
     if (action.grid.is_none && helix.position_ == null) {
@@ -665,9 +666,11 @@ BuiltMap<int, Helix> relax_helix_rolls_reducer(
   var new_helices_map = helices.toMap();
   for (var helix_idx in helix_idxs_to_relax) {
     var helix = new_helices_map[helix_idx]!;
+    var group = state.design.groups[helix.group]!;
+    var geometry = group.geometry ?? state.design.geometry;
     var crossover_addresses =
         state.design.helix_to_crossover_addresses_disallow_intrahelix_disallow_intergroup[helix_idx]!;
-    var helix_relaxed = helix.relax_roll(helices, crossover_addresses);
+    var helix_relaxed = helix.relax_roll(helices, crossover_addresses, geometry);
     new_helices_map[helix_idx] = helix_relaxed;
   }
 
@@ -726,6 +729,7 @@ BuiltMap<int, Helix> helix_position_set_reducer(
 // groups_reducer.dart file, which processes this same Action on the groups map.
 BuiltMap<int, Helix> move_helices_to_group_helices_reducer(
     BuiltMap<int, Helix> helices, actions.MoveHelicesToGroup action) {
+  //TODO: make this global and set helix.geometry if new group geometry is not null
   var helices_map = helices.toMap();
   for (int idx in action.helix_idxs) {
     assert(helices_map.keys.contains(idx));

lib/src/reducers/mouseover_datas_reducer.dart

@@ -47,7 +47,8 @@ BuiltList<MouseoverData> helix_rotation_set_at_other_mouseover_reducer(
     BuiltList<MouseoverData> mouseover_datas, AppState state, actions.HelixRollSetAtOther action) {
   Helix helix = state.design.helices[action.helix_idx]!;
   Helix helix_other = state.design.helices[action.helix_other_idx]!;
-  var geometry = state.design.geometry;
+  var group = state.design.groups[helix.group]!;
+  var geometry = group.geometry ?? state.design.geometry;
   double rotation = util.rotation_between_helices(helix, helix_other, action.forward, geometry);
   return _update_mouseover_datas_with_helix_rotation(
     model: state,