Merge pull request #909 from UC-Davis-molecular-computing/dev

Dev

lib/src/constants.dart

@@ -8,12 +8,12 @@ import 'state/grid.dart';
 
 // WARNING: Do not modify line below, except for the version string
 //          (and also add new version string to scadnano_versions_to_link).
-const String CURRENT_VERSION = "0.18.5";
+const String CURRENT_VERSION = "0.18.6";
 const String INITIAL_VERSION = "0.1.0";
 
 // scadnano versions that we deploy so that older versions can be used.
 final scadnano_older_versions_to_link = [
-  "0.18.4",
+  "0.18.5",
   "0.17.14",
   // "0.17.13",
   // "0.17.12",

lib/src/state/design.dart

@@ -2367,21 +2367,30 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
         var domains_on_strand = strand.domains;
         var num_domains = domains_on_strand.length;
         var domain_idx = domains_on_strand.indexOf(domain);
+        var domain_idx_in_substrands = strand.substrands.indexOf(domain);
 
         // if not first domain, then there is a crossover to the previous domain
         if (domain_idx > 0) {
-          var offset = domain.offset_5p;
-          var other_domain = domains_on_strand[domain_idx - 1];
-          var other_helix_idx = other_domain.helix;
-          ret[helix_idx].add(Address(helix_idx: other_helix_idx, offset: offset, forward: domain.forward));
+          // ... unless there's a loopout between them
+          var previous_substrand = strand.substrands[domain_idx_in_substrands - 1];
+          if (previous_substrand.is_domain()) {
+            var offset = domain.offset_5p;
+            var other_domain = domains_on_strand[domain_idx - 1];
+            var other_helix_idx = other_domain.helix;
+            ret[helix_idx].add(Address(helix_idx: other_helix_idx, offset: offset, forward: domain.forward));
+          }
         }
 
         // if not last domain, then there is a crossover to the next domain
         if (domain_idx < num_domains - 1) {
-          var offset = domain.offset_3p;
-          var other_domain = domains_on_strand[domain_idx + 1];
-          var other_helix_idx = other_domain.helix;
-          ret[helix_idx].add(Address(helix_idx: other_helix_idx, offset: offset, forward: domain.forward));
+          // ... unless there's a loopout between them
+          var next_substrand = strand.substrands[domain_idx_in_substrands + 1];
+          if (next_substrand.is_domain()) {
+            var offset = domain.offset_3p;
+            var other_domain = domains_on_strand[domain_idx + 1];
+            var other_helix_idx = other_domain.helix;
+            ret[helix_idx].add(Address(helix_idx: other_helix_idx, offset: offset, forward: domain.forward));
+          }
         }
       }
     }

lib/src/state/helix.dart

@@ -415,12 +415,12 @@ abstract class Helix with BuiltJsonSerializable, UnusedFields implements Built<H
   }
 
   Helix relax_roll(BuiltMap<int, Helix> helices, BuiltList<Address> crossover_addresses) {
-    var roll = compute_relaxed_roll(helices, crossover_addresses);
-    var new_helix = this.rebuild((b) => b..roll = roll);
+    var roll_delta = compute_relaxed_roll_delta(helices, crossover_addresses);
+    var new_helix = this.rebuild((b) => b..roll = roll + roll_delta);
     return new_helix;
   }
 
-  double compute_relaxed_roll(BuiltMap<int, Helix> helices, BuiltList<Address> crossover_addresses) {
+  double compute_relaxed_roll_delta(BuiltMap<int, Helix> helices, BuiltList<Address> crossover_addresses) {
     List<Tuple2<double, double>> angles = [];
     for (var address in crossover_addresses) {
       var other_helix = helices[address.helix_idx];

lib/src/view/design_main_base_pair_lines.dart

@@ -40,6 +40,12 @@ class DesignMainBasePairLinesComponent extends UiComponent2<DesignMainBasePairLi
     for (int helix_idx in base_pairs.keys) {
       if (!props.only_display_selected_helices || props.side_selected_helix_idxs.contains(helix_idx)) {
         var helix = props.design.helices[helix_idx];
+        HelixGroup group = props.design.groups[helix.group];
+        String transform_str = group.transform_str(props.design.geometry);
+
+        // code below draws one line for each base pair, should render somewhat slowly
+        // however, this makes it easier to associate base pair lines to individual strands,
+        // convenient when exporting SVG
         List<ReactElement> helix_components = [];
         for (int offset in base_pairs[helix_idx]) {
           var svg_position_y = props.helix_idx_to_svg_position_y_map[helix_idx];
@@ -55,13 +61,30 @@ class DesignMainBasePairLinesComponent extends UiComponent2<DesignMainBasePairLi
             ..key = 'base-pair-line-H${helix_idx}-${offset}')();
           helix_components.add(base_pair_line);
         }
-        HelixGroup group = props.design.groups[helix.group];
-        String transform_str = group.transform_str(props.design.geometry);
         var helix_dom_group = (Dom.g()
           ..transform = transform_str
           ..className = 'base-pair-lines-components-in-helix'
           ..key = 'base-pair-lines-components-in-helix-H${helix_idx}')(helix_components);
         base_pair_lines_components.add(helix_dom_group);
+
+        // // code below draws one long disconnected path for base pairs in each helix; should render faster
+        // // however, it's not clear how to use this when exporting SVG for only some selected strands
+        // // since it puts all the base pair lines for the whole helix in one single SVG path
+        // var d = StringBuffer();
+        // for (int offset in base_pairs[helix_idx]) {
+        //   var svg_position_y = props.helix_idx_to_svg_position_y_map[helix_idx];
+        //   var base_svg_forward_pos = helix.svg_base_pos(offset, true, svg_position_y);
+        //   var base_svg_reverse_pos = helix.svg_base_pos(offset, false, svg_position_y);
+        //   d.write(" M ${base_svg_forward_pos.x} ${base_svg_forward_pos.y}"
+        //       " L ${base_svg_reverse_pos.x} ${base_svg_reverse_pos.y}");
+        // }
+        // var helix_lines_path = (Dom.path()
+        //   ..d = d.toString()
+        //   ..transform = transform_str
+        //   ..stroke = 'black'
+        //   ..className = constants.css_selector_base_pair_line
+        //   ..key = 'base-pair-lines-H${helix_idx}')();
+        // base_pair_lines_components.add(helix_lines_path);
       }
     }
 

lib/src/view/menu.dart

@@ -480,6 +480,7 @@ It uses cadnano code that crashes on many designs, so it is not guaranteed to wo
           }
         }
         ..display = 'Copy'
+        ..key = 'edit_menu_copy-paste_copy'
         ..keyboard_shortcut = 'Ctrl+C'
         ..tooltip = '''\
 Copy the currently selected strand(s). They can be pasted into this design,
@@ -493,6 +494,7 @@ a text document to see a JSON description of the copied strand(s).'''
           }
         }
         ..display = 'Copy image'
+        ..key = 'edit_menu_copy-paste_copy-image'
         ..keyboard_shortcut = 'Ctrl+I'
         ..tooltip = '''\
 Copy a (PNG bitmap) image of the currently selected strand(s) to the system
@@ -506,6 +508,7 @@ to save an SVG file of the selected strands.'''
         ..on_click =
             ((_) => window.dispatchEvent(new KeyEvent('keydown', keyCode: KeyCode.V, ctrlKey: true).wrapped))
         ..display = 'Paste'
+        ..key = 'edit_menu_copy-paste_paste'
         ..tooltip = '''\
 Paste the previously copied strand(s). They can be pasted into this design,
 or into another design in another browser or tab. You can also paste into
@@ -515,6 +518,7 @@ a text document to see a JSON description of the copied strand(s).
       (MenuDropdownItem()
         ..on_click = ((_) => paste_strands_auto())
         ..display = 'Autopaste'
+        ..key = 'edit_menu_copy-paste_autopaste'
         ..tooltip = '''\
 This automatically pastes copied strands to an automatically selected position
 in the design, which can be faster to create many copies of strand(s) than
@@ -536,18 +540,21 @@ with some default direction chosen. Play with it and see!
         ..on_click =
             ((_) => window.dispatchEvent(new KeyEvent('keydown', keyCode: KeyCode.A, ctrlKey: true).wrapped))
         ..display = 'Select All'
+        ..key = 'edit_menu_copy-select-all'
         ..tooltip = '''\
 Select all strands in the design.'''
         ..keyboard_shortcut = 'Ctrl+A')(),
       (MenuDropdownItem()
         ..on_click = ((_) => props.dispatch(actions.SelectAllSelectable(current_helix_group_only: true)))
         ..display = 'Select All in Helix Group'
+        ..key = 'edit_menu_copy-select-all-in-helix-groups'
         ..tooltip = '''\
 Select all selectable strands in the current helix group.'''
         ..keyboard_shortcut = 'Ctrl+Shift+A')(),
       (MenuBoolean()
         ..value = props.strand_paste_keep_color
         ..display = 'Pasted strands keep original color'
+        ..key = 'edit_menu_copy-paste_Pasted strands keep original color'
         ..tooltip = '''\
 If checked, when copying and pasting a strand, the color is preserved.
 If unchecked, then a new color is generated.'''
@@ -605,6 +612,7 @@ directly at the adjoining helix.''')(),
       (MenuBoolean()
         ..value = props.default_crossover_type_scaffold_for_setting_helix_rolls
         ..display = 'default to leftmost scaffold crossover'
+        ..key = 'edit_menu_helix-rolls_default to leftmost scaffold crossover'
         ..tooltip = '''\
 When selecting "Set helix coordinates based on crossovers", if two adjacent 
 helices do not have a crossover selected, determines which types to select 
@@ -627,6 +635,7 @@ Ignored if design is not an origami (i.e., does not have at least one scaffold).
       (MenuBoolean()
         ..value = props.default_crossover_type_staple_for_setting_helix_rolls
         ..display = 'default to leftmost staple crossover'
+        ..key = 'edit_menu_helix-rolls_default to leftmost staple crossover'
         ..tooltip = '''\
 When selecting "Set helix coordinates based on crossovers", if two adjacent 
 helices do not have a crossover selected, determines which types to select 

test/helix_relax_rolls_test.dart

@@ -120,6 +120,105 @@ main() {
       expect(design3h.helices[2].roll, closeTo(exp_h2_roll, epsilon));
     });
 
+    test('3_helix_2_crossovers_1_loopout_crossovers_method', () {
+      /*
+          0         1          2
+          012345678901234567890
+        0 [---+[------+[------+
+              |       |        \
+        1 [---+       |        |
+                      |        /
+        2      <------+<------+
+      */
+      List<Helix> helices = [];
+      [];
+      for (int i = 0; i < 3; i++) {
+        var helix = Helix(max_offset: 60, grid: Grid.square, idx: i, grid_position: GridPosition(0, i));
+        if (i == 2) {
+          helix = helix.rebuild((b) => b..grid_position.replace(GridPosition(1, 0)));
+        }
+        helices.add(helix);
+      }
+      var design3h = Design(helices: helices, grid: Grid.square);
+
+      design3h = design3h.draw_strand(0, 0).move(5).cross(1).move(-5).commit();
+      design3h = design3h.draw_strand(0, 5).move(8).cross(2).move(-8).commit();
+      design3h = design3h.draw_strand(0, 13).move(8).loopout(2, 3).move(-8).commit();
+
+      var crossover_addresses = design3h.helix_to_crossover_addresses;
+      var crossover_addresses_h0 = crossover_addresses[0];
+      var crossover_addresses_h1 = crossover_addresses[1];
+      var crossover_addresses_h2 = crossover_addresses[2];
+
+      expect(crossover_addresses_h0.length, 2);
+      expect(crossover_addresses_h1.length, 1);
+      expect(crossover_addresses_h2.length, 1);
+
+      expect(crossover_addresses_h0[0], Address(helix_idx: 1, offset: 4, forward: true));
+      expect(crossover_addresses_h0[1], Address(helix_idx: 2, offset: 12, forward: true));
+
+      expect(crossover_addresses_h1[0], Address(helix_idx: 0, offset: 4, forward: false));
+
+      expect(crossover_addresses_h2[0], Address(helix_idx: 0, offset: 12, forward: false));
+    });
+
+    test('3_helix_2_crossovers_1_loopout', () {
+      /*
+          0         1          2
+          012345678901234567890
+        0 [---+[------+[------+
+              |       |        \
+        1 [---+       |        |
+                      |        /
+        2      <------+<------+
+      */
+      List<Helix> helices = [];
+      [];
+      for (int i = 0; i < 3; i++) {
+        var helix = Helix(max_offset: 60, grid: Grid.square, idx: i, grid_position: GridPosition(0, i));
+        if (i == 2) {
+          helix = helix.rebuild((b) => b..grid_position.replace(GridPosition(1, 0)));
+        }
+        helices.add(helix);
+      }
+      var design3h = Design(helices: helices, grid: Grid.square);
+
+      design3h = design3h.draw_strand(0, 0).move(5).cross(1).move(-5).commit();
+      design3h = design3h.draw_strand(0, 5).move(8).cross(2).move(-8).commit();
+      design3h = design3h.draw_strand(0, 13).move(8).loopout(2, 3).move(-8).commit();
+
+      var crossover_addresses_h0 = design3h.helix_to_crossover_addresses[0].toList();
+      var crossover_addresses_h1 = design3h.helix_to_crossover_addresses[1].toList();
+      var crossover_addresses_h2 = design3h.helix_to_crossover_addresses[2].toList();
+      expect(crossover_addresses_h0.length, 2);
+      expect(crossover_addresses_h1.length, 1);
+      expect(crossover_addresses_h2.length, 1);
+
+      var f1 = 4 / 10.5;
+      var f2 = 12 / 10.5;
+      var a1 = f1 * 360 % 360;
+      var a2 = f2 * 360 % 360;
+
+      // rules for angles:
+      // - add 150 if on reverse strand to account of minor groove
+      // - subtract angle of helix crossover is connecting to
+
+      var ave_h0 = (a1 - 180 + a2 - 90) / 2; // helix 1 at 180 degrees, helix 2 at 90 degrees
+      var exp_h0_roll = (-ave_h0) % 360;
+
+      var ave_h1 = a1 + 150; // helix 0 at 0 degrees relative to helix 1
+      var exp_h1_roll = (-ave_h1) % 360;
+
+      var ave_h2 = a2 + 150 - (-90); // helix 0 at -90 degrees relative to helix 2
+      var exp_h2_roll = (-ave_h2) % 360;
+
+      design3h = design3h.relax_helix_rolls();
+
+      expect(design3h.helices[0].roll, closeTo(exp_h0_roll, epsilon));
+      expect(design3h.helices[1].roll, closeTo(exp_h1_roll, epsilon));
+      expect(design3h.helices[2].roll, closeTo(exp_h2_roll, epsilon));
+    });
+
     test('2_helix_no_crossovers', () {
       /*
           0         1         2
@@ -164,7 +263,6 @@ main() {
         2                            <------+<--------+<--------+
       */
       List<Helix> helices = [];
-      [];
       for (int i = 0; i < 3; i++) {
         var helix = Helix(max_offset: 60, grid: Grid.square, idx: i, grid_position: GridPosition(0, i));
         if (i == 2) {
@@ -237,7 +335,39 @@ main() {
       expect(design2h.helices[1].roll, closeTo(exp_h1_roll, epsilon));
     });
 
-    test('helix_crossovers', () {
+    test('2_helix_2_crossover_call_relax_twice', () {
+      /*
+          0         1
+          012345678901234
+        0 [---+[-----+
+              |      |
+        1 [---+<-----+
+    */
+      List<Helix> helices = [];
+      for (int i = 0; i < 2; i++) {
+        var helix = Helix(max_offset: 60, grid: Grid.square, idx: i, grid_position: GridPosition(0, i));
+        helices.add(helix);
+      }
+      var design2h = Design(helices: helices, grid: Grid.square);
+      design2h = design2h.draw_strand(0, 0).move(5).cross(1).move(-5).commit();
+      design2h = design2h.draw_strand(0, 5).move(6).cross(1).move(-6).commit();
+
+      var exp_h0_roll = 120.0;
+      var exp_h1_roll = 150.0;
+
+      design2h = design2h.relax_helix_rolls();
+
+      expect(exp_h0_roll, design2h.helices[0].roll);
+      expect(exp_h1_roll, design2h.helices[1].roll);
+
+      // test for bug that reset roll; if called twice in a row it should have no effect the second time
+      design2h = design2h.relax_helix_rolls();
+
+      expect(exp_h0_roll, design2h.helices[0].roll);
+      expect(exp_h1_roll, design2h.helices[1].roll);
+    });
+
+    test('helix_crossover_addresses', () {
       //////////////////////////////////////////
       // 3-helix design with 3 strands
       var xs0 = design3helix3strand.helix_to_crossover_addresses[0];