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fixed bug in relaxing helix rolls with loopouts
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@dave-doty
dave-doty committed Aug 20, 2023
1 parent fca783f commit 30ffaca
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Showing 2 changed files with 116 additions and 8 deletions.
25 changes: 17 additions & 8 deletions lib/src/state/design.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -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));
}
}
}
}
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99 changes: 99 additions & 0 deletions test/helix_relax_rolls_test.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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