diff --git a/src/extensions/dnatco/behavior.ts b/src/extensions/dnatco/behavior.ts
index 57ca11ca03eef315f8b9677fbbd995c922c68c02..bbe33f8e9c5c8d700a08926962303d2bc5a7e620 100644
--- a/src/extensions/dnatco/behavior.ts
+++ b/src/extensions/dnatco/behavior.ts
@@ -39,11 +39,15 @@ export const DnatcoNtCs = PluginBehavior.create<{ autoAttach: boolean, showToolT
}
unregister() {
+ this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
this.ctx.customModelProperties.unregister(NtCTubeProvider.descriptor.name);
+ this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
+ this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
this.ctx.representation.structure.registry.remove(NtCTubeRepresentationProvider);
this.ctx.representation.structure.themes.colorThemeRegistry.remove(NtCTubeColorThemeProvider);
+ this.ctx.builders.structure.representation.unregisterPreset(ConfalPyramidsPreset);
this.ctx.builders.structure.representation.unregisterPreset(NtCTubePreset);
}
},
diff --git a/src/extensions/dnatco/confal-pyramids/representation.ts b/src/extensions/dnatco/confal-pyramids/representation.ts
index f55cb6ef923bbd28f7e7a26c94498b5b95b3e19b..80d9e852af43a66b32f01d1634fbbca0463cc5ec 100644
--- a/src/extensions/dnatco/confal-pyramids/representation.ts
+++ b/src/extensions/dnatco/confal-pyramids/representation.ts
@@ -88,6 +88,8 @@ function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Str
const it = new ConfalPyramidsIterator(structure, unit);
while (it.hasNext) {
const allPoints = it.move();
+ if (!allPoints)
+ continue;
for (const points of allPoints) {
const { O3, P, OP1, OP2, O5, confalScore } = points;
diff --git a/src/extensions/dnatco/confal-pyramids/util.ts b/src/extensions/dnatco/confal-pyramids/util.ts
index 6ab28c6f5c9ed549ca7651ec811ed12da11aa28b..c35f3270e893d684bc86e0eb082a64e2c0b9ca69 100644
--- a/src/extensions/dnatco/confal-pyramids/util.ts
+++ b/src/extensions/dnatco/confal-pyramids/util.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Michal MalĂ˝ <michal.maly@ibt.cas.cz>
* @author Jiřà Černý <jiri.cerny@ibt.cas.cz>
@@ -48,6 +48,10 @@ export class ConfalPyramidsIterator {
this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+ // Check for discontinuity
+ if (this.residueTwo.index !== (this.residueOne!.index + 1))
+ return void 0;
+
return this.toPyramids(this.residueOne!, this.residueTwo);
}
diff --git a/src/extensions/dnatco/ntc-tube/util.ts b/src/extensions/dnatco/ntc-tube/util.ts
index 84d4f341b2468892e8ea009b2a4a7b18212c8dbe..36f436358cd5eaa059010413efa2dc22a3ed72ca 100644
--- a/src/extensions/dnatco/ntc-tube/util.ts
+++ b/src/extensions/dnatco/ntc-tube/util.ts
@@ -74,23 +74,59 @@ export type NtCTubeSegment = {
export class NtCTubeSegmentsIterator {
private chainIt: Segmentation.SegmentIterator<ChainIndex>;
private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
+
+ /* Second residue of the previous step, may be undefined
+ * if we are at the beginning of a chain or right after a discontinuity */
private residuePrev?: DnatcoUtil.Residue;
+ /* First residue of the current step */
private residueOne?: DnatcoUtil.Residue;
+ /* Second residue of the current step */
private residueTwo: DnatcoUtil.Residue;
+ /* First residue of the next step, may be undefined
+ * if we are at the end of a chain.
+ * Undefined value indicates that the iterator has reached the end.*/
+ private residueNext?: DnatcoUtil.Residue;
+
private data?: NTT.Data;
private altIdOne = '';
private insCodeOne = '';
private loc: StructureElement.Location;
private moveStep() {
- this.residuePrev = DnatcoUtil.copyResidue(this.residueOne);
- this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
- this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+ if (!this.residueNext)
+ return void 0;
+
+ /* Assume discontinuity of the ResidueIndex of the residue that would become residue one (= first residue of the corresponding step)
+ * does not equal to ResidueIndex of what would be residue two (= second residue of the corresponding step). */
+ if (this.residueTwo.index + 1 === this.residueNext.index) {
+ this.residuePrev = DnatcoUtil.copyResidue(this.residueOne);
+ this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
+ this.residueTwo = DnatcoUtil.copyResidue(this.residueNext)!;
+ this.residueNext = this.residueIt.hasNext ? DnatcoUtil.copyResidue(this.residueIt.move())! : void 0;
+ } else {
+ if (!this.residueIt.hasNext) {
+ this.residueNext = void 0;
+ return void 0;
+ }
+
+ // There is discontinuity, act as if we were at the beginning of a chain
+ this.residuePrev = void 0;
+ this.residueOne = DnatcoUtil.copyResidue(this.residueNext);
+ this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+ this.residueNext = this.residueIt.hasNext ? DnatcoUtil.copyResidue(this.residueIt.move())! : void 0;
+ }
+
+ return this.toSegment(this.residuePrev, this.residueOne!, this.residueTwo, this.residueNext);
+ }
- return this.toSegment(this.residuePrev, this.residueOne!, this.residueTwo);
+ private prime() {
+ if (this.residueIt.hasNext)
+ this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+ if (this.residueIt.hasNext)
+ this.residueNext = this.residueIt.move();
}
- private toSegment(r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue): NtCTubeSegment | undefined {
+ private toSegment(r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue, r3: DnatcoUtil.Residue | undefined): NtCTubeSegment | undefined {
const indices = DnatcoUtil.getStepIndices(this.data!.data, this.loc, r1);
if (indices.length === 0)
return void 0;
@@ -105,13 +141,14 @@ export class NtCTubeSegmentsIterator {
const altIdTwo = step.label_alt_id_2;
const insCodeTwo = step.PDB_ins_code_2;
const followsGap = !!r0 && hasGapElements(r0, this.loc.unit) && hasGapElements(r1, this.loc.unit);
+ const precedesDiscontinuity = r3 ? r3.index !== r2.index + 1 : false;
return {
...getPoints(this.loc, r0, r1, r2, altIdPrev, this.altIdOne, altIdTwo, insCodePrev, this.insCodeOne, insCodeTwo),
stepIdx,
followsGap,
firstInChain: !r0,
- capEnd: !this.residueIt.hasNext || hasGapElements(r2, this.loc.unit),
+ capEnd: !this.residueNext || precedesDiscontinuity || hasGapElements(r2, this.loc.unit),
};
}
@@ -124,8 +161,7 @@ export class NtCTubeSegmentsIterator {
if (this.chainIt.hasNext) {
this.residueIt.setSegment(this.chainIt.move());
- if (this.residueIt.hasNext)
- this.residueTwo = this.residueIt.move();
+ this.prime();
}
this.loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
@@ -134,19 +170,21 @@ export class NtCTubeSegmentsIterator {
get hasNext() {
if (!this.data)
return false;
- return this.residueIt.hasNext
+ return !!this.residueNext
? true
: this.chainIt.hasNext;
}
move() {
- if (this.residueIt.hasNext) {
+ if (!!this.residueNext) {
return this.moveStep();
} else {
this.residuePrev = void 0; // Assume discontinuity when we switch chains
+ this.residueNext = void 0;
+
this.residueIt.setSegment(this.chainIt.move());
- if (this.residueIt.hasNext)
- this.residueTwo = this.residueIt.move();
+ this.prime();
+
return this.moveStep();
}
}