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Merge pull request #778 from MadCatX/ntc-tube-missing-atoms

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Fix rendering of NtC tube when some of the required atoms are missing
This commit is contained in:
Alexander Rose
2023-04-08 09:55:51 -07:00
committed by GitHub
parent 2994caf411 0b2889bb99
commit 5e1bb4b106
2 changed files with 35 additions and 11 deletions
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1
CHANGELOG.md
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@@ -9,6 +9,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Avoid `renderMarkingDepth` for fully transparent renderables
- Remove `camera.far` doubling workaround
- Add `ModifiersKeys.areNone` helper function
- Do not render NtC tube segments unless all required atoms are present in the structure
- Fix rendering issues caused by VAO reuse
- Add "Zoom All", "Orient Axes", "Reset Axes" buttons to the "Reset Camera" button
- Improve trackball move-state handling when key bindings use modifiers

45
src/extensions/dnatco/ntc-tube/util.ts
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@@ -14,11 +14,12 @@ import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, Un
function getAtomPosition(vec: Vec3, loc: StructureElement.Location, residue: DnatcoUtil.Residue, names: string[], altId: string, insCode: string) {
const eI = DnatcoUtil.getAtomIndex(loc, residue, names, altId, insCode);
if (eI !== -1)
if (eI !== -1) {
loc.unit.conformation.invariantPosition(eI, vec);
else {
vec[0] = 0; vec[1] = 0; vec[2] = 0;
return true;
}
return false; // Atom not found
}
const p_1 = Vec3();
@@ -29,19 +30,38 @@ const p3 = Vec3();
const p4 = Vec3();
const pP = Vec3();
const C5PrimeNames = ['C5\'', 'C5*'];
const O3PrimeNames = ['O3\'', 'O3*'];
const O5PrimeNames = ['O5\'', 'O5*'];
const PNames = ['P'];
function getPoints(
loc: StructureElement.Location,
r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue,
altId0: string, altId1: string, altId2: string,
insCode0: string, insCode1: string, insCode2: string,
) {
if (r0) getAtomPosition(p_1, loc, r0, ['C5\'', 'C5*'], altId0, insCode0);
r0 ? getAtomPosition(p0, loc, r0, ['O3\'', 'O3*'], altId0, insCode0) : getAtomPosition(p0, loc, r1, ['O5\'', 'O5*'], altId1, insCode1);
getAtomPosition(p1, loc, r1, ['C5\'', 'C5*'], altId1, insCode1);
getAtomPosition(p2, loc, r1, ['O3\'', 'O3*'], altId1, insCode1);
getAtomPosition(p3, loc, r2, ['C5\'', 'C5*'], altId2, insCode2);
getAtomPosition(p4, loc, r2, ['O3\'', 'O3*'], altId2, insCode2);
getAtomPosition(pP, loc, r2, ['P'], altId2, insCode2);
if (r0) {
if (!getAtomPosition(p_1, loc, r0, C5PrimeNames, altId0, insCode0))
return void 0;
if (!getAtomPosition(p0, loc, r0, O3PrimeNames, altId0, insCode0))
return void 0;
} else {
if (!getAtomPosition(p0, loc, r1, O5PrimeNames, altId1, insCode1))
return void 0;
}
if (!getAtomPosition(p1, loc, r1, C5PrimeNames, altId1, insCode1))
return void 0;
if (!getAtomPosition(p2, loc, r1, O3PrimeNames, altId1, insCode1))
return void 0;
if (!getAtomPosition(p3, loc, r2, C5PrimeNames, altId2, insCode2))
return void 0;
if (!getAtomPosition(p4, loc, r2, O3PrimeNames, altId2, insCode2))
return void 0;
if (!getAtomPosition(pP, loc, r2, PNames, altId2, insCode2))
return void 0;
return { p_1, p0, p1, p2, p3, p4, pP };
}
@@ -142,9 +162,12 @@ export class NtCTubeSegmentsIterator {
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;
const points = getPoints(this.loc, r0, r1, r2, altIdPrev, this.altIdOne, altIdTwo, insCodePrev, this.insCodeOne, insCodeTwo);
if (!points)
return void 0;
return {
...getPoints(this.loc, r0, r1, r2, altIdPrev, this.altIdOne, altIdTwo, insCodePrev, this.insCodeOne, insCodeTwo),
...points,
stepIdx,
followsGap,
firstInChain: !r0,