molstar
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A comprehensive macromolecular library.
152 lines (151 loc) • 6.22 kB
JavaScript
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Michal Malý <michal.maly@ibt.cas.cz>
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
*/
import { NtCTubeProvider } from './property';
import { DnatcoUtil } from '../util';
import { Segmentation, SortedArray } from '../../../mol-data/int';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { StructureElement } from '../../../mol-model/structure';
function getAtomPosition(vec, loc, residue, names, altId, insCode) {
const eI = DnatcoUtil.getAtomIndex(loc, residue, names, altId, insCode);
if (eI !== -1) {
loc.unit.conformation.invariantPosition(eI, vec);
return true;
}
return false; // Atom not found
}
const p_1 = Vec3();
const p0 = Vec3();
const p1 = Vec3();
const p2 = Vec3();
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, r0, r1, r2, altId0, altId1, altId2, insCode0, insCode1, 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 };
}
function hasGapElements(r, unit) {
for (let xI = r.start; xI < r.end; xI++) {
const eI = unit.elements[xI];
if (SortedArray.has(unit.gapElements, eI)) {
return true;
}
}
return false;
}
export class NtCTubeSegmentsIterator {
moveStep() {
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);
}
prime() {
if (this.residueIt.hasNext)
this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move());
if (this.residueIt.hasNext)
this.residueNext = this.residueIt.move();
}
toSegment(r0, r1, r2, r3) {
const indices = DnatcoUtil.getStepIndices(this.data.data, this.loc, r1);
if (indices.length === 0)
return void 0;
const stepIdx = indices[0];
const step = this.data.data.steps[stepIdx];
const altIdPrev = this.altIdOne;
const insCodePrev = this.insCodeOne;
this.altIdOne = step.label_alt_id_1;
this.insCodeOne = step.PDB_ins_code_1;
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;
const points = getPoints(this.loc, r0, r1, r2, altIdPrev, this.altIdOne, altIdTwo, insCodePrev, this.insCodeOne, insCodeTwo);
if (!points)
return void 0;
return {
...points,
stepIdx,
followsGap,
firstInChain: !r0,
capEnd: !this.residueNext || precedesDiscontinuity || hasGapElements(r2, this.loc.unit),
};
}
constructor(structure, unit) {
this.altIdOne = '';
this.insCodeOne = '';
this.chainIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
const prop = NtCTubeProvider.get(unit.model).value;
this.data = prop === null || prop === void 0 ? void 0 : prop.data;
if (this.chainIt.hasNext) {
this.residueIt.setSegment(this.chainIt.move());
this.prime();
}
this.loc = StructureElement.Location.create(structure, unit, -1);
}
get hasNext() {
if (!this.data)
return false;
return !!this.residueNext
? true
: this.chainIt.hasNext;
}
move() {
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());
this.prime();
return this.moveStep();
}
}
}