molstar
Version:
A comprehensive macromolecular library.
114 lines (113 loc) • 4.78 kB
JavaScript
;
Object.defineProperty(exports, "__esModule", { value: true });
exports.eachPolymerBackboneLink = eachPolymerBackboneLink;
exports.eachPolymerBackboneElement = eachPolymerBackboneElement;
exports.eachAtomicPolymerBackboneElement = eachAtomicPolymerBackboneElement;
/**
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
const int_1 = require("../../../../../mol-data/int");
const sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
const polymer_1 = require("../polymer");
function eachPolymerBackboneLink(unit, callback) {
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */: return eachAtomicPolymerBackboneLink(unit, callback);
case 1 /* Unit.Kind.Spheres */:
case 2 /* Unit.Kind.Gaussians */:
return eachCoarsePolymerBackboneLink(unit, callback);
}
}
function eachAtomicPolymerBackboneLink(unit, callback) {
const cyclicPolymerMap = unit.model.atomicRanges.cyclicPolymerMap;
const polymerIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getPolymerRanges)(unit), unit.elements);
const residueIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex; // can assume it won't be -1 for polymer residues
const { moleculeType } = unit.model.atomicHierarchy.derived.residue;
let indexA = -1;
let indexB = -1;
let isFirst = true;
let firstGroup = -1;
let i = 0;
while (polymerIt.hasNext) {
isFirst = true;
firstGroup = i;
residueIt.setSegment(polymerIt.move());
while (residueIt.hasNext) {
if (isFirst) {
const index_1 = residueIt.move().index;
++i;
if (!residueIt.hasNext)
continue;
isFirst = false;
indexB = index_1;
}
const index = residueIt.move().index;
indexA = indexB;
indexB = index;
callback(traceElementIndex[indexA], traceElementIndex[indexB], i - 1, i, moleculeType[indexA]);
++i;
}
if (cyclicPolymerMap.has(indexB)) {
indexA = indexB;
indexB = cyclicPolymerMap.get(indexA);
callback(traceElementIndex[indexA], traceElementIndex[indexB], i - 1, firstGroup, moleculeType[indexA]);
}
}
}
function eachCoarsePolymerBackboneLink(unit, callback) {
const polymerIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getPolymerRanges)(unit), unit.elements);
const { elements } = unit;
let isFirst = true;
let i = 0;
while (polymerIt.hasNext) {
isFirst = true;
const _a = polymerIt.move(), start = _a.start, end = _a.end;
for (let j = start, jl = end; j < jl; ++j) {
if (isFirst) {
++j;
++i;
if (j > jl)
continue;
isFirst = false;
}
callback(elements[j - 1], elements[j], i - 1, i, 0 /* Unknown */);
++i;
}
}
}
function eachPolymerBackboneElement(unit, callback) {
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */: return eachAtomicPolymerBackboneElement(unit, callback);
case 1 /* Unit.Kind.Spheres */:
case 2 /* Unit.Kind.Gaussians */:
return eachCoarsePolymerBackboneElement(unit, callback);
}
}
function eachAtomicPolymerBackboneElement(unit, callback) {
const polymerIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getPolymerRanges)(unit), unit.elements);
const residueIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex; // can assume it won't be -1 for polymer residues
let i = 0;
while (polymerIt.hasNext) {
residueIt.setSegment(polymerIt.move());
while (residueIt.hasNext) {
const index = residueIt.move().index;
callback(traceElementIndex[index], i);
++i;
}
}
}
function eachCoarsePolymerBackboneElement(unit, callback) {
const polymerIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getPolymerRanges)(unit), unit.elements);
const { elements } = unit;
let i = 0;
while (polymerIt.hasNext) {
const _a = polymerIt.move(), start = _a.start, end = _a.end;
for (let j = start, jl = end; j < jl; ++j) {
callback(elements[j], i);
++i;
}
}
}