molstar
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A comprehensive macromolecular library.
74 lines • 3.27 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.assignBridges = void 0;
var common_1 = require("./common");
/**
* Two nonoverlapping stretches of three residues each, i - 1, i, i + 1 and j - 1, j, j + 1,
* form either a parallel or antiparallel bridge, depending on which of
* two basic patterns is matched. We assign a bridge between residues i and j
* if there are two H bonds characteristic of P-structure; in particular,
*
* Parallel Bridge(i, j) =:
* [Hbond(i - 1, j) and Hbond(j, i + 1)] or
* [Hbond(j - 1, i) and Hbond(i, j + 1)]
*
* Antiparallel Bridge(i, j) =:
* [Hbond(i, j) and Hbond(j, i)] or
* [Hbond(i - 1, j + 1) and Hbond(j - 1, i + l)]
*
* Type: B
*/
function assignBridges(ctx) {
var proteinInfo = ctx.proteinInfo, hbonds = ctx.hbonds, flags = ctx.flags, bridges = ctx.bridges;
var offset = hbonds.offset, b = hbonds.b;
var i, j;
for (var k = 0, kl = proteinInfo.residueIndices.length; k < kl; ++k) {
for (var t = offset[k], _t = offset[k + 1]; t < _t; t++) {
var l = b[t];
if (k > l)
continue;
// Parallel Bridge(i, j) =: [Hbond(i - 1, j) and Hbond(j, i + 1)]
i = k + 1; // k is i - 1
j = l;
if (i !== j && hbonds.getDirectedEdgeIndex(j, i + 1) !== -1) {
flags[i] |= 2 /* B */;
flags[j] |= 2 /* B */;
// TODO move to constructor, actually omit object all together
bridges[bridges.length] = new common_1.Bridge(i, j, 0 /* PARALLEL */);
}
// Parallel Bridge(i, j) =: [Hbond(j - 1, i) and Hbond(i, j + 1)]
i = k;
j = l - 1; // l is j + 1
if (i !== j && hbonds.getDirectedEdgeIndex(j - 1, i) !== -1) {
flags[i] |= 2 /* B */;
flags[j] |= 2 /* B */;
bridges[bridges.length] = new common_1.Bridge(j, i, 0 /* PARALLEL */);
}
// Antiparallel Bridge(i, j) =: [Hbond(i, j) and Hbond(j, i)]
i = k;
j = l;
if (i !== j && hbonds.getDirectedEdgeIndex(j, i) !== -1) {
flags[i] |= 2 /* B */;
flags[j] |= 2 /* B */;
bridges[bridges.length] = new common_1.Bridge(j, i, 1 /* ANTI_PARALLEL */);
}
// Antiparallel Bridge(i, j) =: [Hbond(i - 1, j + 1) and Hbond(j - 1, i + l)]
i = k + 1;
j = l - 1;
if (i !== j && hbonds.getDirectedEdgeIndex(j - 1, i + 1) !== -1) {
flags[i] |= 2 /* B */;
flags[j] |= 2 /* B */;
bridges[bridges.length] = new common_1.Bridge(j, i, 1 /* ANTI_PARALLEL */);
}
}
}
bridges.sort(function (a, b) { return a.partner1 > b.partner1 ? 1 : a.partner1 < b.partner1 ? -1 : 0; });
}
exports.assignBridges = assignBridges;
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