molstar
Version:
A comprehensive macromolecular library.
208 lines • 8.8 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>
*/
import { __awaiter, __generator } from "tslib";
import { SecondaryStructure } from '../../../mol-model/structure/model/properties/seconday-structure';
import { SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { assignBends } from './dssp/bends';
import { calcUnitBackboneHbonds } from './dssp/backbone-hbonds';
import { DSSPType } from './dssp/common';
import { assignTurns } from './dssp/turns';
import { assignHelices } from './dssp/helices';
import { assignLadders } from './dssp/ladders';
import { assignBridges } from './dssp/bridges';
import { assignSheets } from './dssp/sheets';
import { calculateUnitDihedralAngles } from './dssp/dihedral-angles';
import { calcUnitProteinTraceLookup3D } from './dssp/trace-lookup';
import { getUnitProteinInfo } from './dssp/protein-info';
import { SortedArray } from '../../../mol-data/int';
/**
* TODO bugs to fix:
* - some turns are not detected correctly: see e.g. pdb:1acj - maybe more than 2 hbonds require some residue to donate electrons
* - some sheets are not extended correctly: see e.g. pdb:1acj
* - validate new helix definition
* - validate new ordering of secondary structure elements
*/
export var DSSPComputationParams = {
oldDefinition: PD.Boolean(true, { description: 'Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter' }),
oldOrdering: PD.Boolean(true, { description: 'Alpha-helices are preferred over 3-10 helices' })
};
export function computeUnitDSSP(unit, params) {
return __awaiter(this, void 0, void 0, function () {
var proteinInfo, residueIndices, lookup3d, hbonds, residueCount, flags, torsionAngles, ladders, bridges, getResidueFlag, getFlagName, ctx, assignment, type, keys, elements, getIndex, i, il, assign, flag;
return __generator(this, function (_a) {
proteinInfo = getUnitProteinInfo(unit);
residueIndices = proteinInfo.residueIndices;
lookup3d = calcUnitProteinTraceLookup3D(unit, residueIndices);
hbonds = calcUnitBackboneHbonds(unit, proteinInfo, lookup3d);
residueCount = residueIndices.length;
flags = new Uint32Array(residueCount);
torsionAngles = calculateUnitDihedralAngles(unit, proteinInfo);
ladders = [];
bridges = [];
getResidueFlag = params.oldDefinition ? getOriginalResidueFlag : getUpdatedResidueFlag;
getFlagName = params.oldOrdering ? getOriginalFlagName : getUpdatedFlagName;
ctx = {
params: params,
getResidueFlag: getResidueFlag,
getFlagName: getFlagName,
unit: unit,
proteinInfo: proteinInfo,
flags: flags,
hbonds: hbonds,
torsionAngles: torsionAngles,
ladders: ladders,
bridges: bridges
};
assignTurns(ctx);
assignHelices(ctx);
assignBends(ctx);
assignBridges(ctx);
assignLadders(ctx);
assignSheets(ctx);
assignment = getDSSPAssignment(flags, getResidueFlag);
type = new Uint32Array(residueCount);
keys = [];
elements = [];
getIndex = function (rI) { return SortedArray.indexOf(residueIndices, rI); };
for (i = 0, il = residueIndices.length; i < il; ++i) {
assign = assignment[i];
type[i] = assign;
flag = getResidueFlag(flags[i]);
// console.log(i, SortedArray.indexOf(residueIndices, i), getFlagName(flags[i]))
// TODO is this expected behavior? elements will be strictly split depending on 'winning' flag
if (elements.length === 0 /* would fail at very start */ || flag !== elements[elements.length - 1].flags /* flag changed */) {
elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag);
}
keys[i] = elements.length - 1;
}
return [2 /*return*/, SecondaryStructure(type, keys, elements, getIndex)];
});
});
}
function createElement(kind, flag, getResidueFlag) {
// TODO would be nice to add more detailed information
if (kind === 'helix') {
return {
kind: 'helix',
flags: getResidueFlag(flag)
};
}
else if (kind === 'sheet') {
return {
kind: 'sheet',
flags: getResidueFlag(flag)
};
}
else if (kind === 'turn' || kind === 'bend') {
return {
kind: 'turn',
flags: getResidueFlag(flag)
};
}
else {
return {
kind: 'none'
};
}
}
function mapToKind(assignment) {
if (assignment === SecondaryStructureType.SecondaryStructureDssp.H || assignment === SecondaryStructureType.SecondaryStructureDssp.G || assignment === SecondaryStructureType.SecondaryStructureDssp.I) {
return 'helix';
}
else if (assignment === SecondaryStructureType.SecondaryStructureDssp.B || assignment === SecondaryStructureType.SecondaryStructureDssp.E) {
return 'sheet';
}
else if (assignment === SecondaryStructureType.SecondaryStructureDssp.T) {
return 'turn';
}
else if (assignment === SecondaryStructureType.SecondaryStructureDssp.S) {
return 'bend';
}
else {
return 'none';
}
}
/** Original priority: H,B,E,G,I,T,S */
function getOriginalResidueFlag(f) {
if (DSSPType.is(f, 1 /* H */))
return SecondaryStructureType.SecondaryStructureDssp.H;
if (DSSPType.is(f, 4 /* E */))
return SecondaryStructureType.SecondaryStructureDssp.E;
if (DSSPType.is(f, 2 /* B */))
return SecondaryStructureType.SecondaryStructureDssp.B;
if (DSSPType.is(f, 8 /* G */))
return SecondaryStructureType.SecondaryStructureDssp.G;
if (DSSPType.is(f, 16 /* I */))
return SecondaryStructureType.SecondaryStructureDssp.I;
if (DSSPType.is(f, 64 /* T */))
return SecondaryStructureType.SecondaryStructureDssp.T;
if (DSSPType.is(f, 32 /* S */))
return SecondaryStructureType.SecondaryStructureDssp.S;
return 0 /* None */;
}
function getOriginalFlagName(f) {
if (DSSPType.is(f, 1 /* H */))
return 'H';
if (DSSPType.is(f, 4 /* E */))
return 'E';
if (DSSPType.is(f, 2 /* B */))
return 'B';
if (DSSPType.is(f, 8 /* G */))
return 'G';
if (DSSPType.is(f, 16 /* I */))
return 'I';
if (DSSPType.is(f, 64 /* T */))
return 'T';
if (DSSPType.is(f, 32 /* S */))
return 'S';
return '-';
}
/** Version 2.1.0 priority: I,H,B,E,G,T,S */
function getUpdatedResidueFlag(f) {
if (DSSPType.is(f, 16 /* I */))
return SecondaryStructureType.SecondaryStructureDssp.I;
if (DSSPType.is(f, 1 /* H */))
return SecondaryStructureType.SecondaryStructureDssp.H;
if (DSSPType.is(f, 4 /* E */))
return SecondaryStructureType.SecondaryStructureDssp.E;
if (DSSPType.is(f, 2 /* B */))
return SecondaryStructureType.SecondaryStructureDssp.B;
if (DSSPType.is(f, 8 /* G */))
return SecondaryStructureType.SecondaryStructureDssp.G;
if (DSSPType.is(f, 64 /* T */))
return SecondaryStructureType.SecondaryStructureDssp.T;
if (DSSPType.is(f, 32 /* S */))
return SecondaryStructureType.SecondaryStructureDssp.S;
return 0 /* None */;
}
function getUpdatedFlagName(f) {
if (DSSPType.is(f, 16 /* I */))
return 'I';
if (DSSPType.is(f, 1 /* H */))
return 'H';
if (DSSPType.is(f, 4 /* E */))
return 'E';
if (DSSPType.is(f, 2 /* B */))
return 'B';
if (DSSPType.is(f, 8 /* G */))
return 'G';
if (DSSPType.is(f, 64 /* T */))
return 'T';
if (DSSPType.is(f, 32 /* S */))
return 'S';
return '-';
}
function getDSSPAssignment(flags, getResidueFlag) {
var type = new Uint32Array(flags.length);
for (var i = 0, il = flags.length; i < il; ++i) {
var f = DSSPType.create(flags[i]);
type[i] = getResidueFlag(f);
}
return type;
}
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