diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index 802bdb325903ecbf9128fe84968225449b67f42c..d7326e63f49a701d361305ce31228fb5606af452 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -19,17 +19,12 @@ interface SecondaryStructure {
}
namespace SecondaryStructure {
- export type Element = None | Bend | Turn | Helix | Sheet
+ export type Element = None | Turn | Helix | Sheet
export interface None {
kind: 'none'
}
- export interface Bend {
- kind: 'bend',
- flags: SecondaryStructureType
- }
-
export interface Turn {
kind: 'turn',
flags: SecondaryStructureType
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.ts b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
index bcd5f07d3dd50a4bad3dd0ca0a8dce0b16d1b4ca..d21ef0b8c9054a6b62f98269124d3fbdc2536e8e 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -2,6 +2,7 @@
* 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 { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
@@ -14,6 +15,7 @@ import { IntAdjacencyGraph } from 'mol-math/graph';
import { BitFlags } from 'mol-util';
import { ElementIndex } from 'mol-model/structure/model/indexing';
import { AtomicHierarchy, AtomicConformation } from '../atomic';
+import { ParamDefinition as PD } from 'mol-util/param-definition'
/**
* TODO bugs to fix:
@@ -44,8 +46,7 @@ const hbondEnergyCutoff = -0.5
const hbondEnergyMinimal = -9.9
interface DSSPContext {
- oldDefinition: boolean,
- oldOrdering: boolean,
+ params: PD.Values<SecondaryStructureComputationParams>,
getResidueFlag: (f: DSSPType) => SecondaryStructureType,
getFlagName: (f: DSSPType) => String,
@@ -111,14 +112,15 @@ namespace DSSPType {
}
}
-export interface SecondaryStructureComputationParams {
- oldDefinition: boolean
- oldOrdering: boolean
+export const SecondaryStructureComputationParams = {
+ 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 type SecondaryStructureComputationParams = typeof SecondaryStructureComputationParams
export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
conformation: AtomicConformation,
- params?: Partial<SecondaryStructureComputationParams>): SecondaryStructure {
+ params: PD.Values<SecondaryStructureComputationParams>): SecondaryStructure {
// TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
const { lookup3d, proteinResidues } = calcAtomicTraceLookup3D(hierarchy, conformation)
const backboneIndices = calcBackboneAtomIndices(hierarchy, proteinResidues)
@@ -127,21 +129,18 @@ export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
const residueCount = proteinResidues.length
const flags = new Uint32Array(residueCount)
- const oldDefinition: boolean = (params && params.oldDefinition) || true
- const oldOrdering: boolean = (params && params.oldOrdering) || true
- console.log(`calculating secondary structure elements using ${ oldDefinition ? 'old' : 'revised'} definition and ${ oldOrdering ? 'old' : 'revised'} ordering of secondary structure elements`)
+ console.log(`calculating secondary structure elements using ${ params.oldDefinition ? 'old' : 'revised'} definition and ${ params.oldOrdering ? 'old' : 'revised'} ordering of secondary structure elements`)
const torsionAngles = calculateDihedralAngles(hierarchy, conformation, proteinResidues, backboneIndices)
const ladders: Ladder[] = []
const bridges: Bridge[] = []
- const getResidueFlag = oldDefinition ? getOriginalResidueFlag : getUpdatedResidueFlag
- const getFlagName = oldOrdering ? getOriginalFlagName : getUpdatedFlagName
+ const getResidueFlag = params.oldDefinition ? getOriginalResidueFlag : getUpdatedResidueFlag
+ const getFlagName = params.oldOrdering ? getOriginalFlagName : getUpdatedFlagName
const ctx: DSSPContext = {
- oldDefinition,
- oldOrdering,
+ params,
getResidueFlag,
getFlagName,
@@ -174,7 +173,7 @@ export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
type[proteinResidues[i]] = assign
const flag = getResidueFlag(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] as SecondaryStructure.Helix | SecondaryStructure.Sheet).flags /* flag changed */) {
+ if (elements.length === 0 /* would fail at very start */ || flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet | SecondaryStructure.Turn).flags /* flag changed */) {
elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
}
keys[i] = elements.length - 1
@@ -211,16 +210,11 @@ function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DS
kind: 'sheet',
flags: getResidueFlag(flag)
} as SecondaryStructure.Sheet
- } else if (kind === 'turn') {
+ } else if (kind === 'turn' || kind === 'bend') {
return {
kind: 'turn',
flags: getResidueFlag(flag)
}
- } else if (kind === 'bend') {
- return {
- kind: 'bend',
- flags: getResidueFlag(flag)
- }
} else {
return {
kind: 'none'
@@ -377,8 +371,9 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
// ignore C-terminal residue as acceptor
if (index.findAtomOnResidue(proteinResidues[i], 'OXT') !== -1) continue
- phi[phi.length] = calculatePhi(cPosPrev, nPos, caPos, cPos)
- psi[psi.length] = calculatePsi(nPos, caPos, cPos, nPosNext)
+ // returns NaN for missing atoms
+ phi[i] = Vec3.dihedralAngle(cPosPrev, nPos, caPos, cPos)
+ psi[i] = Vec3.dihedralAngle(nPos, caPos, cPos, nPosNext)
cPosPrev = cPos, caPosPrev = caPos, nPosPrev = nPos
cPos = cPosNext, caPos = caPosNext, nPos = nPosNext
@@ -389,15 +384,6 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
return { phi, psi };
}
-// angle calculations return NaN upon missing atoms
-function calculatePhi(c: Vec3, nNext: Vec3, caNext: Vec3, cNext: Vec3) {
- return Vec3.dihedralAngle(c, nNext, caNext, cNext);
-}
-
-function calculatePsi(n: Vec3, ca: Vec3, c: Vec3, nNext: Vec3) {
- return Vec3.dihedralAngle(n, ca, c, nNext);
-}
-
function calcBackboneHbonds(hierarchy: AtomicHierarchy, conformation: AtomicConformation, proteinResidues: SortedArray<ResidueIndex>, backboneIndices: BackboneAtomIndices, lookup3d: GridLookup3D): DsspHbonds {
const { cIndices, hIndices, nIndices, oIndices } = backboneIndices
const { index } = hierarchy
@@ -599,7 +585,7 @@ function assignTurns(ctx: DSSPContext) {
// check if hbond exists
if (hbonds.getDirectedEdgeIndex(i, i + idx + 3) !== -1) {
flags[i] |= turnFlag[idx + 3] | turnFlag[idx]
- if (ctx.oldDefinition) {
+ if (ctx.params.oldDefinition) {
for (let k = 1; k < idx + 3; ++k) {
flags[i + k] |= turnFlag[idx + 3] | DSSPType.Flag.T
}
@@ -699,7 +685,7 @@ function assignHelices(ctx: DSSPContext) {
const turnFlag = [DSSPType.Flag.T3S, DSSPType.Flag.T4S, DSSPType.Flag.T5S, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5]
const helixFlag = [0, 0, 0, DSSPType.Flag.G, DSSPType.Flag.H, DSSPType.Flag.I]
- const helixCheckOrder = ctx.oldOrdering ? [4, 3, 5] : [3, 4, 5]
+ const helixCheckOrder = ctx.params.oldOrdering ? [4, 3, 5] : [3, 4, 5]
for (let ni = 0; ni < helixCheckOrder.length; ni++) {
const n = helixCheckOrder[ni]
@@ -709,7 +695,7 @@ function assignHelices(ctx: DSSPContext) {
const fI2 = DSSPType.create(flags[i + 1])
// TODO rework to elegant solution which will not break instantly
- if (ctx.oldOrdering) {
+ if (ctx.params.oldOrdering) {
if ((n === 3 && (DSSPType.is(fI, DSSPType.Flag.H) || DSSPType.is(fI2, DSSPType.Flag.H)) || // for 3-10 yield to alpha helix
(n === 5 && ((DSSPType.is(fI, DSSPType.Flag.H) || DSSPType.is(fI, DSSPType.Flag.G)) || (DSSPType.is(fI2, DSSPType.Flag.H) || DSSPType.is(fI2, DSSPType.Flag.G)))))) { // for pi yield to all other helices
continue
@@ -723,7 +709,7 @@ function assignHelices(ctx: DSSPContext) {
if (DSSPType.is(fI, turnFlag[n]) && DSSPType.is(fI, turnFlag[n - 3]) && // check fI for turn start of proper type
DSSPType.is(fI1, turnFlag[n]) && DSSPType.is(fI1, turnFlag[n - 3])) { // check fI1 accordingly
- if (ctx.oldDefinition) {
+ if (ctx.params.oldDefinition) {
for (let k = 0; k < n; k++) {
flags[i + k] |= helixFlag[n]
}
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 146ef8c6e1fe3dee3138f0d9f891aaa7e476b6fe..4fcdd704d0557c9073165155b2f2c3a3ef17c182 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -12,7 +12,8 @@ import { ColorTheme } from 'mol-theme/color';
import { SizeTheme } from 'mol-theme/size';
import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
-import { computeSecondaryStructure } from 'mol-model/structure/model/properties/utils/secondary-structure';
+import { computeSecondaryStructure, SecondaryStructureComputationParams } from 'mol-model/structure/model/properties/utils/secondary-structure';
+import { ParamDefinition as PD } from 'mol-util/param-definition'
const parent = document.getElementById('app')!
parent.style.width = '100%'
@@ -66,7 +67,8 @@ async function init() {
const models = await getModels(cif)
console.time('computeModelDSSP')
const secondaryStructure = computeSecondaryStructure(models[0].atomicHierarchy,
- models[0].atomicConformation)
+ models[0].atomicConformation,
+ PD.getDefaultValues(SecondaryStructureComputationParams) /*{ oldDefinition: false, oldOrdering: false }*/)
console.timeEnd('computeModelDSSP');
(models[0].properties as any).secondaryStructure = secondaryStructure
const structure = await getStructure(models[0])