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 e21e4e24b265632e4ddddc821615d19525651f0f..5192456d500f7f3dc77130fd2ef82be861565cf1 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -162,7 +162,7 @@ interface DSSPContext {
flags: Uint32Array
hbonds: DsspHbonds,
- torsionAngles: { phi: number[], psi: number[], omega: number[] },
+ torsionAngles: { phi: number[], psi: number[]/*, omega: number[]*/ },
backboneIndices: BackboneAtomIndices,
conformation: AtomicConformation,
ladders: Ladder[],
@@ -184,10 +184,16 @@ const enum BridgeType {
ANTI_PARALLEL = 0x1
}
-interface Bridge {
- partner1: number,
- partner2: number,
- type: BridgeType
+class Bridge {
+ partner1: number;
+ partner2: number;
+ type: BridgeType;
+
+ constructor(p1: number, p2: number, type: BridgeType) {
+ this.partner1 = Math.min(p1, p2)
+ this.partner2 = Math.max(p1, p2)
+ this.type = type
+ }
}
type DSSPType = BitFlags<DSSPType.Flag>
@@ -331,7 +337,7 @@ function assignBends(ctx: DSSPContext) {
// console.log(bends + ' bends')
}
-function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: AtomicConformation, proteinResidues: SortedArray<ResidueIndex>, backboneIndices: BackboneAtomIndices): { phi: number[], psi: number[], omega: number[] } {
+function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: AtomicConformation, proteinResidues: SortedArray<ResidueIndex>, backboneIndices: BackboneAtomIndices): { phi: number[], psi: number[]/*, omega: number[]*/ } {
const { cIndices, nIndices } = backboneIndices
const { x, y, z } = conformation
const { traceElementIndex } = hierarchy.derived.residue
@@ -351,7 +357,7 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
const phi: number[] = []
const psi: number[] = []
- const omega: number[] = []
+ // const omega: number[] = []
for (let i = 0; i < residueCount - 1; ++i) {
const oPIprev = i - 1
@@ -384,22 +390,22 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
position(caAtomNext, caPosNext)
position(nAtomNext, nPosNext)
- const tPhi = calculatePhi(cPosPrev, nPos, caPos, cPos)
- const tPsi = calculatePsi(nPos, caPos, cPos, nPosNext)
- const tOmega = calculateOmega(caPos, cPos, nPosNext, caPosNext)
+ // const tPhi = calculatePhi(cPosPrev, nPos, caPos, cPos)
+ // const tPsi = calculatePsi(nPos, caPos, cPos, nPosNext)
+ // const tOmega = calculateOmega(caPos, cPos, nPosNext, caPosNext)
// console.log(`phi: ${ tPhi }, psi: ${ tPsi }, omega: ${ tOmega }`)
- phi[phi.length] = tPhi
- psi[psi.length] = tPsi
- omega[omega.length] = tOmega
+ phi[phi.length] = calculatePhi(cPosPrev, nPos, caPos, cPos)
+ psi[psi.length] = calculatePsi(nPos, caPos, cPos, nPosNext)
+ // omega[omega.length] = calculateOmega(caPos, cPos, nPosNext, caPosNext)
}
- return { phi, psi, omega };
+ return { phi, psi/*, omega*/ };
}
// angle calculations return NaN upon missing atoms
-
+// TODO would be nice to be provided elsewhere, omega is related but not needed here
function calculatePhi(c: Vec3, nNext: Vec3, caNext: Vec3, cNext: Vec3) {
return angle(c, nNext, caNext, cNext);
}
@@ -408,9 +414,9 @@ function calculatePsi(n: Vec3, ca: Vec3, c: Vec3, nNext: Vec3) {
return angle(n, ca, c, nNext);
}
-function calculateOmega(ca: Vec3, c: Vec3, nNext: Vec3, caNext: Vec3) {
- return angle(ca, c, nNext, caNext);
-}
+// function calculateOmega(ca: Vec3, c: Vec3, nNext: Vec3, caNext: Vec3) {
+// return angle(ca, c, nNext, caNext);
+// }
function calcBackboneHbonds(hierarchy: AtomicHierarchy, conformation: AtomicConformation, proteinResidues: SortedArray<ResidueIndex>, backboneIndices: BackboneAtomIndices, lookup3d: GridLookup3D): DsspHbonds {
const { cIndices, hIndices, nIndices, oIndices } = backboneIndices
@@ -695,7 +701,7 @@ function assignBridges(ctx: DSSPContext) {
flags[i] |= DSSPType.Flag.B
flags[j] |= DSSPType.Flag.B
// TODO move to constructor, actually omit object all together
- bridges[bridges.length] = { partner1: Math.min(i, j), partner2: Math.max(i, j), type: BridgeType.PARALLEL }
+ bridges[bridges.length] = new Bridge(i, j, BridgeType.PARALLEL)
}
// Parallel Bridge(i, j) =: [Hbond(j - 1, i) and Hbond(i, j + 1)]
@@ -704,7 +710,7 @@ function assignBridges(ctx: DSSPContext) {
if (i !== j && hbonds.getDirectedEdgeIndex(j - 1, i) !== -1) {
flags[i] |= DSSPType.Flag.B
flags[j] |= DSSPType.Flag.B
- bridges[bridges.length] = { partner1: Math.min(j, i), partner2: Math.max(j, i), type: BridgeType.PARALLEL }
+ bridges[bridges.length] = new Bridge(j, i, BridgeType.PARALLEL)
}
// Antiparallel Bridge(i, j) =: [Hbond(i, j) and Hbond(j, i)]
@@ -713,7 +719,7 @@ function assignBridges(ctx: DSSPContext) {
if (i !== j && hbonds.getDirectedEdgeIndex(j, i) !== -1) {
flags[i] |= DSSPType.Flag.B
flags[j] |= DSSPType.Flag.B
- bridges[bridges.length] = { partner1: Math.min(j, i), partner2: Math.max(j, i), type: BridgeType.ANTI_PARALLEL }
+ bridges[bridges.length] = new Bridge(j, i, BridgeType.ANTI_PARALLEL)
}
// Antiparallel Bridge(i, j) =: [Hbond(i - 1, j + 1) and Hbond(j - 1, i + l)]
@@ -722,7 +728,7 @@ function assignBridges(ctx: DSSPContext) {
if (i !== j && hbonds.getDirectedEdgeIndex(j - 1, i + 1) !== -1) {
flags[i] |= DSSPType.Flag.B
flags[j] |= DSSPType.Flag.B
- bridges[bridges.length] = { partner1: Math.min(j, i), partner2: Math.max(j, i), type: BridgeType.ANTI_PARALLEL }
+ bridges[bridges.length] = new Bridge(j, i, BridgeType.ANTI_PARALLEL)
}
}
}
@@ -814,9 +820,8 @@ function angle(a: Vec3, b: Vec3, c: Vec3, d: Vec3) {
const angle = Vec3.angle(abc, bcd) * 360.0 / (2 * Math.PI);
const cross = Vec3.zero();
Vec3.cross(cross, abc, bcd);
- const value = Vec3.dot(cb, cross);
- return value > 0 ? angle : -angle;
+ return Vec3.dot(cb, cross) > 0 ? angle : -angle;
}
/**