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@@ -48,7 +48,7 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy, conformation: Atomi
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for (let i = 0, il = proteinResidues.length; i < il; ++i) {
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type[proteinResidues[i]] = assignment[i]
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}
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-
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+
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const secondaryStructure: SecondaryStructure = {
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type,
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key: [], // TODO
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@@ -287,7 +287,7 @@ function getDSSPAssignment(flags: Uint32Array, useOriginal = false) {
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* Q = -332 * 0.42 * 0.20
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*
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* f is the dimensional factor
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- *
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+ *
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* q1 and q2 are partial charges which are placed on the C,O
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* (+q1,-q1) and N,H (-q2,+q2)
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*/
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@@ -306,7 +306,7 @@ function calcHbondEnergy(oPos: Vec3, cPos: Vec3, nPos: Vec3, hPos: Vec3) {
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const distON = Vec3.distance(oPos, nPos)
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const e1 = Q / distOH - Q / distCH
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- const e2 = Q / distCN - Q / distON
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+ const e2 = Q / distCN - Q / distON
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return e1 + e2
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}
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@@ -314,7 +314,7 @@ function calcHbondEnergy(oPos: Vec3, cPos: Vec3, nPos: Vec3, hPos: Vec3) {
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* The basic turn pattern is a single H bond of type (i, i + n).
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* We assign an n-turn at residue i if there is an H bond from CO(i) to NH(i + n),
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* i.e., “n-turn(i)=: Hbond(i, i + n), n = 3, 4, 5.”
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- *
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+ *
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* Type: T
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*/
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function assignTurns(ctx: DSSPContext) {
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@@ -322,7 +322,7 @@ function assignTurns(ctx: DSSPContext) {
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const { chains, residueAtomSegments, chainAtomSegments } = hierarchy
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const { label_asym_id } = chains
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- const turnFlag = [ 0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5 ]
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+ const turnFlag = [0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5]
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for (let i = 0, il = proteinResidues.length; i < il; ++i) {
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const rI = proteinResidues[i]
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@@ -347,18 +347,18 @@ function assignTurns(ctx: DSSPContext) {
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/**
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* Two nonoverlapping stretches of three residues each, i - 1, i, i + 1 and j - 1, j, j + 1,
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- * form either a parallel or antiparallel bridge, depending on which of
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+ * form either a parallel or antiparallel bridge, depending on which of
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* two basic patterns is matched. We assign a bridge between residues i and j
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* if there are two H bonds characteristic of P-structure; in particular,
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- *
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+ *
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* Parallel Bridge(i, j) =:
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* [Hbond(i - 1, j) and Hbond(j, i + 1)] or
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* [Hbond(j - 1, i) and Hbond(i, j + 1)]
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- *
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+ *
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* Antiparallel Bridge(i, j) =:
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* [Hbond(i, j) and Hbond(j, i)] or
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* [Hbond(i - 1, j + 1) and Hbond(j - 1, i + l)]
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- *
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+ *
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* Type: B
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*/
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function assignBridges(ctx: DSSPContext) {
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@@ -371,7 +371,7 @@ function assignBridges(ctx: DSSPContext) {
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for (let t = offset[k], _t = offset[k + 1]; t < _t; t++) {
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const l = b[t]
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if (k > l) continue
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-
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+
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// Parallel Bridge(i, j) =: [Hbond(i - 1, j) and Hbond(j, i + 1)]
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i = k + 1 // k is i - 1
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j = l
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@@ -411,18 +411,18 @@ function assignBridges(ctx: DSSPContext) {
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* A minimal helix is defined by two consecutive n-turns.
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* For example, a 4-helix, of minimal length 4 from residues i to i + 3,
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* requires 4-turns at residues i - 1 and i,
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- *
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+ *
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* 3-helix(i,i + 2)=: [3-turn(i - 1) and 3-turn(i)]
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* 4-helix(i,i + 3)=: [4-turn(i - 1) and 4-turn(i)]
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* 5-helix(i,i + 4)=: [5-turn(i - 1) and 5-turn(i)]
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- *
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+ *
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* Type: G (n=3), H (n=4), I (n=5)
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*/
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function assignHelices(ctx: DSSPContext) {
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const { proteinResidues, flags } = ctx
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-
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- const turnFlag = [ 0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5 ]
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- const helixFlag = [ 0, 0, 0, DSSPType.Flag.G, DSSPType.Flag.H, DSSPType.Flag.I ]
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+
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+ const turnFlag = [0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5]
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+ const helixFlag = [0, 0, 0, DSSPType.Flag.G, DSSPType.Flag.H, DSSPType.Flag.I]
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for (let i = 1, il = proteinResidues.length; i < il; ++i) {
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const fI = DSSPType.create(flags[i])
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@@ -440,7 +440,7 @@ function assignHelices(ctx: DSSPContext) {
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/**
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* ladder=: set of one or more consecutive bridges of identical type
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- *
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+ *
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* Type: E
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*/
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function assignLadders(ctx: DSSPContext) {
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@@ -449,7 +449,7 @@ function assignLadders(ctx: DSSPContext) {
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/**
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* sheet=: set of one or more ladders connected by shared residues
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- *
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+ *
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* Type: E
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*/
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function assignSheets(ctx: DSSPContext) {
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@@ -458,7 +458,7 @@ function assignSheets(ctx: DSSPContext) {
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/**
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* Bend(i) =: [angle ((CW - Ca(i - 2)),(C"(i + 2) - C"(i))) > 70"]
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- *
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+ *
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* Type: S
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*/
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function assignBends(ctx: DSSPContext) {
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David Sehnal