diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index 45f9a41cf78b1efe985889b10e3127e2170df469..bbadc038b15dd391c09fdae5debc08d021dcbd2d 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -13,7 +13,9 @@ interface SecondaryStructure {
/** index into the elements array */
readonly key: ArrayLike<number>,
/** indexed by key */
- readonly elements: ReadonlyArray<SecondaryStructure.Element>
+ readonly elements: ReadonlyArray<SecondaryStructure.Element>,
+ /** string representation of DSSP annotation */
+ readonly dsspString: String
}
namespace SecondaryStructure {
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 cbc23b4db5f283a2dbbc3a4ba38529e754ddf78f..afb3f4aedb619d48313ae02d8c623f6bf0e03d54 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -85,10 +85,8 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy,
const assign = assignment[i]
type[proteinResidues[i]] = assign
const flag = getResidueFlag(flags[i])
- // const kind = mapToKind(assign)
// TODO is this expected behavior? elements will be strictly split depending on 'winning' flag
if (elements.length === 0 || // check ought to fail at very start
- // elements[elements.length - 1].kind !== kind || // new element if overall kind changed
flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet).flags) { // exact flag changed
elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
}
@@ -98,24 +96,21 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy,
const secondaryStructure: SecondaryStructure = {
type,
key: keys,
- elements: elements
+ elements: elements,
+ dsspString: composeDSSPString(flags, getFlagName)
}
- // console.log(keys)
- // console.log(elements)
- // printDSSPString(flags, getFlagName)
-
return secondaryStructure
}
-// function printDSSPString(flags: Uint32Array, getFlagName: (f: DSSPType) => String) {
-// let out = ''
-// for (let i = 0, il = flags.length; i < il; ++i) {
-// const f = DSSPType.create(flags[i])
-// out += getFlagName(f)
-// }
-// console.log(out)
-// }
+function composeDSSPString(flags: Uint32Array, getFlagName: (f: DSSPType) => String) {
+ let out = ''
+ for (let i = 0, il = flags.length; i < il; ++i) {
+ const f = DSSPType.create(flags[i])
+ out += getFlagName(f)
+ }
+ return out
+}
function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DSSPType) => SecondaryStructureType): SecondaryStructure.Element {
// TODO would be nice to add more detailed information
@@ -390,22 +385,14 @@ 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)
-
- // console.log(`phi: ${ tPhi }, psi: ${ tPsi }, omega: ${ 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 };
}
// 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 Vec3.dihedralAngle(c, nNext, caNext, cNext);
}
@@ -414,10 +401,6 @@ function calculatePsi(n: Vec3, ca: Vec3, c: Vec3, nNext: Vec3) {
return Vec3.dihedralAngle(n, ca, c, nNext);
}
-// 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
const { index } = hierarchy
@@ -463,7 +446,7 @@ function calcBackboneHbonds(hierarchy: AtomicHierarchy, conformation: AtomicConf
const { indices, count } = lookup3d.find(caPos[0], caPos[1], caPos[2], caMaxDist)
for (let j = 0; j < count; ++j) {
- // if (squaredDistances[j] < caMinDistSq) continue
+ // if (squaredDistances[j] < caMinDist * caMinDist) continue
const nPI = indices[j]
@@ -498,7 +481,6 @@ function calcBackboneHbonds(hierarchy: AtomicHierarchy, conformation: AtomicConf
const e = calcHbondEnergy(oPos, cPos, nPos, hPos)
if (e > hbondEnergyCutoff) continue
- // console.log(`detected hbond between ${ oPI } and ${ nPI } with energy ${ e }`)
oAtomResidues[oAtomResidues.length] = oPI
nAtomResidues[nAtomResidues.length] = nPI
energies[energies.length] = e
@@ -628,7 +610,6 @@ function assignTurns(ctx: DSSPContext) {
const { proteinResidues, hbonds, flags, hierarchy } = ctx
const { chains, residueAtomSegments, chainAtomSegments } = hierarchy
const { label_asym_id } = chains
- // let turns = 0, turnOpenings = 0
const turnFlag = [DSSPType.Flag.T3S, DSSPType.Flag.T4S, DSSPType.Flag.T5S, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5]
@@ -644,27 +625,20 @@ function assignTurns(ctx: DSSPContext) {
if (!label_asym_id.areValuesEqual(cI, cN)) continue
// check if hbond exists
- // console.log(`${ i } has ${ idx + 3}-turn opening: ${ hbonds.getDirectedEdgeIndex(i, i + idx + 3) !== -1 }`)
if (hbonds.getDirectedEdgeIndex(i, i + idx + 3) !== -1) {
- // console.log(`${ idx + 3 }-turn opening at ${ i } to ${ i + idx + 3 }`)
flags[i] |= turnFlag[idx + 3] | turnFlag[idx]
- // turnOpenings++
if (ctx.oldDefinition) {
for (let k = 1; k < idx + 3; ++k) {
flags[i + k] |= turnFlag[idx + 3] | DSSPType.Flag.T
- // turns++
}
} else {
for (let k = 0; k <= idx + 3; ++k) {
flags[i + k] |= turnFlag[idx + 3] | DSSPType.Flag.T
- // turns++
}
}
}
}
}
-
- // console.log(`${ turns } turns, ${ turnOpenings } turn openings`)
}
/**
@@ -734,8 +708,6 @@ function assignBridges(ctx: DSSPContext) {
}
bridges.sort((a, b) => a.partner1 > b.partner1 ? 1 : a.partner1 < b.partner1 ? -1 : 0)
- // console.log(`${ bridges.length } bridges`)
- // bridges.forEach(b => console.log(b))
}
/**
@@ -756,7 +728,6 @@ function assignHelices(ctx: DSSPContext) {
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 count = [0, 0, 0, 0, 0, 0]
for (let ni = 0; ni < helixCheckOrder.length; ni++) {
const n = helixCheckOrder[ni]
@@ -769,35 +740,29 @@ function assignHelices(ctx: DSSPContext) {
if (ctx.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
- // console.log('skipping in favor of more preferable helix already present')
continue
}
} else {
if ((n === 4 && (DSSPType.is(fI, DSSPType.Flag.G) || DSSPType.is(fI2, DSSPType.Flag.G)) || // for alpha helix yield to 3-10
(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
- // console.log('skipping in favor of more preferable helix already present')
continue
}
}
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
- // console.log(`valid hit for ${n} from ${i} to ${i+n}`)
if (ctx.oldDefinition) {
for (let k = 0; k < n; k++) {
flags[i + k] |= helixFlag[n]
- // count[n]++
}
} else {
for (let k = -1; k <= n; k++) {
flags[i + k] |= helixFlag[n]
- // count[n]++
}
}
}
}
}
- // console.log(`${ count[3] + count[4] + count[5] } helix elements - ${ count[3] } 3-10, ${ count[4] } alpha, ${ count[5] } pi`)
}
/**
@@ -808,7 +773,6 @@ function assignHelices(ctx: DSSPContext) {
function assignLadders(ctx: DSSPContext) {
const { bridges, ladders } = ctx
- // let ext = 0
// create ladders
for (let bridgeIndex = 0; bridgeIndex < bridges.length; bridgeIndex++) {
const bridge = bridges[bridgeIndex]
@@ -816,7 +780,6 @@ function assignLadders(ctx: DSSPContext) {
for (let ladderIndex = 0; ladderIndex < ladders.length; ladderIndex++) {
const ladder = ladders[ladderIndex]
if (shouldExtendLadder(ladder, bridge)) {
- // ext++
found = true
ladder.firstEnd++
if (bridge.type === BridgeType.PARALLEL) {
@@ -840,7 +803,6 @@ function assignLadders(ctx: DSSPContext) {
}
}
}
- // console.log(`${ ext } extension operations`)
// connect ladders
for (let ladderIndex1 = 0; ladderIndex1 < ladders.length; ladderIndex1++) {
@@ -848,14 +810,11 @@ function assignLadders(ctx: DSSPContext) {
for (let ladderIndex2 = ladderIndex1; ladderIndex2 < ladders.length; ladderIndex2++) {
const ladder2 = ladders[ladderIndex2]
if (resemblesBulge(ladder1, ladder2)) {
- // console.log(`connecting ladders ${ ladderIndex1 } and ${ ladderIndex2 } with inbetween bulge`)
ladder1.nextLadder = ladderIndex2
ladder2.previousLadder = ladderIndex1
}
}
}
-
- // console.log(`${ ladders.length } ladders`)
}
/**
@@ -883,18 +842,15 @@ function shouldExtendLadder(ladder: Ladder, bridge: Bridge): boolean {
// in order to extend ladders, same type must be present
if (bridge.type !== ladder.type) return false
- // console.log(`${ bridge.partner1 }-${ bridge.partner2 } ${ ladder.firstEnd }`)
// only extend if residue 1 is sequence neighbor with regard to ladder
if (bridge.partner1 !== ladder.firstEnd + 1) return false
if (bridge.type === BridgeType.PARALLEL) {
if (bridge.partner2 === ladder.secondEnd + 1) {
- // console.log(ladder)
return true
}
} else {
if (bridge.partner2 === ladder.secondStart - 1) {
- // console.log(ladder)
return true
}
}
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.validation b/src/mol-model/structure/model/properties/utils/secondary-structure.validation
index 9b76268f33343c71b216674b79e99e6e76d1cf24..4f1a1f1bba2be14065663ee39ef36e21fb2d575a 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.validation
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.validation
@@ -70,4 +70,6 @@ DSSP: -------TT----------TT----------------GGGTT------------------------------TT
# all #
Mol*: --SEEEETTEEEE-EEEEETTEEEEEEEEEE-EE---GGGTTS--EE----SSEEE--S---B-------TTTT-HHHHTTS--S-B-S---EEEEEE-SS--SSEEEEEEE--STTT---S-SGGG-THHHHHHHT-EEEE-----SHHHH---TT-SSS-S-HHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHH-HHHHTT-SEEEEES--TTSTTSEEEHHHHHHHHHHHHHHTT---S-HHHHHHHHHHS-HHHHHHHHGGG-SS--SS--S--EEE-SSSSSS-HHHHHHHT-S--S-EEEEEESB-SHHHHHHHSTT--TTS-----HHHHHHHHHHHTTT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTTSS-EEEEEE----TT--S-GGG-SBTTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHTSSSS---------SSS-EEEEESSSS--EEESTTHHHHHHHHTHHHHHHHH-
DSSP: --SEEEETTEEEE-EEEEETTEEEEEEEEEE-EE---GGGTTS--EE----SSEEE--S---B-------SSTT-HHHHTTS--S-B-S---EEEEEE-SS--SSEEEEEEE--STTT---S-SGGG-THHHHHHHT-EEEE-----SHHHH---TT-SSS-S-HHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHH-HHHHTT-SEEEEES--TTSTTS-EEHHHHHHHHHHHHHHTT---S-HHHHHHHHHHS-HHHHHHHHGGG-SS--SS--S---EE-SSSSSS-HHHHHHHT-S--S-EEEEEESB-SHHHHHHHSTT--TTS-----HHHHHHHHHHH-TT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTTSS-EEEEEE----TT--S-GGG-SBTTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHTSSSS---------SSS-EEEEESSSS--EEESTTHHHHHHHHTHHHHHHHH-
-TODO fix mismatches e.g. here
\ No newline at end of file
+
+TODO fix mismatches e.g. here
+TODO move to spec.ts once tests are running
\ No newline at end of file
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index e3732508f43a79e42d4aab8db5b558e067a7768a..927e24c14132b9746c37f2d90b2764b6c47652ad 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -62,7 +62,7 @@ function getCartoonRepr() {
}
async function init() {
- const cif = await downloadFromPdb('3j3q')
+ const cif = await downloadFromPdb('1acj')
const models = await getModels(cif)
console.time('computeModelDSSP')
const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy,
@@ -72,6 +72,8 @@ async function init() {
const structure = await getStructure(models[0])
const cartoonRepr = getCartoonRepr()
+ console.log(secondaryStructure.dsspString)
+
cartoonRepr.setTheme({
color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
size: reprCtx.sizeThemeRegistry.create('uniform', { structure })