fixes to DSSP impl, detection of bends and sheets

src/mol-math/linear-algebra/3d/vec3.ts

@@ -414,6 +414,7 @@ namespace Vec3 {
     }
 
     const angleTempA = zero(), angleTempB = zero();
+    /** Computes the angle between 2 vectors, reports in rad. */
     export function angle(a: Vec3, b: Vec3) {
         copy(angleTempA, a);
         copy(angleTempB, b);

src/mol-math/linear-algebra/_spec/vec3.spec.ts

+import { Vec3 } from '../3d'
+
+describe('vec3', () => {
+    const vec1 = [ 1, 2, 3 ] as Vec3;
+    const vec2 = [ 2, 3, 1 ] as Vec3;
+    const orthVec1 = [ 0, 1, 0 ] as Vec3;
+    const orthVec2 = [ 1, 0, 0 ] as Vec3;
+
+    it('angle calculation', () => {
+        expect(Vec3.angle(vec1, vec1) * 360 / (2 * Math.PI)).toBe(0.0);
+        expect(Vec3.angle(orthVec1, orthVec2) * 360 / (2 * Math.PI)).toBe(90.0);
+        expect(Vec3.angle(vec1, vec2)).toBeCloseTo(0.666946);
+    });
+})
\ No newline at end of file

src/mol-model/structure/model/properties/seconday-structure.ts

@@ -20,7 +20,8 @@ namespace SecondaryStructure {
     export type Element = None | Helix | Sheet
 
     export interface None {
-        kind: 'none'
+        kind: 'none',
+        flags?: SecondaryStructureType // TODO should this level of detail be added to non-defined secondary structure elements?
     }
 
     export interface Helix {

src/mol-model/structure/model/properties/utils/secondary-structure.validation

+compares Mol* port of DSSP (with default parameters) to the BioJava implementation
+
+### pdb:1pga ###
+# turns #
+Mol*: ----------------------TTTTTTTTTTTTTTTT--------TTTT------
+53 turns, 18 openings
+DSSP: ----------------------TTTTTTTTTTTTTTTT--------TTTT------
+53 turns, 18 openings
+
+# bends #
+Mol*: ---------SS---------SSSSSSSSSSSSSSSSSS--------SSS-------
+23 bends
+DSSP: ---------SS---------SSSSSSSSSSSSSSSSSS--------SSS-------
+23 bends
+
+# helices #
+Mol*: ----------------------HHHHHHHHHHHHHHTT--------TTTT------
+44 helix elements - 0 3-10, 44 alpha, 0 pi
+DSSP: ----------------------HHHHHHHHHHHHHHTT--------TTTT------
+44 helix elements - 0 3-10, 44 alpha, 0 pi
+
+# all #
+Mol*: -EEEEEEE-SS-EEEEEEE-SSHHHHHHHHHHHHHHTT---EEEEETTTTEEEEE-
+DSSP: -EEEEEEE-SS-EEEEEEE-SSHHHHHHHHHHHHHHTT---EEEEETTTTEEEEE-
+
+
+### pdb:1bta ###
+# turns #
+Mol*: ------TTT---TTTTTTTTTTTTT--TT----TTTTTTTTTTT-----------TTTTTTTTT--TTTTTTTTTTTTTTT--------
+127 turns, 44 openings
+DSSP: ------TTT---TTTTTTTTTTTTT--TT----TTTTTTTTTTT-----------TTTTTTTTT--TTTTTTTTTTTTTTT--------
+127 turns, 44 openings
+
+# bends #
+Mol*: ------SSS--SSSSSSSSSSSSS---SS---SSSSSSSSSSSSS-SS------SSSSSSSSSSSSSSSSSSSSSSSSSSS--------
+60 bends
+DSSP: ------SSS--SSSSSSSSSSSSS---SS---SSSSSSSSSSSSS-SS------SSSSSSSSSSSSSSSSSSSSSSSSSSS--------
+60 bends
+
+# helices #
+Mol*: ------TTT---HHHHHHHHHHHHT--TT----HHHHHHHHTTT-----------TTHHHHTTT--HHHHHHHHHHHHHTT--------
+100 helix elements - 0 3-10, 100 alpha, 0 pi
+DSSP: ------TTT---HHHHHHHHHHHHT--TT----HHHHHHHHTTT-----------TTHHHHTTT--HHHHHHHHHHHHHTT--------
+100 helix elements - 0 3-10, 100 alpha, 0 pi
+
+# all #
+Mol*: -EEEEETTT--SHHHHHHHHHHHHT--TT---SHHHHHHHHTTTS-SSEEEEEESTTHHHHTTTSSHHHHHHHHHHHHHTT--EEEEE-
+DSSP: -EEEEETTT--SHHHHHHHHHHHHT--TT---SHHHHHHHHTTTS-SSEEEEEESTTHHHHTTTSSHHHHHHHHHHHHHTT--EEEEE-
+
+
+### pdb:1acj ###
+# turns #
+Mol*: -------TT----------TT----------------TTTTT----------------------------TTTT-TTTTTT----------------------------------TTT------TTT-TTTTTTTTT-----------TTTT---TT-------TTTTTTTTTTTTTTTTTTTTT--TT-------TTTTTTTTTTTT-TTTTTT----------TT-TT----TTTTTTTTTTTTTTTT-----TTTTTTTTTT--TTTTTTTTTTT-----------------------TTTTTTTT----------------TTTTTTT-TT--TT------TTTTTTTTTTTTTT--TTTTTTTTTTT--TTTTT-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-------------TT----TTT---TTTTTTTTTTTTT-TTT---TTTTTTTTTTTTTTTTTTTT--------------------------------TTTTTTTTTTTTTTTTTTT-
+614 turns, 223 openings
+DSSP: -------TT----------TT----------------TTTTT------------------------------TT-TTTTTT----------------------------------TTT------TTT-TTTTTTTTT-----------TTTT---TT-------TTTTTTTTTTTTTTTTTTTTT--TT-------TTTTTTTTTTTT-TTTTTT----------TT-TT----TTTTTTTTTTTTTTTT-----TTTTTTTTTT--TTTTTTTTTTT-----------------------TTTTTTTT----------------TTTTTTT-TT--TT------TTTTTTTTTTT-TT--TTTTTTTTTTT--TTTTT-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-------------TT----TTT---TTTTTTTTTTTTT-TTT---TTTTTTTTTTTTTTTTTTTT--------------------------------TTTTTTTTTTTTTTTTTTT-
+606 turns, 220 openings
+
+# bends #
+Mol*: --S----SS----------SSS----------S----SS-SSS--------SS-----S-----------SSSS-SSSSSSS--S---S----------SS--SS---------SSSS---S-SSSS--SSSSSSS-----------SSSS----SS-SSS-S-SSSSSSSSSSSSSSSSSSSSS--SSS------SSSSSSSSSSSS-SSSSSS-S----SS--SSSSSS---SSSSSSSSSSSSSSS----S-SSSSSSSSSSS-SSSSSSSSSS--SS--SS--S------SSSSSS-SSSSSSS--S--S-------S--SSSSSSSSSSS--SSS-----SSSSSSSSSSS-SS--SSSSSSSSSSS--SSSSS-SSSSSSSSSSSSSSSSS----SSSSSSSSSSSS-----------SS--S-SSS-S-SS-SSSSSS--SS-SSS---SSSSSSSSSSSSSSSSSSSSSSSS---------SSS------SSSS----SSSS-S----SSSSSSSSSS--
+305 bends
+DSSP: --S----SS----------SSS----------S----SS-SSS--------SS-----S-----------SSSS-SSSSSSS--S---S----------SS--SS---------SSSS---S-SSSS--SSSSSSS-----------SSSS----SS-SSS-S-SSSSSSSSSSSSSSSSSSSSS--SSS------SSSSSSSSSSSS-SSSSSS-S----SS--SSSSSS---SSSSSSSSSSSSSSS----S-SSSSSSSSSSS-SSSSSSSSSS--SS--SS--S------SSSSSS-SSSSSSS--S--S-------S--SSSSSSSSSSS--SSS-----SSSSSSSSSSS-SS--SSSSSSSSSSS--SSSSS-SSSSSSSSSSSSSSSSS----SSSSSSSSSSSS-----------SS--S-SSS-S-SS-SSSSSS--SS-SSS---SSSSSSSSSSSSSSSSSSSSSSSS---------SSS------SSSS----SSSS-S----SSSSSSSSSS--
+305 bends
+
+# helices #
+Mol*: -------TT----------TT----------------GGGTT----------------------------TTTT-HHHHTT----------------------------------TTT------GGG-THHHHHHHT-----------HHHH---TT-------HHHHHHHHHHHHHHHHGGGGT--TT-------THHHHHHHHHHH-HHHHTT----------TT-TT----HHHHHHHHHHHHHHTT-----HHHHHHHHHH--HHHHHHHHGGG-----------------------HHHHHHHT----------------HHHHHHH-TT--TT------HHHHHHHHHHHTTT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTT-------------TT----GGG---TTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHT--------------------------------TTHHHHHHHHTHHHHHHHH-
+523 helix elements - 27 3-10, 496 alpha, 0 pi
+DSSP: -------TT----------TT----------------GGGTT------------------------------TT-HHHHTT----------------------------------TTT------GGG-THHHHHHHT-----------HHHH---TT-------HHHHHHHHHHHHHHHHGGGGT--TT-------THHHHHHHHHHH-HHHHTT----------TT-TT----HHHHHHHHHHHHHHTT-----HHHHHHHHHH--HHHHHHHHGGG-----------------------HHHHHHHT----------------HHHHHHH-TT--TT------HHHHHHHHHHH-TT--HHHHHHHHHHH--GGGTT-HHHHHHHHHHHHHHHHTHHHHHHHHHHHHTT-------------TT----GGG---TTTTHHHHTTGGG-GGG---HHHHHHHHHHHHHHHHHHHT--------------------------------TTHHHHHHHHTHHHHHHHH-
+523 helix elements - 27 3-10, 496 alpha, 0 pi
+
+# 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

src/mol-model/structure/model/types.ts

@@ -275,41 +275,42 @@ export namespace SecondaryStructureType {
         DoubleHelix = 0x1,
         Helix = 0x2,
         Beta = 0x4,
-        Turn = 0x8,
+        Bend = 0x8,
+        Turn = 0x10,
 
         // category variant
-        LeftHanded = 0x10,  // helix
-        RightHanded = 0x20,
+        LeftHanded = 0x20,  // helix
+        RightHanded = 0x40,
 
-        ClassicTurn = 0x40,  // turn
-        InverseTurn = 0x80,
+        ClassicTurn = 0x80,  // turn
+        InverseTurn = 0x100,
 
         // sub-category
-        HelixOther = 0x100,  // protein
-        Helix27 = 0x200,
-        Helix3Ten = 0x400,
-        HelixAlpha = 0x800,
-        HelixGamma = 0x1000,
-        HelixOmega = 0x2000,
-        HelixPi = 0x4000,
-        HelixPolyproline = 0x8000,
-
-        DoubleHelixOther = 0x10000,  // nucleic
-        DoubleHelixZ = 0x20000,
-        DoubleHelixA = 0x40000,
-        DoubleHelixB = 0x80000,
-
-        BetaOther = 0x100000,  // protein
-        BetaStrand = 0x200000,  // single strand
-        BetaSheet = 0x400000,  // multiple hydrogen bonded strands
-        BetaBarell = 0x800000,  // closed series of sheets
-
-        TurnOther = 0x1000000,  // protein
-        Turn1 = 0x2000000,
-        Turn2 = 0x4000000,
-        Turn3 = 0x8000000,
-
-        NA = 0x10000000,  // not applicable/available
+        HelixOther = 0x200,  // protein
+        Helix27 = 0x400,
+        Helix3Ten = 0x800,
+        HelixAlpha = 0x1000,
+        HelixGamma = 0x2000,
+        HelixOmega = 0x4000,
+        HelixPi = 0x8000,
+        HelixPolyproline = 0x10000,
+
+        DoubleHelixOther = 0x20000,  // nucleic
+        DoubleHelixZ = 0x40000,
+        DoubleHelixA = 0x80000,
+        DoubleHelixB = 0x100000,
+
+        BetaOther = 0x200000,  // protein
+        BetaStrand = 0x400000,  // single strand
+        BetaSheet = 0x800000,  // multiple hydrogen bonded strands
+        BetaBarell = 0x1000000,  // closed series of sheets
+
+        TurnOther = 0x2000000,  // protein
+        Turn1 = 0x4000000,
+        Turn2 = 0x8000000,
+        Turn3 = 0x10000000,
+
+        NA = 0x20000000,  // not applicable/available
     }
 
     export const SecondaryStructureMmcif: { [value: string]: number } = {
@@ -386,7 +387,7 @@ export namespace SecondaryStructureType {
         G: Flag.Helix | Flag.Helix3Ten,  // 3-helix (310 helix)
         I: Flag.Helix | Flag.HelixPi,  // 5 helix (pi-helix)
         T: Flag.Turn,  // hydrogen bonded turn
-        S: Flag.Turn,  // bend
+        S: Flag.Bend,  // bend
     }
 }
 

src/mol-theme/color/secondary-structure.ts

@@ -22,6 +22,8 @@ const SecondaryStructureColors = ColorMap({
     'betaTurn': 0x6080FF,
     'betaStrand': 0xFFC800,
     'coil': 0xFFFFFF,
+    'bend': 0x66D8C9 /* biting original color used 0x00FF00 */,
+    'turn': 0x00B266,
 
     'dna': 0xAE00FE,
     'rna': 0xFD0162,
@@ -53,8 +55,10 @@ export function secondaryStructureColor(unit: Unit, element: ElementIndex): Colo
         return SecondaryStructureColors.alphaHelix
     } else if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Beta)) {
         return SecondaryStructureColors.betaStrand
+    } else if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Bend)) {
+        return SecondaryStructureColors.bend
     } else if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Turn)) {
-        return SecondaryStructureColors.coil
+        return SecondaryStructureColors.turn
     } else {
         const moleculeType = getElementMoleculeType(unit, element)
         if (moleculeType === MoleculeType.DNA) {

src/tests/browser/render-structure.ts

@@ -65,9 +65,10 @@ async function init() {
     const cif = await downloadFromPdb('3j3q')
     const models = await getModels(cif)
     console.time('computeModelDSSP')
-    const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy, models[0].atomicConformation)
-    console.timeEnd('computeModelDSSP')
-    ;(models[0].properties as any).secondaryStructure = secondaryStructure
+    const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy,
+        models[0].atomicConformation)
+    console.timeEnd('computeModelDSSP');
+    (models[0].properties as any).secondaryStructure = secondaryStructure
     const structure = await getStructure(models[0])
     const cartoonRepr = getCartoonRepr()
 
@@ -76,7 +77,7 @@ async function init() {
         size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
     })
     await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
-    
+
     canvas3d.add(cartoonRepr)
     canvas3d.resetCamera()
 }