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Commit 2bb40d91 authored by Sebastian Bittrich's avatar Sebastian Bittrich
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indention and code order

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src/mol-model/structure/model/properties/utils/secondary-structure.ts
+ 100
− 108
View file @ 2bb40d91
......@@ -23,12 +23,102 @@ import { AtomicHierarchy, AtomicConformation } from '../atomic';
* - validate new ordering of secondary structure elements
*/
/** max distance between two C-alpha atoms to check for hbond */
const caMaxDist = 9.0;
/**
* Constant for electrostatic energy in kcal/mol
* f * q1 * q2
* Q = -332 * 0.42 * 0.20
*
* f is the dimensional factor
*
* q1 and q2 are partial charges which are placed on the C,O
* (+q1,-q1) and N,H (-q2,+q2)
*/
const Q = -27.888
/** cutoff for hbonds in kcal/mol, must be lower to be consider as an hbond */
const hbondEnergyCutoff = -0.5
/** prevent extremely low hbond energies */
const hbondEnergyMinimal = -9.9
export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
conformation: AtomicConformation): SecondaryStructure {
// TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
return computeModelDSSP(hierarchy, conformation)
}
interface DSSPContext {
/** Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter */
oldDefinition: boolean,
/** alpha-helices are preferred over 3-10 helix */
oldOrdering: boolean,
getResidueFlag: (f: DSSPType) => SecondaryStructureType,
getFlagName: (f: DSSPType) => String,
hierarchy: AtomicHierarchy
proteinResidues: SortedArray<ResidueIndex>
/** flags for each residue */
flags: Uint32Array
hbonds: DsspHbonds,
torsionAngles: { phi: number[], psi: number[] },
backboneIndices: BackboneAtomIndices,
conformation: AtomicConformation,
ladders: Ladder[],
bridges: Bridge[]
}
interface Ladder {
previousLadder: number,
nextLadder: number,
firstStart: number,
secondStart: number,
secondEnd: number,
firstEnd: number,
type: BridgeType
}
const enum BridgeType {
PARALLEL = 0x0,
ANTI_PARALLEL = 0x1
}
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>
namespace DSSPType {
export const is: (t: DSSPType, f: Flag) => boolean = BitFlags.has
export const create: (f: Flag) => DSSPType = BitFlags.create
export const enum Flag {
_ = 0x0,
H = 0x1,
B = 0x2,
E = 0x4,
G = 0x8,
I = 0x10,
S = 0x20,
T = 0x40,
T3 = 0x80,
T4 = 0x100,
T5 = 0x200,
T3S = 0x400, // marks 3-turn start
T4S = 0x800,
T5S = 0x1000
}
}
export function computeModelDSSP(hierarchy: AtomicHierarchy,
conformation: AtomicConformation,
oldDefinition = true,
......@@ -75,9 +165,7 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy,
assignSheets(ctx)
const assignment = getDSSPAssignment(flags, getResidueFlag)
const type = new Uint32Array(hierarchy.residues._rowCount) as unknown as SecondaryStructureType[]
const keys: number[] = []
const elements: SecondaryStructure.Element[] = []
......@@ -86,8 +174,7 @@ export function computeModelDSSP(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 || // check ought to fail at very start
flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet).flags) { // exact flag changed
if (elements.length === 0 /* would fail at very start */ || flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet).flags /* flag changed */) {
elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
}
keys[i] = elements.length - 1
......@@ -133,8 +220,7 @@ function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DS
}
function mapToKind(assignment: SecondaryStructureType.Flag) {
if (assignment === SecondaryStructureType.SecondaryStructureDssp.H || assignment === SecondaryStructureType.SecondaryStructureDssp.G ||
assignment === SecondaryStructureType.SecondaryStructureDssp.I) {
if (assignment === SecondaryStructureType.SecondaryStructureDssp.H || assignment === SecondaryStructureType.SecondaryStructureDssp.G || assignment === SecondaryStructureType.SecondaryStructureDssp.I) {
return 'helix'
} else if (assignment === SecondaryStructureType.SecondaryStructureDssp.B || assignment === SecondaryStructureType.SecondaryStructureDssp.E) {
return 'sheet'
......@@ -143,79 +229,6 @@ function mapToKind(assignment: SecondaryStructureType.Flag) {
}
}
interface DSSPContext {
/** Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter */
oldDefinition: boolean,
/** alpha-helices are preferred over 3-10 helix */
oldOrdering: boolean,
getResidueFlag: (f: DSSPType) => SecondaryStructureType,
getFlagName: (f: DSSPType) => String,
hierarchy: AtomicHierarchy
proteinResidues: SortedArray<ResidueIndex>
/** flags for each residue */
flags: Uint32Array
hbonds: DsspHbonds,
torsionAngles: { phi: number[], psi: number[]/*, omega: number[]*/ },
backboneIndices: BackboneAtomIndices,
conformation: AtomicConformation,
ladders: Ladder[],
bridges: Bridge[]
}
interface Ladder {
previousLadder: number,
nextLadder: number,
firstStart: number,
secondStart: number,
secondEnd: number,
firstEnd: number,
type: BridgeType
}
const enum BridgeType {
PARALLEL = 0x0,
ANTI_PARALLEL = 0x1
}
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>
namespace DSSPType {
export const is: (t: DSSPType, f: Flag) => boolean = BitFlags.has
export const create: (f: Flag) => DSSPType = BitFlags.create
export const enum Flag {
_ = 0x0,
H = 0x1,
B = 0x2,
E = 0x4,
G = 0x8,
I = 0x10,
S = 0x20,
T = 0x40,
T3 = 0x80,
T4 = 0x100,
T5 = 0x200,
T3S = 0x400, // marks 3-turn start
T4S = 0x800,
T5S = 0x1000
}
}
/** max distance between two C-alpha atoms to check for hbond */
const caMaxDist = 9.0;
function calcAtomicTraceLookup3D(hierarchy: AtomicHierarchy, conformation: AtomicConformation) {
const { x, y, z } = conformation;
const { moleculeType, traceElementIndex } = hierarchy.derived.residue
......@@ -284,7 +297,6 @@ function assignBends(ctx: DSSPContext) {
const caPosPrev2 = Vec3.zero()
const caPos = Vec3.zero()
const caPosNext2 = Vec3.zero()
// let bends = 0
const nIndices = ctx.backboneIndices.nIndices
const cPos = Vec3.zero()
......@@ -321,16 +333,14 @@ function assignBends(ctx: DSSPContext) {
const angle = Vec3.angle(caMinus2, caPlus2) * 360 / (2 * Math.PI)
if (angle && angle > 70.00) {
// console.log(`found bend at ${ i } with kappa ${ angle }`)
flags[i] |= DSSPType.Flag.S
// bends++
}
}
// console.log(bends + ' bends')
}
function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: AtomicConformation, proteinResidues: SortedArray<ResidueIndex>, backboneIndices: BackboneAtomIndices): { phi: number[], psi: number[]/*, omega: number[]*/ } {
const { cIndices, nIndices } = backboneIndices
const { index } = hierarchy
const { x, y, z } = conformation
const { traceElementIndex } = hierarchy.derived.residue
......@@ -349,7 +359,6 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
const phi: number[] = []
const psi: number[] = []
// const omega: number[] = []
for (let i = 0; i < residueCount - 1; ++i) {
const oPIprev = i - 1
......@@ -370,7 +379,7 @@ function calculateDihedralAngles(hierarchy: AtomicHierarchy, conformation: Atomi
const nAtomNext = nIndices[oRInext]
// ignore C-terminal residue as acceptor
// if (index.findAtomOnResidue(oRI, 'OXT') !== -1) continue
if (index.findAtomOnResidue(oRI, 'OXT') !== -1) continue
position(cAtomPrev, cPosPrev)
position(caAtomPrev, caPosPrev)
......@@ -551,23 +560,6 @@ function getDSSPAssignment(flags: Uint32Array, getResidueFlag: (f: DSSPType) =>
return type as unknown as ArrayLike<SecondaryStructureType>
}
/**
* Constant for electrostatic energy in kcal/mol
* f * q1 * q2
* Q = -332 * 0.42 * 0.20
*
* f is the dimensional factor
*
* q1 and q2 are partial charges which are placed on the C,O
* (+q1,-q1) and N,H (-q2,+q2)
*/
const Q = -27.888
/** cutoff for hbonds in kcal/mol, must be lower to be consider as an hbond */
const hbondEnergyCutoff = -0.5
const hbondEnergyMinimal = -9.9
/**
* E = Q * (1/r(ON) + l/r(CH) - l/r(OH) - l/r(CN))
*/
......
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