From 606ef255e8815bd13960028614e8350d92c50b9d Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 24 Apr 2019 11:07:17 -0700
Subject: [PATCH] per-unit dssp as structure property
---
.../structure/mmcif/secondary-structure.ts | 9 ++++++---
.../computed/secondary-structure.ts | 3 ++-
.../computed/secondary-structure/dssp.ts | 11 +++++-----
.../secondary-structure/dssp/trace-lookup.ts | 2 +-
.../model/properties/seconday-structure.ts | 7 +++++--
.../visual/util/polymer/trace-iterator.ts | 20 ++++++++++++++-----
src/mol-theme/color/secondary-structure.ts | 2 +-
7 files changed, 36 insertions(+), 18 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/secondary-structure.ts b/src/mol-model-formats/structure/mmcif/secondary-structure.ts
index bb3f4fabb..ca06a9b65 100644
--- a/src/mol-model-formats/structure/mmcif/secondary-structure.ts
+++ b/src/mol-model-formats/structure/mmcif/secondary-structure.ts
@@ -19,14 +19,17 @@ export function getSecondaryStructure(data: mmCIF_Database, hierarchy: AtomicHie
// must add Helices 1st because of 'key' value assignment.
addSheets(data.struct_sheet_range, map, data.struct_conf._rowCount, elements);
+ const n = hierarchy.residues._rowCount
+ const getIndex = (rI: ResidueIndex) => rI
+
const secStruct: SecondaryStructureData = {
- type: new Int32Array(hierarchy.residues._rowCount) as any,
- key: new Int32Array(hierarchy.residues._rowCount) as any,
+ type: new Int32Array(n) as any,
+ key: new Int32Array(n) as any,
elements
};
if (map.size > 0) assignSecondaryStructureRanges(hierarchy, map, secStruct);
- return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements);
+ return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements, getIndex);
}
type SecondaryStructureEntry = {
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index d45ff6952..784be59d3 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.ts
@@ -59,7 +59,8 @@ export type SecondaryStructureComputationProps = PD.Values<SecondaryStructureCom
async function computeSecondaryStructure(structure: Structure, params: Partial<SecondaryStructureComputationProps>): Promise<ComputedSecondaryStructure.Property> {
const p = { ...PD.getDefaultValues(SecondaryStructureComputationParams), params }
- // TODO take inter-unit hbonds into account
+ // TODO take inter-unit hbonds into account for bridge, ladder, sheet assignment
+ // TODO store unit-only secStruc as custom unit property???
// TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
const map = new Map<number, SecondaryStructure>()
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
diff --git a/src/mol-model-props/computed/secondary-structure/dssp.ts b/src/mol-model-props/computed/secondary-structure/dssp.ts
index 0d9504586..7838724f5 100644
--- a/src/mol-model-props/computed/secondary-structure/dssp.ts
+++ b/src/mol-model-props/computed/secondary-structure/dssp.ts
@@ -20,6 +20,8 @@ import { calculateUnitDihedralAngles } from './dssp/dihedral-angles';
import { calcUnitProteinTraceLookup3D } from './dssp/trace-lookup';
import { Unit } from 'mol-model/structure';
import { getUnitProteinInfo } from './dssp/protein-info';
+import { ResidueIndex } from 'mol-model/structure/model';
+import { SortedArray } from 'mol-data/int';
/**
* TODO bugs to fix:
@@ -37,7 +39,6 @@ export type DSSPComputationParams = typeof DSSPComputationParams
export type DSSPComputationProps = PD.Values<DSSPComputationParams>
export async function computeUnitDSSP(unit: Unit.Atomic, params: DSSPComputationProps): Promise<SecondaryStructure> {
-
const proteinInfo = getUnitProteinInfo(unit)
const { residueIndices } = proteinInfo
const lookup3d = calcUnitProteinTraceLookup3D(unit, residueIndices)
@@ -83,20 +84,20 @@ export async function computeUnitDSSP(unit: Unit.Atomic, params: DSSPComputation
const type = new Uint32Array(residueCount) as unknown as SecondaryStructureType[]
const keys: number[] = []
const elements: SecondaryStructure.Element[] = []
+ const getIndex = (rI: ResidueIndex) => SortedArray.indexOf(residueIndices, rI)
for (let i = 0, il = residueIndices.length; i < il; ++i) {
const assign = assignment[i]
- type[residueIndices[i]] = assign
+ type[i] = assign
const flag = getResidueFlag(flags[i])
+ // console.log(i, SortedArray.indexOf(residueIndices, i), getFlagName(flags[i]))
// TODO is this expected behavior? elements will be strictly split depending on 'winning' flag
if (elements.length === 0 /* would fail at very start */ || flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet | SecondaryStructure.Turn).flags /* flag changed */) {
elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
}
keys[i] = elements.length - 1
}
- // TODO expose model to unit residueIndex mapping
-
- return SecondaryStructure(type, keys, elements)
+ return SecondaryStructure(type, keys, elements, getIndex)
}
function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DSSPType) => SecondaryStructureType): SecondaryStructure.Element {
diff --git a/src/mol-model-props/computed/secondary-structure/dssp/trace-lookup.ts b/src/mol-model-props/computed/secondary-structure/dssp/trace-lookup.ts
index bfda77c36..e889ddf8c 100644
--- a/src/mol-model-props/computed/secondary-structure/dssp/trace-lookup.ts
+++ b/src/mol-model-props/computed/secondary-structure/dssp/trace-lookup.ts
@@ -14,7 +14,7 @@ export function calcUnitProteinTraceLookup3D(unit: Unit.Atomic, unitProteinResid
const { traceElementIndex } = unit.model.atomicHierarchy.derived.residue
const indices = new Uint32Array(unitProteinResidues.length)
for (let i = 0, il = unitProteinResidues.length; i < il; ++i) {
- indices[indices.length] = traceElementIndex[unitProteinResidues[i]]
+ indices[i] = traceElementIndex[unitProteinResidues[i]]
}
return GridLookup3D({ x, y, z, indices: SortedArray.ofSortedArray(indices) });
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index 64fcb890f..82a44214d 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -5,6 +5,7 @@
*/
import { SecondaryStructureType } from '../types';
+import { ResidueIndex } from '../indexing';
/** Secondary structure "indexed" by residues. */
interface SecondaryStructure {
@@ -13,10 +14,12 @@ interface SecondaryStructure {
readonly key: ArrayLike<number>,
/** indexed by key */
readonly elements: ReadonlyArray<SecondaryStructure.Element>
+ /** mapping from residue index */
+ readonly getIndex: (rI: ResidueIndex) => number,
}
-function SecondaryStructure(type: SecondaryStructure['type'], key: SecondaryStructure['key'], elements: SecondaryStructure['elements']) {
- return { type, key, elements }
+function SecondaryStructure(type: SecondaryStructure['type'], key: SecondaryStructure['key'], elements: SecondaryStructure['elements'], getIndex: SecondaryStructure['getIndex']) {
+ return { type, key, elements, getIndex }
}
namespace SecondaryStructure {
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index e0ae05d72..68b46ca5e 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -14,6 +14,7 @@ import { CoarseSphereConformation, CoarseGaussianConformation } from 'mol-model/
import { getPolymerRanges } from '../polymer';
import { AtomicConformation } from 'mol-model/structure/model/properties/atomic';
import { ComputedSecondaryStructure } from 'mol-model-props/computed/secondary-structure';
+import { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
/**
* Iterates over individual residues/coarse elements in polymers of a unit while
@@ -69,7 +70,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
private residueIt: Segmentation.SegmentIterator<ResidueIndex>
private polymerSegment: Segmentation.Segment<ResidueIndex>
private cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
- private secondaryStructureType: ArrayLike<SecondaryStructureType>
+ private secondaryStructureType: SecondaryStructure['type']
+ private secondaryStructureGetIndex: SecondaryStructure['getIndex']
private residueSegmentMin: ResidueIndex
private residueSegmentMax: ResidueIndex
private prevSecStrucType: SecondaryStructureType
@@ -133,8 +135,12 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
return residueIndex as ResidueIndex
}
+ private getSecStruc(residueIndex: number) {
+ return this.secondaryStructureType[this.secondaryStructureGetIndex(residueIndex as ResidueIndex)]
+ }
+
private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
- const ss = this.secondaryStructureType[residueIndex]
+ const ss = this.getSecStruc(residueIndex)
if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p3, Vec3.add(out, p2, p2))), 1/4)
} else {
@@ -153,7 +159,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (residueIt.hasNext) {
this.state = AtomicPolymerTraceIteratorState.nextResidue
this.currSecStrucType = SecStrucTypeNA
- this.nextSecStrucType = this.secondaryStructureType[this.residueSegmentMin]
+ this.nextSecStrucType = this.getSecStruc(this.residueSegmentMin)
this.currCoarseBackbone = false
this.nextCoarseBackbone = this.directionElementIndex[this.residueSegmentMin] === -1
break
@@ -165,7 +171,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
const { index: residueIndex } = residueIt.move();
this.prevSecStrucType = this.currSecStrucType
this.currSecStrucType = this.nextSecStrucType
- this.nextSecStrucType = residueIt.hasNext ? this.secondaryStructureType[residueIndex + 1] : SecStrucTypeNA
+ this.nextSecStrucType = residueIt.hasNext ? this.getSecStruc(residueIndex + 1) : SecStrucTypeNA
this.prevCoarseBackbone = this.currCoarseBackbone
this.currCoarseBackbone = this.nextCoarseBackbone
@@ -250,10 +256,14 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
this.secondaryStructureType = unit.model.properties.secondaryStructure.type
+ this.secondaryStructureGetIndex = unit.model.properties.secondaryStructure.getIndex
const computedSecondaryStructure = ComputedSecondaryStructure.get(structure)
if (computedSecondaryStructure) {
const secondaryStructure = computedSecondaryStructure.map.get(unit.invariantId)
- if (secondaryStructure) this.secondaryStructureType = secondaryStructure.type
+ if (secondaryStructure) {
+ this.secondaryStructureType = secondaryStructure.type
+ this.secondaryStructureGetIndex = secondaryStructure.getIndex
+ }
}
}
}
diff --git a/src/mol-theme/color/secondary-structure.ts b/src/mol-theme/color/secondary-structure.ts
index 50d77eab4..9f1034f34 100644
--- a/src/mol-theme/color/secondary-structure.ts
+++ b/src/mol-theme/color/secondary-structure.ts
@@ -47,7 +47,7 @@ export function secondaryStructureColor(unit: Unit, element: ElementIndex, compu
secStrucType = unit.model.properties.secondaryStructure.type[unit.residueIndex[element]]
if (computedSecondaryStructure) {
const secondaryStructure = computedSecondaryStructure.map.get(unit.invariantId)
- if (secondaryStructure) secStrucType = secondaryStructure.type[unit.residueIndex[element]]
+ if (secondaryStructure) secStrucType = secondaryStructure.type[secondaryStructure.getIndex(unit.residueIndex[element])]
}
}
--
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