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Commit 3b00d25c authored by Sebastian Bittrich's avatar Sebastian Bittrich
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more memory-efficient way to store atom radii

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src/mol-model/structure/structure/accessible-surface-area.ts
+ 55
− 42
View file @ 3b00d25c
......@@ -14,19 +14,19 @@ import { VdwRadius } from '../model/properties/atomic';
import { isHydrogen, getElementIdx } from './unit/links/common';
namespace AccessibleSurfaceArea {
// Chothia's amino acid atoms vdw radii
const trigonalCarbonVdw = 1.76;
const tetrahedralCarbonVdw = 1.87;
const trigonalNitrogenVdw = 1.65;
const tetrahedralNitrogenVdw = 1.50;
// deviating radii from definition in types.ts
const oxygenVdw = 1.40;
const sulfurVdw = 1.85;
// Chothia's nucleotide atom vdw radii
const nucCarbonVdw = 1.80;
const nucNitrogenVdw = 1.60;
const nucPhosphorusVdw = 1.40;
export const missingValue = -1.0;
// Chothia's amino acid and nucleotide atom vdw radii
export const VdWLookup = [
-1.0, // 0: missing
1.76, // 1: trigonal C
1.87, // 2: tetrahedral C
1.65, // 3: trigonal N
1.50, // 4: tetrahedral N
1.40, // 5: O
1.85, // 6: S
1.80, // 7: C (nucleic)
1.60, // 8: N (nucleic)
1.40 // 9: P (nucleic)
] // can still be appended on-the-fly for rare elements like selenium
/**
* Adapts the BioJava implementation by Jose Duarte. That implementation is based on the publication by Shrake, A., and
......@@ -48,7 +48,6 @@ namespace AccessibleSurfaceArea {
normalizeAccessibleSurfaceArea(ctx);
return {
atomRadius: ctx.atomRadius!,
accessibleSurfaceArea: ctx.accessibleSurfaceArea!,
relativeAccessibleSurfaceArea: ctx.relativeAccessibleSurfaceArea!,
buried: (index: number) => ctx.relativeAccessibleSurfaceArea![index] < 0.16 // TODO this doesnt seem super elegant
......@@ -62,7 +61,7 @@ namespace AccessibleSurfaceArea {
spherePoints: Vec3[],
cons: number,
maxLookupRadius: number,
atomRadius?: Float32Array, // TODO there are only 5-10 unique values in this array - rather than storing values, a int pointing to a dictionary will be far more memory efficient
atomRadius?: Int8Array,
accessibleSurfaceArea?: Float32Array,
relativeAccessibleSurfaceArea?: Float32Array
}
......@@ -98,14 +97,13 @@ namespace AccessibleSurfaceArea {
for (let aI = 0; aI < atomCount; ++aI) {
if (aI % 10000 === 0) {
console.log(`calculating accessible surface area, current: ${ aI }, max: ${ atomCount }`);
if (ctx.rtctx.shouldUpdate) {
await ctx.rtctx.update({ message: 'calculating accessible surface area', current: aI, max: atomCount });
}
}
const radius1 = atomRadius![aI];
if (radius1 === missingValue) continue;
const radius1 = VdWLookup[atomRadius![aI]];
if (radius1 === VdWLookup[0]) continue;
// pre-filter by lookup3d
// 36275 ms - lookup ~3000 ms
......@@ -116,8 +114,8 @@ namespace AccessibleSurfaceArea {
const neighbors = [];
for (let iI = 0; iI < count; ++iI) {
const bI = units[iI].elements[indices[iI]];
const radius2 = atomRadius![bI];
if (aI === bI || radius2 === missingValue) continue;
const radius2 = VdWLookup[atomRadius![bI]];
if (aI === bI || radius2 === VdWLookup[0]) continue;
const cutoff2 = (cutoff1 + radius2) * (cutoff1 + radius2);
if (squaredDistances[iI] < cutoff2) {
......@@ -137,7 +135,8 @@ namespace AccessibleSurfaceArea {
for (let _nI = 0; _nI < neighbors.length; ++_nI) {
const nI = neighbors[_nI];
position(nI, bPos);
const cutoff3 = (atomRadius![nI] + probeSize!) * (atomRadius![nI] + probeSize!);
const radius3 = VdWLookup[atomRadius![nI]];
const cutoff3 = (radius3 + probeSize!) * (radius3 + probeSize!);
if (Vec3.squaredDistance(testPoint, bPos) < cutoff3) {
accessible = false;
break;
......@@ -161,7 +160,7 @@ namespace AccessibleSurfaceArea {
const residueCount = moleculeType.length;
// with atom and residue count at hand: initialize arrays
ctx.atomRadius = new Float32Array(atomCount - 1);
ctx.atomRadius = new Int8Array(atomCount - 1);
ctx.accessibleSurfaceArea = new Float32Array(residueCount - 1);
ctx.relativeAccessibleSurfaceArea = new Float32Array(residueCount - 1);
......@@ -171,7 +170,7 @@ namespace AccessibleSurfaceArea {
const elementIdx = getElementIdx(element);
// skip hydrogen atoms
if (isHydrogen(elementIdx)) {
ctx.atomRadius[aI] = missingValue;
ctx.atomRadius[aI] = VdWLookup[0];
continue;
}
......@@ -179,7 +178,7 @@ namespace AccessibleSurfaceArea {
// skip non-polymer groups
if (!ctx.params.nonPolymer) {
if (!isPolymer(residueType)) {
ctx.atomRadius[aI] = missingValue;
ctx.atomRadius[aI] = VdWLookup[0];
continue;
}
}
......@@ -196,7 +195,7 @@ namespace AccessibleSurfaceArea {
} else if (residueType === MoleculeType.protein) {
ctx.atomRadius[aI] = determineRadiusAmino(atomId, element, compId);
} else {
ctx.atomRadius[aI] = VdwRadius(element);
ctx.atomRadius[aI] = handleNonStandardCase(element);
}
}
}
......@@ -209,43 +208,58 @@ namespace AccessibleSurfaceArea {
function determineRadiusAmino(atomId: string, element: ElementSymbol, compId: string): number {
switch (element) {
case 'O':
return oxygenVdw;
return 5;
case 'S':
return sulfurVdw;
return 6;
case 'N':
return atomId === 'NZ' ? tetrahedralNitrogenVdw : trigonalNitrogenVdw;
return atomId === 'NZ' ? 4 : 3;
case 'C':
switch (atomId) {
case 'C': case 'CE1': case'CE2': case 'CE3': case 'CH2': case 'CZ': case 'CZ2': case 'CZ3':
return trigonalCarbonVdw;
return 1;
case 'CA': case 'CB': case 'CE': case 'CG1': case 'CG2':
return tetrahedralCarbonVdw;
return 2;
default:
switch (compId) {
case 'PHE': case 'TRP': case 'TYR': case 'HIS': case 'ASP': case 'ASN':
return trigonalCarbonVdw;
return 1;
case 'PRO': case 'LYS': case 'ARG': case 'MET': case 'ILE': case 'LEU':
return tetrahedralCarbonVdw;
return 2;
case 'GLU': case 'GLN':
return atomId === 'CD' ? trigonalCarbonVdw : tetrahedralCarbonVdw;
return atomId === 'CD' ? 1 : 2;
}
}
}
return VdwRadius(element);
return handleNonStandardCase(element);
}
function determineRadiusNucl(atomId: string, element: ElementSymbol, compId: string): number {
switch (element) {
case 'C':
return nucCarbonVdw;
return 7;
case 'N':
return nucNitrogenVdw;
return 8;
case 'P':
return nucPhosphorusVdw;
return 9;
case 'O':
return oxygenVdw;
return 5;
}
return VdwRadius(element);
return handleNonStandardCase(element);
}
function handleNonStandardCase(element: ElementSymbol): number {
const radius = VdwRadius(element);
let index = VdWLookup.indexOf(radius);
console.log(radius);
console.log(index);
console.log(VdWLookup);
if (index === -1) {
// add novel value to lookup array
console.log(`novel value ${radius} for ${element}`)
index = VdWLookup.length;
VdWLookup[index] = radius;
}
return index;
}
function initialize(rtctx: RuntimeContext, structure: Structure, params: Partial<PD.Values<AccessibleSurfaceAreaComputationParams>>): AccessibleSurfaceAreaContext {
......@@ -255,7 +269,7 @@ namespace AccessibleSurfaceArea {
params: params,
spherePoints: generateSpherePoints(params.numberOfSpherePoints!),
cons: 4.0 * Math.PI / params.numberOfSpherePoints!,
maxLookupRadius: 2 * params.probeSize! + 2 * tetrahedralCarbonVdw // 2x probe size + 2x largest VdW
maxLookupRadius: 2 * params.probeSize! + 2 * VdWLookup[2] // 2x probe size + 2x largest VdW
}
}
......@@ -318,7 +332,6 @@ namespace AccessibleSurfaceArea {
}
interface AccessibleSurfaceArea {
readonly atomRadius?: ArrayLike<number>
readonly accessibleSurfaceArea?: ArrayLike<number>
readonly relativeAccessibleSurfaceArea?: ArrayLike<number>
buried(index: number): boolean
......
src/tests/browser/render-structure.ts
+ 4
− 3
View file @ 3b00d25c
......@@ -69,9 +69,10 @@ function getCartoonRepr() {
let accessibleSurfaceArea: AccessibleSurfaceArea;
async function init(props = {}) {
const cif = await downloadFromPdb(
'3j3q'
// '1aon'
// '3j3q'
'1aon'
// '1acj'
// '1pga'
)
const models = await getModels(cif)
const structure = await getStructure(models[0])
......@@ -117,7 +118,7 @@ export function AccessibleSurfaceAreaColorTheme(ctx: ThemeDataContext, props: PD
if (StructureElement.isLocation(location)) {
if (Unit.isAtomic(location.unit)) {
const value = accessibleSurfaceArea.relativeAccessibleSurfaceArea![location.unit.residueIndex[location.element]];
return value !== AccessibleSurfaceArea.missingValue ? scale.color(value) : DefaultColor;
return value !== AccessibleSurfaceArea.VdWLookup[0] /* signals missing value */ ? scale.color(value) : DefaultColor;
}
}
......
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