From 696b188b91359593065978af007548dbc4cd0e6c Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Fri, 22 Mar 2019 13:26:49 -0700
Subject: [PATCH] wrong assignment of values resolved
---
.../unit/accessible-surface-area/compute.ts | 13 ++++++------
.../color/accessible-surface-area.ts | 2 +-
src/tests/browser/render-structure.ts | 20 ++++++++++++++-----
3 files changed, 23 insertions(+), 12 deletions(-)
diff --git a/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts b/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts
index 198f0af73..4fa2225a7 100644
--- a/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts
+++ b/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts
@@ -46,8 +46,7 @@ function normalizeAccessibleSurfaceArea(ctx: AccessibleSurfaceAreaContext) {
function computePerResidue(ctx: AccessibleSurfaceAreaContext) {
const { atomRadius, accessibleSurfaceArea, maxLookupRadius, spherePoints, cons } = ctx;
const { probeSize } = ctx.params;
- const { elements: atoms } = ctx.unit;
- const { residueAtomSegments } = ctx.unit.model.atomicHierarchy;
+ const { elements: atoms, residueIndex } = ctx.unit;
const { x, y, z } = ctx.unit.model.atomicConformation;
const atomCount = ctx.unit.elements.length;
const { lookup3d } = ctx.unit;
@@ -57,6 +56,7 @@ function computePerResidue(ctx: AccessibleSurfaceAreaContext) {
const a2Pos = Vec3.zero();
for (let _aI = 0; _aI < atomCount; ++_aI) {
+ // map the atom index of this unit to the actual 'global' atom index
const aI = atoms[_aI];
const radii1 = atomRadius[aI];
if (radii1 === missingAccessibleSurfaceAreaValue) continue;
@@ -104,7 +104,7 @@ function computePerResidue(ctx: AccessibleSurfaceAreaContext) {
}
const value = cons * accessiblePointCount * r * r;
- accessibleSurfaceArea[residueAtomSegments.index[aI]] += value;
+ accessibleSurfaceArea[residueIndex[aI]] += value;
}
}
@@ -136,11 +136,11 @@ function assignRadiusForHeavyAtoms(ctx: AccessibleSurfaceAreaContext) {
const element = type_symbol.value(aI);
const resn = label_comp_id.value(raI)!;
- ctx.atomRadius[ctx.atomRadius.length] = determineRadius(atomId, element, resn);
+ ctx.atomRadius[aI] = determineRadius(atomId, element, resn);
// while having atom->parent mapping at hand, initialize residue-level of information
- ctx.accessibleSurfaceArea[ctx.accessibleSurfaceArea.length] = 0.0;
- ctx.relativeAccessibleSurfaceArea[ctx.relativeAccessibleSurfaceArea.length] = 0.0;
+ ctx.accessibleSurfaceArea[raI] = 0.0;
+ ctx.relativeAccessibleSurfaceArea[raI] = 0.0;
}
}
@@ -202,6 +202,7 @@ function initialize(unit: Unit.Atomic, params: AccessibleSurfaceAreaComputationP
}
function computeAccessibleSurfaceArea(unit: Unit.Atomic, params?: Partial<AccessibleSurfaceAreaComputationParameters>): AccessibleSurfaceArea {
+ console.log(`computing accessible surface area for unit #${ unit.id + 1 }`);
return _computeAccessibleSurfaceArea(unit, {
numberOfSpherePoints: (params && params.numberOfSpherePoints) || 960,
probeSize: (params && params.probeSize) || 1.4
diff --git a/src/mol-theme/color/accessible-surface-area.ts b/src/mol-theme/color/accessible-surface-area.ts
index 2dfd70eb7..3593c7b76 100644
--- a/src/mol-theme/color/accessible-surface-area.ts
+++ b/src/mol-theme/color/accessible-surface-area.ts
@@ -13,7 +13,7 @@ import { ColorListOptions, ColorListName, ColorScale } from 'mol-util/color/scal
import { StructureElement, Unit } from 'mol-model/structure';
import { missingAccessibleSurfaceAreaValue } from 'mol-model/structure/structure/unit/accessible-surface-area/compute';
-const DefaultColor = Color(0xCCCCCC)
+const DefaultColor = Color(0xFFFFFF)
const Description = 'Assigns a color based on the relative accessible surface area of a residue.'
export const AccessibleSurfaceAreaColorThemeParams = {
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 3f14cfcd8..c2b761936 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -61,12 +61,9 @@ function getCartoonRepr() {
}
async function init() {
- const cif = await downloadFromPdb('1acj')
+ const cif = await downloadFromPdb('1brr')
const models = await getModels(cif)
- // console.time('computeModelASA')
- // const asa = computeModelASA(models[0].atomicHierarchy, models[0].atomicConformation)
- // console.timeEnd('computeModelASA');
- // (models[0].properties as any).asa = asa
+
const structure = await getStructure(models[0])
const cartoonRepr = getCartoonRepr()
@@ -76,6 +73,19 @@ async function init() {
})
await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
+ // console.time('computeModelDSSP')
+ // 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()
+
+ // cartoonRepr.setTheme({
+ // color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
+ // size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
+ // })
+ // await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
+
canvas3d.add(cartoonRepr)
canvas3d.resetCamera()
}
--
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