From e403c371e9e83118ec6f5e84113fb6d8e58f3bad Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Thu, 21 Mar 2019 10:37:26 -0700
Subject: [PATCH] cleanup
---
.../utils/accessible-surface-area.ts | 22 ++++++-------------
1 file changed, 7 insertions(+), 15 deletions(-)
diff --git a/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts b/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts
index 8fb4ae37a..40c376d06 100644
--- a/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts
+++ b/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts
@@ -1,6 +1,7 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { AtomicHierarchy, AtomicConformation } from '../atomic';
-import { ElementSymbol, VdwRadii, MaxAsa, DefaultMaxAsa } from '../../types';
+import { ElementSymbol, MaxAsa, DefaultMaxAsa, MoleculeType } from '../../types';
+import { VdwRadius } from '../atomic/measures';
const defaultNumberOfPoints = 960;
const defaultProbeSize = 1.4;
@@ -24,24 +25,14 @@ export function computeModelASA(hierarchy: AtomicHierarchy, conformation: Atomic
conformation
}
- return calculateASA(ctx);
-}
-
-const valueForIgnoredAtom = -1.0;
-
-function calculateASA(ctx: ASAContext) {
const { probeSize, spherePoints, cons } = ctx;
const { atoms, residues, residueAtomSegments, derived } = ctx.hierarchy;
const { type_symbol } = atoms;
const { x, y, z } = ctx.conformation;
const radii: number[] = [];
- // const atomAsa: number[] = [];
const residueAsa: number[] = [];
- console.log(ctx.hierarchy);
- console.log(ctx.conformation);
-
const position = (i: number, v: Vec3) => Vec3.set(v, x[i], y[i], z[i]);
const a1Pos = Vec3.zero();
const a2Pos = Vec3.zero();
@@ -59,7 +50,7 @@ function calculateASA(ctx: ASAContext) {
const groupIndex = residueAtomSegments.index[i];
// skip entities not part of a peptide chain
- if (derived.residue.moleculeType[groupIndex] !== 4) {
+ if (derived.residue.moleculeType[groupIndex] !== MoleculeType.protein) {
radii[radii.length] = valueForIgnoredAtom;
continue;
}
@@ -144,10 +135,12 @@ function calculateASA(ctx: ASAContext) {
residueAsa[i] /= (maxAsa === undefined ? DefaultMaxAsa : maxAsa);
}
- // console.log(residueAsa);
+ console.log(residueAsa);
return residueAsa;
}
+const valueForIgnoredAtom = -1.0;
+
/**
* Gets the van der Waals radius of the given atom following the values defined by Chothia (1976)
* J.Mol.Biol.105,1-14. NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly
@@ -178,8 +171,7 @@ function determineRadius(atomId: string, element: ElementSymbol, compId: string)
}
}
}
- // TODO could potentially use logging or error thrown
- return (VdwRadii as any)[atomId];
+ return VdwRadius(element);
}
/** Creates a collection of points on a sphere by the Golden Section Spiral algorithm. */
--
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