From 0bd7bdfe9f1ea00270dec18493f1aa8b554e4536 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Wed, 20 Mar 2019 17:05:24 -0700
Subject: [PATCH] summing up ASA values for residues
---
.../utils/accessible-surface-area.ts | 23 +++++++++++--------
1 file changed, 13 insertions(+), 10 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 16f9a4c6e..5291218db 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
@@ -36,7 +36,7 @@ function calculateASA(ctx: ASAContext) {
const { x, y, z } = ctx.conformation;
const radii: number[] = [];
- const atomAsa: number[] = [];
+ // const atomAsa: number[] = [];
const residueAsa: number[] = [];
console.log(ctx.hierarchy);
@@ -46,7 +46,7 @@ function calculateASA(ctx: ASAContext) {
const a1Pos = Vec3.zero();
const a2Pos = Vec3.zero();
- // 1. extract all heavy atoms
+ // extract all heavy atoms
// TODO can be more elegant by obtaining residue info once and then using offset to navigate to next residue
for (let i = 0; i < type_symbol.rowCount; ++i) {
// skip hydrogen atoms
@@ -67,11 +67,13 @@ function calculateASA(ctx: ASAContext) {
const atomId = atoms.label_atom_id.value(i);
const compId = residues.label_comp_id.value(groupIndex);
const element = type_symbol.value(i);
- // 2. assign radius to all heavy atoms - depends on element and bonding patterns
+ // assign radius to all heavy atoms - depends on element and bonding patterns
radii[radii.length] = determineRadius(atomId, element, compId);
+ // set ASA of corresponding group to 0
+ residueAsa[groupIndex] = 0.0;
}
- // 3. calculate the individual ASA of each atom
+ // calculate the individual ASA of each atom
// TODO again might be more elegant to use offsets
// TODO distance is symmetric, omit redudant calcuations
for (let i = 0; i < radii.length; ++i) {
@@ -79,7 +81,7 @@ function calculateASA(ctx: ASAContext) {
// skip invalid entries
if (radius === valueForIgnoredAtom) {
- atomAsa[atomAsa.length] = valueForIgnoredAtom;
+ // atomAsa[atomAsa.length] = valueForIgnoredAtom;
continue;
}
@@ -124,13 +126,14 @@ function calculateASA(ctx: ASAContext) {
}
}
- atomAsa[atomAsa.length] = cons * accessiblePoints * r * r;
+ const value = cons * accessiblePoints * r * r;
+ // atomAsa[atomAsa.length] = value;
+ // sum up values for each residue
+ residueAsa[residueAtomSegments.index[i]] += value;
}
- // 3. for each residue
- // 3b. sum up
- // 3c. (optionally) normalize by maximum value expected for a particular amino acid - needs lookup of max values
- console.log(atomAsa);
+ // TODO (optionally) normalize by maximum value expected for a particular amino acid - needs lookup of max values
+ console.log(residueAsa);
}
/**
--
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