From a77d98150cb8627d47fb513a429bc655efcd5ece Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 25 Mar 2019 10:10:53 -0700
Subject: [PATCH] removes minCaDist criterion
---
.../model/properties/utils/secondary-structure.ts | 11 -----------
src/tests/browser/render-structure.ts | 2 +-
2 files changed, 1 insertion(+), 12 deletions(-)
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.ts b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
index 2d6a1153c..bedaa01f0 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -216,9 +216,6 @@ namespace DSSPType {
/** max distance between two C-alpha atoms to check for hbond */
const caMaxDist = 9.0;
-/** min distance between two C-alpha atoms to check for hbond */
-const caMinDist = 0.5;
-
function calcAtomicTraceLookup3D(hierarchy: AtomicHierarchy, conformation: AtomicConformation) {
const { x, y, z } = conformation;
const { moleculeType, traceElementIndex } = hierarchy.derived.residue
@@ -423,8 +420,6 @@ function calcBackboneHbonds(hierarchy: AtomicHierarchy, conformation: AtomicConf
const cPosPrev = Vec3.zero()
const oPosPrev = Vec3.zero()
- // const caMinDistSq = caMinDist * caMinDist
-
for (let i = 0, il = proteinResidues.length; i < il; ++i) {
const oPI = i
const oRI = proteinResidues[i]
@@ -446,8 +441,6 @@ function calcBackboneHbonds(hierarchy: AtomicHierarchy, conformation: AtomicConf
const { indices, count } = lookup3d.find(caPos[0], caPos[1], caPos[2], caMaxDist)
for (let j = 0; j < count; ++j) {
- // if (squaredDistances[j] < caMinDist * caMinDist) continue
-
const nPI = indices[j]
// ignore bonds within a residue or to prev or next residue, TODO take chain border into account
@@ -584,10 +577,6 @@ function calcHbondEnergy(oPos: Vec3, cPos: Vec3, nPos: Vec3, hPos: Vec3) {
const distCN = Vec3.distance(cPos, nPos)
const distON = Vec3.distance(oPos, nPos)
- if (distOH < caMinDist || distCH < caMinDist || distCN < caMinDist || distON < caMinDist) {
- return hbondEnergyMinimal
- }
-
const e1 = Q / distOH - Q / distCH
const e2 = Q / distCN - Q / distON
const e = e1 + e2
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 927e24c14..1436e7517 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -62,7 +62,7 @@ function getCartoonRepr() {
}
async function init() {
- const cif = await downloadFromPdb('1acj')
+ const cif = await downloadFromPdb('3j3q')
const models = await getModels(cif)
console.time('computeModelDSSP')
const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy,
--
GitLab