From a2da7648556d6c735105ba34cb5dfad5edc11781 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 25 Mar 2019 10:40:41 -0700
Subject: [PATCH] omits multiple entrypoints
---
.../model/properties/utils/secondary-structure.ts | 11 +++--------
src/tests/browser/render-structure.ts | 4 ++--
2 files changed, 5 insertions(+), 10 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 655649b57..c9c30919f 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -43,12 +43,6 @@ const hbondEnergyCutoff = -0.5
/** prevent extremely low hbond energies */
const hbondEnergyMinimal = -9.9
-export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
- conformation: AtomicConformation): SecondaryStructure {
- // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
- return computeModelDSSP(hierarchy, conformation)
-}
-
interface DSSPContext {
/** Whether to use the old DSSP convention for the annotation of turns and helices, causes them to be two residues shorter */
oldDefinition: boolean,
@@ -119,10 +113,11 @@ namespace DSSPType {
}
}
-export function computeModelDSSP(hierarchy: AtomicHierarchy,
+export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
conformation: AtomicConformation,
oldDefinition = true,
- oldOrdering = true) {
+ oldOrdering = true): SecondaryStructure {
+ // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
// console.log(`calculating secondary structure elements using ${ oldDefinition ? 'old' : 'revised'} definition and ${ oldOrdering ? 'old' : 'revised'} ordering of secondary structure elements`)
const { lookup3d, proteinResidues } = calcAtomicTraceLookup3D(hierarchy, conformation)
const backboneIndices = calcBackboneAtomIndices(hierarchy, proteinResidues)
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 927e24c14..146ef8c6e 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -12,7 +12,7 @@ import { ColorTheme } from 'mol-theme/color';
import { SizeTheme } from 'mol-theme/size';
import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
-import { computeModelDSSP } from 'mol-model/structure/model/properties/utils/secondary-structure';
+import { computeSecondaryStructure } from 'mol-model/structure/model/properties/utils/secondary-structure';
const parent = document.getElementById('app')!
parent.style.width = '100%'
@@ -65,7 +65,7 @@ async function init() {
const cif = await downloadFromPdb('1acj')
const models = await getModels(cif)
console.time('computeModelDSSP')
- const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy,
+ const secondaryStructure = computeSecondaryStructure(models[0].atomicHierarchy,
models[0].atomicConformation)
console.timeEnd('computeModelDSSP');
(models[0].properties as any).secondaryStructure = secondaryStructure
--
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