From bea4d12b47cb74923cb9c2d5c868b30a0c9beafe Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 25 Mar 2019 11:13:04 -0700
Subject: [PATCH] stub for param integration
---
.../properties/utils/secondary-structure.ts | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 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 c9c30919f..c7d332e61 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -44,9 +44,7 @@ const hbondEnergyCutoff = -0.5
const hbondEnergyMinimal = -9.9
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,
- /** alpha-helices are preferred over 3-10 helix */
oldOrdering: boolean,
getResidueFlag: (f: DSSPType) => SecondaryStructureType,
getFlagName: (f: DSSPType) => String,
@@ -113,12 +111,15 @@ namespace DSSPType {
}
}
+export interface SecondaryStructureComputationParams {
+ oldDefinition: boolean
+ oldOrdering: boolean
+}
+
export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
conformation: AtomicConformation,
- oldDefinition = true,
- oldOrdering = true): SecondaryStructure {
+ params?: Partial<SecondaryStructureComputationParams>): 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)
const hbonds = calcBackboneHbonds(hierarchy, conformation, proteinResidues, backboneIndices, lookup3d)
@@ -126,12 +127,16 @@ export function computeSecondaryStructure(hierarchy: AtomicHierarchy,
const residueCount = proteinResidues.length
const flags = new Uint32Array(residueCount)
+ const oldDefinition: boolean = (params && params.oldDefinition) || true
+ const oldOrdering: boolean = (params && params.oldOrdering) || true
+ console.log(`calculating secondary structure elements using ${ oldDefinition ? 'old' : 'revised'} definition and ${ oldOrdering ? 'old' : 'revised'} ordering of secondary structure elements`)
+
const torsionAngles = calculateDihedralAngles(hierarchy, conformation, proteinResidues, backboneIndices)
const ladders: Ladder[] = []
const bridges: Bridge[] = []
- const getResidueFlag = oldOrdering ? getOriginalResidueFlag : getUpdatedResidueFlag
+ const getResidueFlag = oldDefinition ? getOriginalResidueFlag : getUpdatedResidueFlag
const getFlagName = oldOrdering ? getOriginalFlagName : getUpdatedFlagName
const ctx: DSSPContext = {
--
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