From 09db0abadb10237a453e1dad290ed4509be2654e Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 25 Mar 2019 10:28:57 -0700
Subject: [PATCH] adds turns and bends as dedicated secondary structure
elements
---
.../model/properties/seconday-structure.ts | 15 ++++++++++++---
.../properties/utils/secondary-structure.ts | 17 +++++++++++++++--
src/tests/browser/render-structure.ts | 2 +-
3 files changed, 28 insertions(+), 6 deletions(-)
diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index bbadc038b..802bdb325 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -19,11 +19,20 @@ interface SecondaryStructure {
}
namespace SecondaryStructure {
- export type Element = None | Helix | Sheet
+ export type Element = None | Bend | Turn | Helix | Sheet
export interface None {
- kind: 'none',
- flags?: SecondaryStructureType // TODO should this level of detail be added to non-defined secondary structure elements?
+ kind: 'none'
+ }
+
+ export interface Bend {
+ kind: 'bend',
+ flags: SecondaryStructureType
+ }
+
+ export interface Turn {
+ kind: 'turn',
+ flags: SecondaryStructureType
}
export interface Helix {
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 ff1ba9b4e..655649b57 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -211,11 +211,20 @@ function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DS
kind: 'sheet',
flags: getResidueFlag(flag)
} as SecondaryStructure.Sheet
- } else {
+ } else if (kind === 'turn') {
+ return {
+ kind: 'turn',
+ flags: getResidueFlag(flag)
+ }
+ } else if (kind === 'bend') {
return {
- kind: 'none',
+ kind: 'bend',
flags: getResidueFlag(flag)
}
+ } else {
+ return {
+ kind: 'none'
+ }
}
}
@@ -224,6 +233,10 @@ function mapToKind(assignment: SecondaryStructureType.Flag) {
return 'helix'
} else if (assignment === SecondaryStructureType.SecondaryStructureDssp.B || assignment === SecondaryStructureType.SecondaryStructureDssp.E) {
return 'sheet'
+ } else if (assignment === SecondaryStructureType.SecondaryStructureDssp.T) {
+ return 'turn'
+ } else if (assignment === SecondaryStructureType.SecondaryStructureDssp.S) {
+ return 'bend'
} else {
return 'none'
}
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 1436e7517..927e24c14 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('3j3q')
+ const cif = await downloadFromPdb('1acj')
const models = await getModels(cif)
console.time('computeModelDSSP')
const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy,
--
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