From 72190cf91d7b94768c85ccf6d784a3e28ca38c06 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 5 Jul 2018 15:34:51 +0200
Subject: [PATCH] Renamed SecondaryStructure 'index' back to 'key'
---
src/apps/structure-info/model.ts | 6 +++---
.../export/categories/secondary-structure.ts | 6 +++---
.../model/formats/mmcif/secondary-structure.ts | 14 +++++++-------
.../model/properties/seconday-structure.ts | 2 +-
src/mol-model/structure/structure/properties.ts | 2 +-
5 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index a4f8ddf66..b6a66fcf6 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -49,16 +49,16 @@ export function residueLabel(model: Model, rI: number) {
export function printSecStructure(model: Model) {
console.log('\nSecondary Structure\n=============');
const { residues } = model.atomicHierarchy;
- const { index, elements } = model.properties.secondaryStructure;
+ const { key, elements } = model.properties.secondaryStructure;
const count = residues._rowCount;
let rI = 0;
while (rI < count) {
let start = rI;
- while (rI < count && index[start] === index[rI]) rI++;
+ while (rI < count && key[start] === key[rI]) rI++;
rI--;
- const e = elements[index[start]];
+ const e = elements[key[start]];
if (e.kind !== 'none') console.log(`${e.kind}: ${residueLabel(model, start)} - ${residueLabel(model, rI)}`);
rI++;
}
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index cc27294ab..35936e165 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -75,7 +75,7 @@ interface SSElement<T extends SecondaryStructure.Element> {
}
function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContext, kind: SecondaryStructure.Element['kind']) {
- const { index, elements } = ctx.model.properties.secondaryStructure;
+ const { key, elements } = ctx.model.properties.secondaryStructure;
const ssElements: SSElement<any>[] = [];
@@ -91,7 +91,7 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
if (move) current = residues.move();
const start = current!.index;
- const startIdx = index[start];
+ const startIdx = key[start];
const element = elements[startIdx];
if (element.kind !== kind) {
move = true;
@@ -102,7 +102,7 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
while (residues.hasNext) {
prev = current!.index;
current = residues.move();
- if (startIdx !== index[current.index]) {
+ if (startIdx !== key[current.index]) {
move = false;
ssElements[ssElements.length] = {
start: Element.Location(unit, segs.segments[start]),
diff --git a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
index 15ff80bb2..0c045f605 100644
--- a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
+++ b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
@@ -20,7 +20,7 @@ export function getSecondaryStructureMmCif(data: mmCIF_Database, hierarchy: Atom
const secStruct: SecondaryStructureData = {
type: new Int32Array(hierarchy.residues._rowCount) as any,
- index: new Int32Array(hierarchy.residues._rowCount) as any,
+ key: new Int32Array(hierarchy.residues._rowCount) as any,
elements
};
@@ -34,10 +34,10 @@ type SecondaryStructureEntry = {
endSeqNumber: number,
endInsCode: string | null,
type: SecondaryStructureType,
- index: number
+ key: number
}
type SecondaryStructureMap = Map<string, Map<number, SecondaryStructureEntry>>
-type SecondaryStructureData = { type: SecondaryStructureType[], index: number[], elements: SecondaryStructure.Element[] }
+type SecondaryStructureData = { type: SecondaryStructureType[], key: number[], elements: SecondaryStructure.Element[] }
function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
@@ -66,7 +66,7 @@ function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, eleme
endSeqNumber: end_label_seq_id.value(i),
endInsCode: pdbx_end_PDB_ins_code.value(i),
type,
- index: elements.length
+ key: elements.length
};
elements[elements.length] = element;
@@ -112,7 +112,7 @@ function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap,
endSeqNumber: end_label_seq_id.value(i),
endInsCode: pdbx_end_PDB_ins_code.value(i),
type,
- index: elements.length
+ key: elements.length
};
elements[elements.length] = element;
@@ -131,13 +131,13 @@ function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap,
function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: SecondaryStructureEntry, resStart: number, resEnd: number, data: SecondaryStructureData) {
const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
- const { endSeqNumber, endInsCode, index, type } = entry;
+ const { endSeqNumber, endInsCode, key, type } = entry;
let rI = resStart;
while (rI < resEnd) {
const seqNumber = label_seq_id.value(rI);
data.type[rI] = type;
- data.index[rI] = index;
+ data.key[rI] = key;
if ((seqNumber > endSeqNumber) ||
(seqNumber === endSeqNumber && pdbx_PDB_ins_code.value(rI) === endInsCode)) {
diff --git a/src/mol-model/structure/model/properties/seconday-structure.ts b/src/mol-model/structure/model/properties/seconday-structure.ts
index 5ecfb439c..49618f007 100644
--- a/src/mol-model/structure/model/properties/seconday-structure.ts
+++ b/src/mol-model/structure/model/properties/seconday-structure.ts
@@ -11,7 +11,7 @@ interface SecondaryStructure {
readonly type: ArrayLike<SecondaryStructureType>,
/** index into the elements array */
- readonly index: ArrayLike<number>,
+ readonly key: ArrayLike<number>,
/** indexed by key */
readonly elements: ReadonlyArray<SecondaryStructure.Element>
}
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 7a3e8f789..d13f5ddd8 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -59,7 +59,7 @@ const residue = {
// Properties
secondary_structure_type: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
- secondary_structure_key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.index[l.unit.residueIndex[l.element]]),
+ secondary_structure_key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
}
const chain = {
--
GitLab