Renamed SecondaryStructure 'index' back to 'key'

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++;
     }

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]),

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)) {

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>
 }

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 = {