2.0.0-dev.6

- fixes #123

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.5",
+  "version": "2.0.0-dev.6",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.5",
+  "version": "2.0.0-dev.6",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/apps/viewer/index.html

@@ -48,9 +48,6 @@
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
             if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
-            var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
-            var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();

src/mol-model-formats/structure/basic/atomic.ts

@@ -74,7 +74,7 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
         let cI = 0;
         let seqId = 0;
         for (let i = 0, il = seqIds.length; i < il; ++i) {
-            if (residueOffsets[i] > chainOffsets[cI + 1]) {
+            if (residueOffsets[i] >= chainOffsets[cI + 1]) {
                 cI += 1;
                 seqId = 0;
             }

src/mol-model-formats/structure/xyz.ts

@@ -84,7 +84,7 @@ function getModels(mol: XyzFile, ctx: RuntimeContext) {
         atom_site
     });
 
-    return createModels(basics, MolFormat.create(mol), ctx);
+    return createModels(basics, XyzFormat.create(mol), ctx);
 }
 
 //
@@ -93,9 +93,9 @@ export { XyzFormat };
 
 type XyzFormat = ModelFormat<XyzFile>
 
-namespace MolFormat {
+namespace XyzFormat {
     export function is(x?: ModelFormat): x is XyzFormat {
-        return x?.kind === 'mol';
+        return x?.kind === 'xyz';
     }
 
     export function create(mol: XyzFile): XyzFormat {

src/mol-model-props/computed/secondary-structure.ts

@@ -69,7 +69,7 @@ async function computeDssp(structure: Structure, props: DSSPComputationProps): P
     const map = new Map<number, SecondaryStructure>();
     for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
         const u = structure.unitSymmetryGroups[i].units[0];
-        if (Unit.isAtomic(u)) {
+        if (Unit.isAtomic(u) && !Model.isCoarseGrained(u.model)) {
             const secondaryStructure = await computeUnitDSSP(u, props);
             map.set(u.invariantId, secondaryStructure);
         }

src/mol-model/structure/model/model.ts

@@ -227,7 +227,7 @@ export namespace Model {
 
     const CoarseGrainedProp = '__CoarseGrained__';
     /**
-     * Has typical coarse grained atom names (BB, SC1) or less than twice as many
+     * Has typical coarse grained atom names (BB, SC1) or less than three times as many
      * atoms as polymer residues (C-alpha only models).
      */
     export function isCoarseGrained(model: Model): boolean {
@@ -251,7 +251,7 @@ export namespace Model {
 
         const coarseGrained = (hasBB && hasSC1) || (
             polymerResidueCount && atomCount
-                ? atomCount / polymerResidueCount < 2
+                ? atomCount / polymerResidueCount < 3
                 : false
         );
         model._staticPropertyData[CoarseGrainedProp] = coarseGrained;

src/mol-plugin-state/manager/structure/focus.ts

@@ -164,7 +164,10 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
 
         plugin.state.data.events.object.updated.subscribe(({ oldData, obj, action }) => {
             if (!PluginStateObject.Molecule.Structure.is(obj)) return;
+            // structure NOT changed, keep everything as is; fixes #123
+            if (oldData === obj.data) return;
 
+            // structure changed (e.g. coordinates), try to remap and re-focus
             if (action === 'in-place') {
                 const current = this.state.current;
                 const structure = obj.data as Structure;