add AtomicConformation.xyzDefined & improve getAtomicRanges

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

@@ -69,8 +69,8 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
     const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
 
     // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
     substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
     substUndefinedColumn(residues, 'label_comp_id', 'auth_comp_id');
     substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
 
@@ -83,6 +83,7 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
         atomId: atom_site.id,
         occupancy: atom_site.occupancy,
         B_iso_or_equiv: atom_site.B_iso_or_equiv,
+        xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
         x: atom_site.Cartn_x.toArray({ array: Float32Array }),
         y: atom_site.Cartn_y.toArray({ array: Float32Array }),
         z: atom_site.Cartn_z.toArray({ array: Float32Array }),

src/mol-model/structure/model/properties/atomic/conformation.ts

@@ -34,6 +34,10 @@ export interface AtomicConformation {
     // Coordinates. Generally, not to be accessed directly because the coordinate might be
     // transformed by an operator. Use Unit.getPosition instead.
 
+    /**
+     * Are xyz coordinates defined?
+     */
+    xyzDefined: boolean,
     /**
      * The x coordinate in angstroms specified according to a set of orthogonal Cartesian axes.
      */

src/mol-model/structure/model/properties/utils/atomic-ranges.ts

@@ -70,7 +70,7 @@ export function getAtomicRanges(hierarchy: AtomicHierarchy, entities: Entities,
         const riEnd = hierarchy.residueAtomSegments.index[chainSegment.end - 1]
         const seqIdStart = label_seq_id.value(riStart)
         const seqIdEnd = label_seq_id.value(riEnd)
-        if (seqIdStart === 1 && seqIdEnd === maxSeqId && areBackboneConnected(riStart, riEnd, conformation, index, derived)) {
+        if (seqIdStart === 1 && seqIdEnd === maxSeqId && conformation.xyzDefined && areBackboneConnected(riStart, riEnd, conformation, index, derived)) {
             cyclicPolymerMap.set(riStart, riEnd)
             cyclicPolymerMap.set(riEnd, riStart)
         }
@@ -95,7 +95,7 @@ export function getAtomicRanges(hierarchy: AtomicHierarchy, entities: Entities,
                     } else {
                         const riStart = hierarchy.residueAtomSegments.index[residueSegment.start]
                         const riEnd = hierarchy.residueAtomSegments.index[prevEnd - 1]
-                        if (!areBackboneConnected(riStart, riEnd, conformation, hierarchy.index, derived)) {
+                        if (conformation.xyzDefined && !areBackboneConnected(riStart, riEnd, conformation, hierarchy.index, derived)) {
                             polymerRanges.push(startIndex, prevEnd - 1)
                             startIndex = residueSegment.start
                         }