mol-model: check alt loc in carb fused rings

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

@@ -67,18 +67,6 @@ function getAnomericCarbon(unit: Unit.Atomic, ringAtoms: ArrayLike<StructureElem
                     : elements[ringAtoms[0]]) as ElementIndex
 }
 
-/** Return first non-empty label_alt_id or an empty string */
-function getRingAltId(unit: Unit.Atomic, ringAtoms: SortedArray<StructureElement.UnitIndex>) {
-    const { elements } = unit
-    const { label_alt_id } = unit.model.atomicHierarchy.atoms
-    for (let i = 0, il = ringAtoms.length; i < il; ++i) {
-        const ei = elements[ringAtoms[i]]
-        const altId = label_alt_id.value(ei)
-        if (altId) return altId
-    }
-    return ''
-}
-
 function getAltId(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
     const { elements } = unit
     const { label_alt_id } = unit.model.atomicHierarchy.atoms
@@ -106,6 +94,10 @@ function filterFusedRings(unitRings: UnitRings, rings: UnitRings.Index[] | undef
         const rc = ringCombinations[i];
         const r0 = unitRings.all[rings[rc[0]]], r1 = unitRings.all[rings[rc[1]]];
         if (SortedArray.areIntersecting(r0, r1)) {
+            // TODO: is this a correct check?
+            if (UnitRing.getAltId(unitRings.unit, r0) !== UnitRing.getAltId(unitRings.unit, r1)) {
+                continue;
+            }
             fusedRings.add(rings[rc[0]])
             fusedRings.add(rings[rc[1]])
         }
@@ -201,7 +193,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
                     const direction = getDirection(Vec3.zero(), unit, anomericCarbon, center)
                     Vec3.orthogonalize(direction, normal, direction)
 
-                    const ringAltId = getRingAltId(unit, ringAtoms)
+                    const ringAltId = UnitRing.getAltId(unit, ringAtoms)
                     const elementIndex = elements.length
                     ringElements.push(elementIndex)
                     elementsWithRingMap.set(ringElementKey(residueIndex, unit.id, ringAltId), elementIndex)

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

@@ -97,7 +97,7 @@ namespace UnitRing {
     ] as ElementSymbol[])
     const AromaticRingPlanarityThreshold = 0.05
 
-    export function isAromatic(unit: Unit.Atomic, ring: SortedArray<StructureElement.UnitIndex>): boolean {
+    export function isAromatic(unit: Unit.Atomic, ring: UnitRing): boolean {
         const { elements, bonds: { b, offset, edgeProps: { flags } } } = unit;
         const { type_symbol } = unit.model.atomicHierarchy.atoms;
         const { label_comp_id } = unit.model.atomicHierarchy.residues;
@@ -128,6 +128,20 @@ namespace UnitRing {
         const ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring))
         return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold
     }
+
+    /** Get the alternate location of the 1st non '' alt loc atom. */
+    export function getAltId(unit: Unit.Atomic, ring: UnitRing) {
+        const { label_alt_id } = unit.model.atomicHierarchy.atoms;
+        const { elements } = unit;
+
+        for (let i = 0, il = ring.length; i < il; ++i) {
+            const eI = elements[ring[i]];
+            const altId = label_alt_id.value(eI);
+            if (altId) return altId;
+        }
+
+        return '';
+    }
 }
 
 namespace UnitRings {
@@ -143,9 +157,11 @@ namespace UnitRings {
     /** Creates a mapping ResidueIndex -> list or rings that are on that residue and have one of the specified fingerprints. */
     export function byFingerprintAndResidue(rings: UnitRings, fingerprints: ReadonlyArray<UnitRing.Fingerprint>) {
         const map = new Map<ResidueIndex, Index[]>();
-        for (const fp of fingerprints) {
+    
+        for (let fI = 0, _fI = fingerprints.length; fI < _fI; fI++) {
+            const fp = fingerprints[fI];
             addSingleResidueRings(rings, fp, map);
-        }
+        }        
         return map;
     }
 }
@@ -153,7 +169,8 @@ namespace UnitRings {
 function createByFingerprint(unit: Unit.Atomic, rings: ReadonlyArray<UnitRing>) {
     const byFingerprint = new Map<UnitRing.Fingerprint, UnitRings.Index[]>();
     let idx = 0 as UnitRings.Index;
-    for (const r of rings) {
+    for (let rI = 0, _rI = rings.length; rI < _rI; rI++) {
+        const r = rings[rI];
         const fp = UnitRing.fingerprint(unit, r);
         if (byFingerprint.has(fp)) byFingerprint.get(fp)!.push(idx);
         else byFingerprint.set(fp, [idx]);
@@ -175,7 +192,8 @@ function ringResidueIdx(unit: Unit.Atomic, ring: ArrayLike<StructureElement.Unit
 function addSingleResidueRings(rings: UnitRings, fp: UnitRing.Fingerprint, map: Map<ResidueIndex, UnitRings.Index[]>) {
     const byFp = rings.byFingerprint.get(fp);
     if (!byFp) return;
-    for (const r of byFp) {
+    for (let rI = 0, _rI = byFp.length; rI < _rI; rI++) {
+        const r = byFp[rI];
         const idx = ringResidueIdx(rings.unit, rings.all[r]);
         if (idx >= 0) {
             if (map.has(idx)) map.get(idx)!.push(r);