tweaks for coarse/backbone only models

data/mmcif-field-names.csv

@@ -66,8 +66,8 @@ entity_poly.entity_id
 entity_poly.type
 entity_poly.nstd_linkage
 entity_poly.nstd_monomer
-entity_poly.pdbx_seq_one_letter_code  
-entity_poly.pdbx_seq_one_letter_code_can 
+entity_poly.pdbx_seq_one_letter_code
+entity_poly.pdbx_seq_one_letter_code_can
 entity_poly.pdbx_strand_id
 entity_poly.pdbx_target_identifier
 

src/mol-geo/representation/util.ts

@@ -22,7 +22,8 @@ export function getQualityProps(props: Partial<QualityProps>, structure?: Struct
     let linearSegments = defaults(props.linearSegments, 8)
 
     if (quality === 'auto' && structure) {
-        const score = structure.elementCount
+        let score = structure.elementCount
+        if (structure.isCoarse) score *= 10
         if (score > 500_000) {
             quality = 'lowest'
         } else if (score > 100_000) {

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

@@ -22,13 +22,13 @@ function getMoleculeType(compId: string, chemicalComponentMap: ChemicalComponent
     return cc ? cc.moleculeType : MoleculeType.unknown
 }
 
-function getElementIndexForAtomId(rI: ResidueIndex, atomId: string, data: AtomicData, segments: AtomicSegments, ): ElementIndex {
+function getElementIndexForAtomId(rI: ResidueIndex, atomId: string, data: AtomicData, segments: AtomicSegments): ElementIndex {
     const { offsets } = segments.residueAtomSegments
     const { label_atom_id } = data.atoms
     for (let j = offsets[rI], _j = offsets[rI + 1]; j < _j; j++) {
-        if (label_atom_id.value(j) === atomId) return j as ElementIndex
+        if (label_atom_id.value(j) === atomId) return j
     }
-    return offsets[rI] as ElementIndex
+    return offsets[rI]
 }
 
 function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, chemicalComponentMap: ChemicalComponentMap) {
@@ -46,7 +46,7 @@ function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data:
     const { x, y, z } = conformation
     const pStart = Vec3.create(x[eiStart], y[eiStart], z[eiStart])
     const pEnd = Vec3.create(x[eiEnd], y[eiEnd], z[eiEnd])
-    return Vec3.distance(pStart, pEnd) < 2
+    return Vec3.distance(pStart, pEnd) < 10
 }
 
 export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, chemicalComponentMap: ChemicalComponentMap): AtomicRanges {
@@ -90,6 +90,13 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
                         startIndex = residueSegment.start
                     } else if (!residueIt.hasNext) {
                         polymerRanges.push(startIndex, residueSegment.end - 1)
+                    } else {
+                        const riStart = segments.residueAtomSegments.index[residueSegment.start]
+                        const riEnd = segments.residueAtomSegments.index[prevEnd - 1]
+                        if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, chemicalComponentMap)) {
+                            polymerRanges.push(startIndex, prevEnd - 1)
+                            startIndex = residueSegment.start
+                        }
                     }
                 } else {
                     startIndex = residueSegment.start // start polymer

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

@@ -40,7 +40,8 @@ class Structure {
         models?: ReadonlyArray<Model>,
         hashCode: number,
         elementCount: number,
-    } = { hashCode: -1, elementCount: 0 };
+        polymerResidueCount: number,
+    } = { hashCode: -1, elementCount: 0, polymerResidueCount: 0 };
 
     subsetBuilder(isSorted: boolean) {
         return new StructureSubsetBuilder(this, isSorted);
@@ -51,6 +52,18 @@ class Structure {
         return this._props.elementCount;
     }
 
+    /** Count of all polymer residues in the structure */
+    get polymerResidueCount() {
+        return this._props.polymerResidueCount;
+    }
+
+    /** Coarse structure, defined as Containing less than twice as many elements as polymer residues */
+    get isCoarse() {
+        const ec = this.elementCount
+        const prc = this.polymerResidueCount
+        return prc && ec ? ec / prc < 2 : false
+    }
+
     get hashCode() {
         if (this._props.hashCode !== -1) return this._props.hashCode;
         return this.computeHash();
@@ -123,12 +136,14 @@ class Structure {
     constructor(units: ArrayLike<Unit>) {
         const map = IntMap.Mutable<Unit>();
         let elementCount = 0;
+        let polymerResidueCount = 0;
         let isSorted = true;
         let lastId = units.length > 0 ? units[0].id : 0;
         for (let i = 0, _i = units.length; i < _i; i++) {
             const u = units[i];
             map.set(u.id, u);
             elementCount += u.elements.length;
+            polymerResidueCount += u.polymerElements.length;
             if (u.id < lastId) isSorted = false;
             lastId = u.id;
         }
@@ -136,6 +151,7 @@ class Structure {
         this.unitMap = map;
         this.units = units as ReadonlyArray<Unit>;
         this._props.elementCount = elementCount;
+        this._props.polymerResidueCount = polymerResidueCount;
     }
 }
 

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

@@ -21,7 +21,7 @@ export function getAtomicPolymerElements(unit: Unit.Atomic) {
         while (residueIt.hasNext) {
             const residueSegment = residueIt.move()
             const { start, end, index } = residueSegment
-            if (OrderedSet.areIntersecting(Interval.ofBounds(elements[start], elements[end - 1]), elements)) {
+            if (OrderedSet.areIntersecting(Interval.ofRange(elements[start], elements[end - 1]), elements)) {
                 const elementIndex = getElementIndexForAtomRole(model, index, 'trace')
                 indices.push(elementIndex === -1 ? residueAtomSegments.offsets[index] : elementIndex)
             }