set some IndexPairBonds maxDistance to Infinity

- for MOL/SDF and MOL2 (without symmetry) models
- avoid filtering by element-based rules

CHANGELOG.md

@@ -12,6 +12,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add example mmCIF file with categories necessary to display Confal pyramids
 - Change the lookup logic of NtC steps from residues
 - Add support for download of gzipped files
+- Don't filter IndexPairBonds by element-based rules in MOL/SDF and MOL2 (without symmetry) models
 
 ## [v3.13.0] - 2022-07-24
 

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

@@ -80,7 +80,10 @@ export async function getMolModels(mol: MolFile, format: ModelFormat<any> | unde
         const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
         const indexB = Column.ofIntArray(Column.mapToArray(bonds.atomIdxB, x => x - 1, Int32Array));
         const order = Column.asArrayColumn(bonds.order, Int32Array);
-        const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: atoms.count });
+        const pairBonds = IndexPairBonds.fromData(
+            { pairs: { indexA, indexB, order }, count: atoms.count },
+            { maxDistance: Infinity }
+        );
         IndexPairBonds.Provider.set(models.representative, pairBonds);
     }
 

src/mol-model-formats/structure/mol2.ts

@@ -113,7 +113,10 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
                         return BondType.Flag.Covalent;
                 }
             }, Int8Array));
-            const pairBonds = IndexPairBonds.fromData({ pairs: { key, indexA, indexB, order, flag }, count: atoms.count });
+            const pairBonds = IndexPairBonds.fromData(
+                { pairs: { key, indexA, indexB, order, flag }, count: atoms.count },
+                { maxDistance: crysin ? -1 : Infinity }
+            );
 
             const first = _models.representative;
             IndexPairBonds.Provider.set(first, pairBonds);