show non-polymer residues of polymer entities as ball&stick

src/mol-plugin/util/structure-selection-helper.ts

@@ -112,6 +112,8 @@ const branchedConnectedOnly = MS.struct.modifier.union([
 ])
 
 const ligand = MS.struct.modifier.union([
+    MS.struct.combinator.merge([
+        MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
                 'entity-test': MS.core.logic.and([
                     MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
@@ -125,6 +127,18 @@ const ligand = MS.struct.modifier.union([
                     MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
                 ])
             })
+        ]),
+        // this is to get non-polymer components in polymer entities, e.g. PXZ in 4HIV
+        // one option to optimize this is to expose `_entity_poly.nstd_monomer` in molql
+        // and only check those entities residue by residue
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.str.match([MS.re('non-polymer', 'i'), MS.ammp('chemCompType')])
+            })
+        ])
+    ]),
 ])
 
 // don't innclude branched entities as they have their own link representation