avoid standard polymers misqualified as ligands

- overrule erroneous chem comp type in some files

docs/interesting-pdb-entries.md

@@ -29,6 +29,11 @@
 * Long linear sugar chain (4HG6)
 * Anisotropic B-factors/Ellipsoids (1EJG)
 * NOS bridges (LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
+* Non-polymer components in polymer entities
+    * PN2 in 1F80
+    * ACE (many, e.g. 5AGU, 1E1X)
+    * ACY in 7ABY
+    * NH2 (many, e.g. 6Y13)
 
 Assembly symmetries
 * 5M30 (Assembly 1, C3 local and pseudo)

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

@@ -321,6 +321,12 @@ export function getMoleculeType(compType: string, compId: string): MoleculeType
         if (SaccharideCompIdMap.has(compId)) {
             // trust our saccharide table more than given 'non-polymer' or 'other' component type
             return MoleculeType.Saccharide;
+        } else if (AminoAcidNames.has(compId)) {
+            return MoleculeType.Protein;
+        } else if (RnaBaseNames.has(compId)) {
+            return MoleculeType.RNA;
+        } else if (DnaBaseNames.has(compId)) {
+            return MoleculeType.DNA;
         } else {
             return MoleculeType.Other;
         }

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -7,7 +7,7 @@
 
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { QueryContext, Structure, StructureQuery, StructureSelection, StructureProperties, StructureElement } from '../../mol-model/structure';
-import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol } from '../../mol-model/structure/model/types';
+import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol, PolymerNames } from '../../mol-model/structure/model/types';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { Expression } from '../../mol-script/language/expression';
@@ -320,6 +320,8 @@ const branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate
 ]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
+    MS.struct.modifier.exceptBy({
+        0: MS.struct.modifier.union([
             MS.struct.combinator.merge([
                 MS.struct.modifier.union([
                     MS.struct.generator.atomGroups({
@@ -347,6 +349,17 @@ const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
                     })
                 ])
             ]),
+        ]),
+        by: 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.set.has([
+                    MS.set(...SetUtils.toArray(PolymerNames)), MS.ammp('label_comp_id')
+                ])
+            })
+        ])
+    })
 ]), { category: StructureSelectionCategory.Type });
 
 // don't include branched entities as they have their own link representation