Merge pull request #1830 from josemduarte/ms-fix-omitwater

Fix ModelServer bugs for omitWater param in surroundingLigands endpoint

CHANGELOG.md

@@ -12,6 +12,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add mesoscale representation preset
 - Add presets option to `ObjectList` param definition
 - Fix memory leak in `State.dispose()` not invoking transformer `dispose` callbacks for live cells
+- Fix bugs in ModelServer surroundingLigands endpoint, resulting in omitWater not honored
 - Fix `Volume` and `Isosurface` getBoundingSphere ignoring instances
 
 ## [v5.9.0] - 2026-05-03

src/mol-model/structure/query/queries/modifiers.ts

@@ -545,6 +545,12 @@ export function surroundingLigands({ query, radius, includeWater }: SurroundingL
                     continue;
                 }
 
+                // Water is handled exclusively by the `includeWater` 3D-lookup branch below.
+                // A single water pulled in via a struct_conn metalc/covale edge would
+                // otherwise match every other water in the chain (all share label_seq_id
+                // and label_comp_id) and leak the entire chain.
+                if (StructureProperties.entity.type(l) === 'water') continue;
+
                 residuesIt.setSegment(chainSegment);
                 while (residuesIt.hasNext) {
                     const residueSegment = residuesIt.move();

src/servers/model/CHANGELOG.md

@@ -1,3 +1,7 @@
+# 0.9.13
+* /surroundingLigands: honor `omit_water=true|false` for REST GET requests (boolean parser previously coerced both to `false`)
+* /surroundingLigands: stop leaking the asymmetric unit's water chain into the result when `omit_water=true` (water residues pulled in via struct_conn covale/metalc edges no longer match every other water in the chain)
+
 # 0.9.12
 * add `health-check` endpoint + `healthCheckPath` config prop to report service health
 

src/servers/model/server/api.ts

@@ -295,7 +295,7 @@ function _normalizeQueryParams(params: { [p: string]: string }, paramList: Query
                 case QueryParamType.String: el = value; break;
                 case QueryParamType.Integer: el = parseInt(value); break;
                 case QueryParamType.Float: el = parseFloat(value); break;
-                case QueryParamType.Boolean: el = Boolean(+value); break;
+                case QueryParamType.Boolean: el = isTrue(value); break;
             }
 
             if (p.validation) p.validation(el);

src/servers/model/version.ts

@@ -4,4 +4,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export const VERSION = '0.9.12';
+export const VERSION = '0.9.13';