@cyanheads/protein-mcp-server 0.8.2 → 0.8.3

package/dist/services/shared/identifiers.d.ts

@@ -14,6 +14,13 @@ export declare function isUniProtAccession(value: string): boolean;
 export declare function isAlphaFoldEntryId(value: string): boolean;
 /** True when `value` is a syntactically valid PDB entry ID. */
 export declare function isPdbId(value: string): boolean;
-/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
+/** True when `value` is an RCSB computed-model ID (`AF_*` AlphaFold / `MA_*` ModelArchive). */
+export declare function isComputedModelId(value: string): boolean;
+/**
+ * Extract the entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). A
+ * computed-model ID carries its own underscore after the `AF_`/`MA_` prefix, so
+ * only its trailing `_<entity number>` is stripped (`AF_AFP69905F1_1` →
+ * `AF_AFP69905F1`); a bare computed-model entry ID passes through.
+ */
 export declare function entryIdOf(identifier: string): string;
 //# sourceMappingURL=identifiers.d.ts.map

package/dist/services/shared/identifiers.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}
+{"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,+FAA+F;AAC/F,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAExD;AAED;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAIpD"}

package/dist/services/shared/identifiers.js

@@ -28,8 +28,19 @@ export function isAlphaFoldEntryId(value) {
 export function isPdbId(value) {
     return PDB_RE.test(value.trim());
 }
-/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
+/** True when `value` is an RCSB computed-model ID (`AF_*` AlphaFold / `MA_*` ModelArchive). */
+export function isComputedModelId(value) {
+    return /^(AF|MA)_/i.test(value);
+}
+/**
+ * Extract the entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). A
+ * computed-model ID carries its own underscore after the `AF_`/`MA_` prefix, so
+ * only its trailing `_<entity number>` is stripped (`AF_AFP69905F1_1` →
+ * `AF_AFP69905F1`); a bare computed-model entry ID passes through.
+ */
 export function entryIdOf(identifier) {
+    if (isComputedModelId(identifier))
+        return identifier.replace(/_\d+$/, '').toUpperCase();
     const base = identifier.split(/[_.]/)[0] ?? identifier;
     return base.toUpperCase();
 }

package/dist/services/shared/identifiers.js.map

@@ -1 +1 @@
-{"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,qEAAqE;AACrE,MAAM,YAAY,GAAG,4EAA4E,CAAC;AAElG,4DAA4D;AAC5D,MAAM,UAAU,GAAG,IAAI,MAAM,CAAC,IAAI,YAAY,GAAG,EAAE,GAAG,CAAC,CAAC;AAExD,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,MAAM,CAAC,OAAO,YAAY,SAAS,EAAE,GAAG,CAAC,CAAC;AAElE,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACxC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}
+{"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,qEAAqE;AACrE,MAAM,YAAY,GAAG,4EAA4E,CAAC;AAElG,4DAA4D;AAC5D,MAAM,UAAU,GAAG,IAAI,MAAM,CAAC,IAAI,YAAY,GAAG,EAAE,GAAG,CAAC,CAAC;AAExD,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,MAAM,CAAC,OAAO,YAAY,SAAS,EAAE,GAAG,CAAC,CAAC;AAElE,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACxC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,+FAA+F;AAC/F,MAAM,UAAU,iBAAiB,CAAC,KAAa;IAC7C,OAAO,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AAClC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,IAAI,iBAAiB,CAAC,UAAU,CAAC;QAAE,OAAO,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;IACxF,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.8.2",
+  "version": "0.8.3",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.8.2",
+  "version": "0.8.3",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.2",
+      "version": "0.8.3",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.2",
+      "version": "0.8.3",
       "packageArguments": [
         {
           "type": "positional",