@cyanheads/protein-mcp-server 0.7.0 → 0.8.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +2 -2
- package/CLAUDE.md +2 -2
- package/README.md +6 -4
- package/changelog/0.8.x/0.8.0.md +22 -0
- package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts +9 -0
- package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-similar.tool.js +88 -24
- package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +11 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js +32 -2
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.js +14 -4
- package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
- package/dist/services/foldseek/foldseek-service.d.ts +12 -1
- package/dist/services/foldseek/foldseek-service.d.ts.map +1 -1
- package/dist/services/foldseek/foldseek-service.js +17 -12
- package/dist/services/foldseek/foldseek-service.js.map +1 -1
- package/dist/services/rcsb/rcsb-service.d.ts +31 -1
- package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
- package/dist/services/rcsb/rcsb-service.js +113 -22
- package/dist/services/rcsb/rcsb-service.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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1
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+
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@@ -2,7 +2,9 @@
|
|
|
2
2
|
* @fileoverview Foldseek service — wraps the public Foldseek structural-search
|
|
3
3
|
* ticket API (`/api/ticket` → poll `/api/ticket/{id}` → `/api/result/{id}/{n}`).
|
|
4
4
|
* Submits a query coordinate file against experimental + predicted databases and
|
|
5
|
-
* returns fold-similarity hits
|
|
5
|
+
* returns a page of fold-similarity hits alongside the full hit count, so a
|
|
6
|
+
* completed ticket can be re-paged instead of resubmitted. Backs
|
|
7
|
+
* `protein_find_similar` (`by: structure`).
|
|
6
8
|
* Async: the ticket status field drives completion, not the HTTP code.
|
|
7
9
|
* @module services/foldseek/foldseek-service
|
|
8
10
|
*/
|
|
@@ -40,6 +42,7 @@ export type FoldseekOutcome = {
|
|
|
40
42
|
status: 'complete';
|
|
41
43
|
ticketId: string;
|
|
42
44
|
hits: FoldseekHit[];
|
|
45
|
+
total: number;
|
|
43
46
|
} | {
|
|
44
47
|
status: 'computing';
|
|
45
48
|
ticketId: string;
|
|
@@ -63,6 +66,7 @@ export declare class FoldseekService {
|
|
|
63
66
|
databases: string[];
|
|
64
67
|
mode: string;
|
|
65
68
|
limit: number;
|
|
69
|
+
start: number;
|
|
66
70
|
timeoutMs: number;
|
|
67
71
|
}, ctx: Context): Promise<FoldseekOutcome>;
|
|
68
72
|
/**
|
|
@@ -74,10 +78,17 @@ export declare class FoldseekService {
|
|
|
74
78
|
resume(params: {
|
|
75
79
|
ticketId: string;
|
|
76
80
|
limit: number;
|
|
81
|
+
start: number;
|
|
77
82
|
timeoutMs: number;
|
|
78
83
|
}, ctx: Context): Promise<FoldseekOutcome>;
|
|
79
84
|
private submit;
|
|
80
85
|
private pollTicket;
|
|
86
|
+
/**
|
|
87
|
+
* Read a completed ticket's full alignment set and return the requested page.
|
|
88
|
+
* The whole list is parsed before slicing so the caller learns the real hit
|
|
89
|
+
* count — a page with no total leaves an agent unable to tell a complete result
|
|
90
|
+
* from a truncated one, and unable to ask for the rest.
|
|
91
|
+
*/
|
|
81
92
|
private fetchResults;
|
|
82
93
|
}
|
|
83
94
|
export declare function initFoldseekService(config: AppConfig, storage: StorageService, serverConfig: ServerConfig): void;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"foldseek-service.d.ts","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"foldseek-service.d.ts","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAI9D,oCAAoC;AACpC,MAAM,WAAW,WAAW;IAC1B,sBAAsB;IACtB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,8BAA8B;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IACjB,yBAAyB;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,kCAAkC;IAClC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,+BAA+B;IAC/B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,2BAA2B;IAC3B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,4FAA4F;IAC5F,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,qDAAqD;IACrD,MAAM,EAAE,MAAM,CAAC;IACf,4BAA4B;IAC5B,UAAU,EAAE,KAAK,GAAG,WAAW,GAAG,OAAO,CAAC;IAC1C,6CAA6C;IAC7C,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAaD,uDAAuD;AACvD,MAAM,MAAM,eAAe,GACvB;IAAE,MAAM,EAAE,UAAU,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,WAAW,EAAE,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,GAC5E;IAAE,MAAM,EAAE,WAAW,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,GACzC;IAAE,MAAM,EAAE,WAAW,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,GACzC;IAAE,MAAM,EAAE,QAAQ,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC;AAExC,qBAAa,eAAe;IAC1B,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IAEjC,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY,EAEnF;IAED;;;OAGG;IACG,MAAM,CACV,MAAM,EAAE;QACN,WAAW,EAAE,MAAM,CAAC;QACpB,QAAQ,EAAE,MAAM,CAAC;QACjB,SAAS,EAAE,MAAM,EAAE,CAAC;QACpB,IAAI,EAAE,MAAM,CAAC;QACb,KAAK,EAAE,MAAM,CAAC;QACd,KAAK,EAAE,MAAM,CAAC;QACd,SAAS,EAAE,MAAM,CAAC;KACnB,EACD,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,eAAe,CAAC,CA4B1B;IAED;;;;;OAKG;IACG,MAAM,CACV,MAAM,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAA;KAAE,EAC7E,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,eAAe,CAAC,CAqB1B;YAEa,MAAM;YA4BN,UAAU;IAsBxB;;;;;OAKG;YACW,YAAY;CAuB3B;AA+CD,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,SAAS,EACjB,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,YAAY,GACzB,IAAI,CAEN;AAED,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD"}
|
|
@@ -2,7 +2,9 @@
|
|
|
2
2
|
* @fileoverview Foldseek service — wraps the public Foldseek structural-search
|
|
3
3
|
* ticket API (`/api/ticket` → poll `/api/ticket/{id}` → `/api/result/{id}/{n}`).
|
|
4
4
|
* Submits a query coordinate file against experimental + predicted databases and
|
|
5
|
-
* returns fold-similarity hits
|
|
5
|
+
* returns a page of fold-similarity hits alongside the full hit count, so a
|
|
6
|
+
* completed ticket can be re-paged instead of resubmitted. Backs
|
|
7
|
+
* `protein_find_similar` (`by: structure`).
|
|
6
8
|
* Async: the ticket status field drives completion, not the HTTP code.
|
|
7
9
|
* @module services/foldseek/foldseek-service
|
|
8
10
|
*/
|
|
@@ -28,14 +30,14 @@ export class FoldseekService {
|
|
|
28
30
|
}
|
|
29
31
|
try {
|
|
30
32
|
const outcome = await withAsyncPoll({
|
|
31
|
-
step: () => this.pollTicket(ticketId, params.limit, ctx),
|
|
33
|
+
step: () => this.pollTicket(ticketId, params.start, params.limit, ctx),
|
|
32
34
|
timeoutMs: params.timeoutMs,
|
|
33
35
|
ctx,
|
|
34
36
|
intervalMs: 1500,
|
|
35
37
|
maxIntervalMs: 2500,
|
|
36
38
|
});
|
|
37
39
|
return outcome.status === 'complete'
|
|
38
|
-
? { status: 'complete', ticketId,
|
|
40
|
+
? { status: 'complete', ticketId, ...outcome.value }
|
|
39
41
|
: { status: 'computing', ticketId };
|
|
40
42
|
}
|
|
41
43
|
catch (err) {
|
|
@@ -51,14 +53,14 @@ export class FoldseekService {
|
|
|
51
53
|
async resume(params, ctx) {
|
|
52
54
|
try {
|
|
53
55
|
const outcome = await withAsyncPoll({
|
|
54
|
-
step: () => this.pollTicket(params.ticketId, params.limit, ctx),
|
|
56
|
+
step: () => this.pollTicket(params.ticketId, params.start, params.limit, ctx),
|
|
55
57
|
timeoutMs: params.timeoutMs,
|
|
56
58
|
ctx,
|
|
57
59
|
intervalMs: 1500,
|
|
58
60
|
maxIntervalMs: 2500,
|
|
59
61
|
});
|
|
60
62
|
return outcome.status === 'complete'
|
|
61
|
-
? { status: 'complete', ticketId: params.ticketId,
|
|
63
|
+
? { status: 'complete', ticketId: params.ticketId, ...outcome.value }
|
|
62
64
|
: { status: 'computing', ticketId: params.ticketId };
|
|
63
65
|
}
|
|
64
66
|
catch (err) {
|
|
@@ -90,7 +92,7 @@ export class FoldseekService {
|
|
|
90
92
|
throw new Error('Foldseek did not return a ticket ID');
|
|
91
93
|
return raw.id;
|
|
92
94
|
}
|
|
93
|
-
async pollTicket(ticketId, limit, ctx) {
|
|
95
|
+
async pollTicket(ticketId, start, limit, ctx) {
|
|
94
96
|
const ticket = await fetchJson(`${this.baseUrl}/api/ticket/${encodeURIComponent(ticketId)}`, ctx, {
|
|
95
97
|
operation: 'FoldseekService.pollTicket',
|
|
96
98
|
label: 'Foldseek',
|
|
@@ -102,10 +104,15 @@ export class FoldseekService {
|
|
|
102
104
|
throw new Error('Foldseek reported an error processing the structure');
|
|
103
105
|
if (status !== 'COMPLETE')
|
|
104
106
|
return { ready: false };
|
|
105
|
-
|
|
106
|
-
return { ready: true, value: hits };
|
|
107
|
+
return { ready: true, value: await this.fetchResults(ticketId, start, limit, ctx) };
|
|
107
108
|
}
|
|
108
|
-
|
|
109
|
+
/**
|
|
110
|
+
* Read a completed ticket's full alignment set and return the requested page.
|
|
111
|
+
* The whole list is parsed before slicing so the caller learns the real hit
|
|
112
|
+
* count — a page with no total leaves an agent unable to tell a complete result
|
|
113
|
+
* from a truncated one, and unable to ask for the rest.
|
|
114
|
+
*/
|
|
115
|
+
async fetchResults(ticketId, start, limit, ctx) {
|
|
109
116
|
const raw = await fetchJson(`${this.baseUrl}/api/result/${encodeURIComponent(ticketId)}/0`, ctx, { operation: 'FoldseekService.fetchResults', label: 'Foldseek', baseDelayMs: 400 });
|
|
110
117
|
const hits = [];
|
|
111
118
|
for (const dbResult of raw.results ?? []) {
|
|
@@ -115,12 +122,10 @@ export class FoldseekService {
|
|
|
115
122
|
if (!aln.target)
|
|
116
123
|
continue;
|
|
117
124
|
hits.push(normalizeHit(aln, db));
|
|
118
|
-
if (hits.length >= limit)
|
|
119
|
-
return hits;
|
|
120
125
|
}
|
|
121
126
|
}
|
|
122
127
|
}
|
|
123
|
-
return hits;
|
|
128
|
+
return { total: hits.length, hits: hits.slice(start, start + limit) };
|
|
124
129
|
}
|
|
125
130
|
}
|
|
126
131
|
// ─── Normalizers ──────────────────────────────────────────────────────────────
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"foldseek-service.js","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"foldseek-service.js","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAG3E,OAAO,EAAiB,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAClE,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AA8C9C,MAAM,OAAO,eAAe;IACT,OAAO,CAAS;IAEjC,YAAY,OAAkB,EAAE,QAAwB,EAAE,YAA0B;QAClF,IAAI,CAAC,OAAO,GAAG,YAAY,CAAC,eAAe,CAAC;IAC9C,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,MAAM,CACV,MAQC,EACD,GAAY;QAEZ,IAAI,QAAgB,CAAC;QACrB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAC1B,MAAM,CAAC,WAAW,EAClB,MAAM,CAAC,QAAQ,EACf,MAAM,CAAC,SAAS,EAChB,MAAM,CAAC,IAAI,EACX,GAAG,CACJ,CAAC;QACJ,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACvF,CAAC;QAED,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,aAAa,CAAe;gBAChD,IAAI,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC;gBACtE,SAAS,EAAE,MAAM,CAAC,SAAS;gBAC3B,GAAG;gBACH,UAAU,EAAE,IAAI;gBAChB,aAAa,EAAE,IAAI;aACpB,CAAC,CAAC;YACH,OAAO,OAAO,CAAC,MAAM,KAAK,UAAU;gBAClC,CAAC,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAC,KAAK,EAAE;gBACpD,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAC;QACxC,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACvF,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,MAAM,CACV,MAA6E,EAC7E,GAAY;QAEZ,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,aAAa,CAAe;gBAChD,IAAI,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC;gBAC7E,SAAS,EAAE,MAAM,CAAC,SAAS;gBAC3B,GAAG;gBACH,UAAU,EAAE,IAAI;gBAChB,aAAa,EAAE,IAAI;aACpB,CAAC,CAAC;YACH,OAAO,OAAO,CAAC,MAAM,KAAK,UAAU;gBAClC,CAAC,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,GAAG,OAAO,CAAC,KAAK,EAAE;gBACrE,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC;QACzD,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,yEAAyE;YACzE,qEAAqE;YACrE,4DAA4D;YAC5D,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,aAAa,EAAE,CAAC;gBAC3E,OAAO,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC;YAC5D,CAAC;YACD,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACvF,CAAC;IACH,CAAC;IAEO,KAAK,CAAC,MAAM,CAClB,WAAmB,EACnB,QAAgB,EAChB,SAAmB,EACnB,IAAY,EACZ,GAAY;QAEZ,MAAM,IAAI,GAAG,IAAI,QAAQ,EAAE,CAAC;QAC5B,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,IAAI,CAAC,CAAC,WAAW,CAAC,EAAE,EAAE,IAAI,EAAE,gBAAgB,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAC;QAChF,KAAK,MAAM,EAAE,IAAI,SAAS;YAAE,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;QAC1D,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;QAC1B,8EAA8E;QAC9E,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,IAAI,CAAC,OAAO,aAAa,EAC5B,GAAG,EACH;YACE,MAAM,EAAE,MAAM;YACd,IAAI,EAAE,IAAI;YACV,SAAS,EAAE,wBAAwB;YACnC,KAAK,EAAE,UAAU;YACjB,WAAW,EAAE,IAAI;YACjB,UAAU,EAAE,CAAC;SACd,CACF,CAAC;QACF,IAAI,CAAC,GAAG,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;QACpE,OAAO,GAAG,CAAC,EAAE,CAAC;IAChB,CAAC;IAEO,KAAK,CAAC,UAAU,CACtB,QAAgB,EAChB,KAAa,EACb,KAAa,EACb,GAAY;QAEZ,MAAM,MAAM,GAAG,MAAM,SAAS,CAC5B,GAAG,IAAI,CAAC,OAAO,eAAe,kBAAkB,CAAC,QAAQ,CAAC,EAAE,EAC5D,GAAG,EACH;YACE,SAAS,EAAE,4BAA4B;YACvC,KAAK,EAAE,UAAU;YACjB,SAAS,EAAE,MAAM;YACjB,WAAW,EAAE,GAAG;SACjB,CACF,CAAC;QACF,MAAM,MAAM,GAAG,CAAC,MAAM,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;QACnD,IAAI,MAAM,KAAK,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;QAC/F,IAAI,MAAM,KAAK,UAAU;YAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;QACnD,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,IAAI,CAAC,YAAY,CAAC,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,EAAE,CAAC;IACtF,CAAC;IAED;;;;;OAKG;IACK,KAAK,CAAC,YAAY,CACxB,QAAgB,EAChB,KAAa,EACb,KAAa,EACb,GAAY;QAEZ,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,IAAI,CAAC,OAAO,eAAe,kBAAkB,CAAC,QAAQ,CAAC,IAAI,EAC9D,GAAG,EACH,EAAE,SAAS,EAAE,8BAA8B,EAAE,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,EAAE,CACnF,CAAC;QACF,MAAM,IAAI,GAAkB,EAAE,CAAC;QAC/B,KAAK,MAAM,QAAQ,IAAI,GAAG,CAAC,OAAO,IAAI,EAAE,EAAE,CAAC;YACzC,MAAM,EAAE,GAAG,QAAQ,CAAC,EAAE,IAAI,SAAS,CAAC;YACpC,KAAK,MAAM,KAAK,IAAI,QAAQ,CAAC,UAAU,IAAI,EAAE,EAAE,CAAC;gBAC9C,KAAK,MAAM,GAAG,IAAI,KAAK,IAAI,EAAE,EAAE,CAAC;oBAC9B,IAAI,CAAC,GAAG,CAAC,MAAM;wBAAE,SAAS;oBAC1B,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC;gBACnC,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,GAAG,KAAK,CAAC,EAAE,CAAC;IACxE,CAAC;CACF;AAED,iFAAiF;AAEjF,SAAS,YAAY,CAAC,GAAiB,EAAE,QAAgB;IACvD,MAAM,MAAM,GAAG,GAAG,CAAC,MAAgB,CAAC;IACpC,MAAM,GAAG,GAAgB,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;IACtE,8EAA8E;IAC9E,0EAA0E;IAC1E,6EAA6E;IAC7E,4DAA4D;IAC5D,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ;QAAE,GAAG,CAAC,gBAAgB,GAAG,GAAG,CAAC,KAAK,GAAG,GAAG,CAAC;IAC1E,IAAI,OAAO,GAAG,CAAC,SAAS,KAAK,QAAQ;QAAE,GAAG,CAAC,eAAe,GAAG,GAAG,CAAC,SAAS,CAAC;IAC3E,IAAI,OAAO,GAAG,CAAC,IAAI,KAAK,QAAQ;QAAE,GAAG,CAAC,WAAW,GAAG,GAAG,CAAC,IAAI,CAAC;IAC7D,IAAI,OAAO,GAAG,CAAC,IAAI,KAAK,QAAQ;QAAE,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC;IACxD,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ;QAAE,GAAG,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC;IACzD,OAAO,GAAG,CAAC;AACb,CAAC;AAED,qEAAqE;AACrE,SAAS,WAAW,CAClB,MAAc;IAEd,MAAM,EAAE,GAAG,yBAAyB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAClD,IAAI,EAAE;QAAE,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,gBAAgB,EAAE,EAAE,CAAC,CAAC,CAAW,EAAE,CAAC;IAC9E,MAAM,GAAG,GAAG,uCAAuC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACjE,IAAI,GAAG;QACL,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,KAAK,EAAG,GAAG,CAAC,CAAC,CAAY,CAAC,WAAW,EAAE,EAAE,KAAK,EAAE,GAAG,CAAC,CAAC,CAAW,EAAE,CAAC;IACjG,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,CAAC;AACjC,CAAC;AAgBD,IAAI,QAAqC,CAAC;AAE1C,MAAM,UAAU,mBAAmB,CACjC,MAAiB,EACjB,OAAuB,EACvB,YAA0B;IAE1B,QAAQ,GAAG,IAAI,eAAe,CAAC,MAAM,EAAE,OAAO,EAAE,YAAY,CAAC,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,kBAAkB;IAChC,IAAI,CAAC,QAAQ;QACX,MAAM,IAAI,KAAK,CAAC,yEAAyE,CAAC,CAAC;IAC7F,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
|
@@ -61,7 +61,20 @@ export declare class RcsbService {
|
|
|
61
61
|
* surfaces first — a count-only query (rows 0), no rows or sort pulled.
|
|
62
62
|
*/
|
|
63
63
|
countEntriesWithLigand(compId: string, ctx: Context): Promise<number>;
|
|
64
|
-
/**
|
|
64
|
+
/**
|
|
65
|
+
* Resolve a ligand name, synonym, or molecular formula to candidate chemical
|
|
66
|
+
* component IDs. A formula-shaped query routes to RCSB's `chemical` service,
|
|
67
|
+
* which matches composition; anything else runs the name/synonym search, where
|
|
68
|
+
* a formula would only match components whose *name* contains formula-like
|
|
69
|
+
* tokens.
|
|
70
|
+
*
|
|
71
|
+
* Formula detection is a shape heuristic, so it can claim a string that is
|
|
72
|
+
* really a component ID — an all-caps ID built only from single-letter element
|
|
73
|
+
* symbols and a digit (`SF4`, `H4B`) tokenizes as a formula. An empty formula
|
|
74
|
+
* match therefore falls through to the name/synonym search rather than ending
|
|
75
|
+
* the resolution, which keeps those IDs reaching the path that can resolve
|
|
76
|
+
* them. The extra call happens only when the formula terminal matched nothing.
|
|
77
|
+
*/
|
|
65
78
|
findChemComps(query: string, limit: number, ctx: Context): Promise<string[]>;
|
|
66
79
|
/** Facet-only aggregation over an optional scoping query (no row pull). */
|
|
67
80
|
analyzeFacets(params: StructureSearchParams, facets: FacetSpec[], ctx: Context): Promise<{
|
|
@@ -94,6 +107,23 @@ export declare class RcsbService {
|
|
|
94
107
|
}
|
|
95
108
|
/** Build the RCSB query node from search params (match-all when no constraint given). */
|
|
96
109
|
export declare function buildQuery(params: StructureSearchParams): unknown;
|
|
110
|
+
/**
|
|
111
|
+
* True when `query` is a molecular formula rather than a chemical name or a
|
|
112
|
+
* component ID. Whitespace is insignificant — both the spaced CCD Hill notation
|
|
113
|
+
* and the unspaced form resolve upstream — but every remaining character must
|
|
114
|
+
* belong to an element-symbol token, and at least one element count must be
|
|
115
|
+
* present. The digit requirement carries most of the discrimination: Hill
|
|
116
|
+
* notation omits an implicit `1` only for the leading element, never for all of
|
|
117
|
+
* them, so `STI` (S·Ti) and `HEM` (H·E·M) are IDs, not formulas.
|
|
118
|
+
*
|
|
119
|
+
* It is a shape test, not a decision about what the string means, and it cannot
|
|
120
|
+
* separate every component ID from a formula: an all-caps ID built only from
|
|
121
|
+
* single-letter element symbols plus a digit (`SF4`, `H4B`, `BU1`) satisfies
|
|
122
|
+
* every rule here. `findChemComps` absorbs that by retrying the name/synonym
|
|
123
|
+
* search when the formula terminal matches nothing, so a claimed ID still
|
|
124
|
+
* resolves.
|
|
125
|
+
*/
|
|
126
|
+
export declare function isChemicalFormula(query: string): boolean;
|
|
97
127
|
/** Translate a friendly FacetSpec into the RCSB facet request shape (recursively). */
|
|
98
128
|
export declare function toRcsbFacet(spec: FacetSpec): Record<string, unknown>;
|
|
99
129
|
export declare function initRcsbService(config: AppConfig, storage: StorageService, serverConfig: ServerConfig): void;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"rcsb-service.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/rcsb-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAE9D,OAAO,KAAK,EAEV,WAAW,EACX,QAAQ,EACR,WAAW,EACX,SAAS,EAET,cAAc,EAId,YAAY,EACZ,qBAAqB,EACrB,WAAW,EACZ,MAAM,YAAY,CAAC;AAEpB,iDAAiD;AACjD,MAAM,MAAM,UAAU,GAAG,OAAO,GAAG,gBAAgB,GAAG,gBAAgB,CAAC;AAEvE,+EAA+E;AAC/E,MAAM,WAAW,SAAS;IACxB,wBAAwB;IACxB,WAAW,EAAE,OAAO,GAAG,WAAW,GAAG,gBAAgB,CAAC;IACtD,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,iDAAiD;IACjD,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,qDAAqD;IACrD,SAAS,EAAE,MAAM,CAAC;IAClB,gGAAgG;IAChG,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;CAC5B;AA6BD,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;IACnC,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;IAEnC,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY,EAKnF;IAID,gFAAgF;IAC1E,MAAM,CACV,MAAM,EAAE,qBAAqB,EAC7B,GAAG,EAAE,OAAO,EACZ,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,YAAY,CAAC,CAmBvB;IAED,uEAAuE;IACjE,cAAc,CAClB,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE;QACJ,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,WAAW,CAAC,EAAE,WAAW,EAAE,CAAC;KAC7B,EACD,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC,CAqBvB;IAED;;;;;;OAMG;IACG,cAAc,CAClB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,WAAW,EAAE,CAAA;KAAE,EACrE,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC,CAOvB;IAED;;;;OAIG;IACG,sBAAsB,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAO1E;IAED
|
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1
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+
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@@ -91,28 +91,33 @@ export class RcsbService {
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const raw = await this.postSearch(ligandContainmentQuery(compId, undefined, 0, 0, false), ctx, 'RcsbService.countEntriesWithLigand');
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/**
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* Resolve a ligand name, synonym, or molecular formula to candidate chemical
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* which matches composition; anything else runs the name/synonym search, where
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*
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query: {
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nodes: [chemTerm('chem_comp.name'), chemTerm('rcsb_chem_comp_synonyms.name')],
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request_options: { paginate: { start: 0, rows: limit } },
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const search = async (query_) => {
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query: query_,
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}, ctx, 'RcsbService.findChemComps');
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return normalizeHits(raw.result_set).map((h) => h.id);
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/** Facet-only aggregation over an optional scoping query (no row pull). */
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label: 'RCSB GraphQL API',
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baseDelayMs: 400,
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@@ -293,6 +308,82 @@ export function buildQuery(params) {
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function textNode(attribute, operator, value) {
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* Name/synonym chemical-dictionary query. Matches the term against both the
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* formal component name and its synonyms: common names ("heme", "aspirin") live
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* in synonyms, not the formal name ("PROTOPORPHYRIN IX CONTAINING FE"). A plain
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* full_text search over mol_definition matches far too broadly and buries the
|
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* intended component.
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*/
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function chemNameQuery(query) {
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type: 'terminal',
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service: 'text_chem',
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parameters: { attribute, operator: 'contains_words', value: query },
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return {
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type: 'group',
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nodes: [chemTerm('chem_comp.name'), chemTerm('rcsb_chem_comp_synonyms.name')],
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};
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}
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/**
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* Composition query against RCSB's `chemical` service. The formula terminal
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* accepts both CCD Hill notation (`C29 H31 N7 O`) and the unspaced form
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* (`C29H31N7O`), so the value is passed through unnormalized. `match_subset` is
|
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* left unset for an exact-composition match: the callers that consume the
|
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+
* resolved ID (`structures_with_ligand`, `binding_site`) expect a single
|
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* canonical component, which subset matching would dilute with supersets.
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* The `text_chem` attribute `chem_comp.formula` is not an alternative — RCSB
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+
* rejects it with "search is not enabled on [ chem_comp.formula ] attribute".
|
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+
*/
|
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+
function formulaQuery(query) {
|
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+
return {
|
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type: 'terminal',
|
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+
service: 'chemical',
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+
parameters: { type: 'formula', value: query.trim() },
|
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+
};
|
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+
}
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|
+
/**
|
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348
|
+
* Element symbols in canonical casing — the token vocabulary formula detection
|
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349
|
+
* accepts. Token shape alone is not enough: an all-caps chemical name can
|
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350
|
+
* tokenize as element-shaped letters (`VITAMIN B12` → V·I·T·A·M·I·N·B12), and
|
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351
|
+
* mis-routing a name to the formula terminal returns an empty match set rather
|
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352
|
+
* than an error, so the miss would be silent.
|
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353
|
+
*/
|
|
354
|
+
const ELEMENT_SYMBOLS = new Set(`H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se
|
|
355
|
+
Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb
|
|
356
|
+
Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm
|
|
357
|
+
Bk Cf Es Fm Md No Lr Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og`.split(/\s+/));
|
|
358
|
+
/** One formula token: an element symbol plus an optional count (`C29`, `Fe`). */
|
|
359
|
+
const FORMULA_TOKEN_RE = /[A-Z][a-z]?\d*/g;
|
|
360
|
+
/**
|
|
361
|
+
* True when `query` is a molecular formula rather than a chemical name or a
|
|
362
|
+
* component ID. Whitespace is insignificant — both the spaced CCD Hill notation
|
|
363
|
+
* and the unspaced form resolve upstream — but every remaining character must
|
|
364
|
+
* belong to an element-symbol token, and at least one element count must be
|
|
365
|
+
* present. The digit requirement carries most of the discrimination: Hill
|
|
366
|
+
* notation omits an implicit `1` only for the leading element, never for all of
|
|
367
|
+
* them, so `STI` (S·Ti) and `HEM` (H·E·M) are IDs, not formulas.
|
|
368
|
+
*
|
|
369
|
+
* It is a shape test, not a decision about what the string means, and it cannot
|
|
370
|
+
* separate every component ID from a formula: an all-caps ID built only from
|
|
371
|
+
* single-letter element symbols plus a digit (`SF4`, `H4B`, `BU1`) satisfies
|
|
372
|
+
* every rule here. `findChemComps` absorbs that by retrying the name/synonym
|
|
373
|
+
* search when the formula terminal matches nothing, so a claimed ID still
|
|
374
|
+
* resolves.
|
|
375
|
+
*/
|
|
376
|
+
export function isChemicalFormula(query) {
|
|
377
|
+
const compact = query.trim().replace(/\s+/g, '');
|
|
378
|
+
if (!/\d/.test(compact))
|
|
379
|
+
return false;
|
|
380
|
+
const tokens = compact.match(FORMULA_TOKEN_RE) ?? [];
|
|
381
|
+
// Anything the tokenizer skipped (punctuation, a lowercase-leading word, a
|
|
382
|
+
// digit-leading component ID) leaves the rejoined tokens shorter than the input.
|
|
383
|
+
if (tokens.join('') !== compact)
|
|
384
|
+
return false;
|
|
385
|
+
return tokens.every((token) => ELEMENT_SYMBOLS.has(token.replace(/\d+$/, '')));
|
|
386
|
+
}
|
|
296
387
|
/**
|
|
297
388
|
* Emit the `results_content_type` request option for a content scope. Omitting
|
|
298
389
|
* the option is not a union — RCSB defaults to experimental only — so a caller
|
|
@@ -1 +1 @@
|
|
|
1
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-
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1
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+
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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1
1
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{
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2
2
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"name": "@cyanheads/protein-mcp-server",
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3
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-
"version": "0.
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3
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+
"version": "0.8.0",
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4
4
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"mcpName": "io.github.cyanheads/protein-mcp-server",
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|
5
5
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"description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
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|
6
6
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"type": "module",
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