@delta-infra/cli 1.1.19 → 1.1.23

package/skills/delta-science/references/rdkit.md

@@ -1,141 +1,141 @@
-# RDKit reference
-
-Call this tool only through `delta-cli science invoke`. Business responses are in the top-level
-CLI `data`; read only the fields described here and do not search recursively. This document
-records operation schemas and does not authorise direct HTTP access.
-
-Make only the calls needed to meet the request. To validate, canonicalise and calculate basic
-descriptors in one request, use `batch-parse-describe` with the `molecules:[{id,smiles}]` payload;
-do not split it into parse and descriptors calls. For all-pairs similarity across multiple
-molecules, use one `similarity-matrix` call. Its fixed ranking fields are `a`, `b` and
-`similarity`, not `i`, `j` or `score`.
-
-Report only descriptors actually present in the business response. When rendering a PNG, decode
-only the field specified in the documentation and verify that the bytes begin with
-`89 50 4e 47 0d 0a 1a 0a`; do not save a JSON envelope as an image.
-
-## Health
-
-Operation: `health`; no request body.
-
-## Parse
-
-Operation: `parse`.
-
-```json
-{"input": "CCO", "format": "smiles", "sanitize": true}
-```
-
-Formats: `smiles`, `inchi`, `molblock`.
-
-Key response fields in `data`: `valid`, `canonical_smiles`, `formula`,
-`molecular_weight`, `exact_molecular_weight`, `inchi_key`, `atom_count`,
-`heavy_atom_count`, `bond_count`, `warnings`, `error`.
-
-## Descriptors
-
-Operation: `descriptors`.
-
-```json
-{"smiles": "CCO", "descriptor_set": "basic", "sanitize": true}
-```
-
-`descriptor_set` currently supports `basic`. Descriptor keys include `Formula`,
-`MolWt`, `ExactMolWt`, `HeavyAtomMolWt`, `TPSA`, `MolLogP`, `NumHDonors`,
-`NumHAcceptors`, `NumRotatableBonds`, `RingCount`, `FractionCSP3`,
-`HeavyAtomCount`, `AtomCount`, and `BondCount`.
-
-## Batch Descriptors
-
-Operation: `batch-descriptors`.
-
-```json
-{"smiles": ["CCO", "c1ccccc1"], "descriptor_set": "basic", "sanitize": true}
-```
-
-Limits: 1-500 SMILES.
-
-## Batch Parse Describe
-
-Operation: `batch-parse-describe`.
-
-```json
-{
-  "molecules": [
-    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
-    {"id": "caffeine", "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C"}
-  ],
-  "descriptor_set": "basic",
-  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
-  "sanitize": true
-}
-```
-
-Limits: 1-500 molecules. Returns per-item `valid`, `canonical_smiles`, parse
-fields, `descriptors`, optional `fingerprint_metadata`, `on_bits`, `bit_count`,
-`warnings`, and `error`.
-
-## Render
-
-Operation: `render`.
-
-```json
-{"smiles": "CCO", "image_format": "svg", "width": 450, "height": 320}
-```
-
-Image formats: `svg`, `png`. SVG returns text; PNG returns base64.
-Width/height range: 150-2000.
-
-## Fingerprint
-
-Operation: `fingerprint`.
-
-```json
-{"smiles": "CCO", "radius": 2, "n_bits": 2048}
-```
-
-Morgan fingerprint parameters: `radius` 1-6, `n_bits` 128-8192.
-
-## Similarity
-
-Operation: `similarity`.
-
-```json
-{"query_smiles": "CCO", "target_smiles": "CCCO", "radius": 2, "n_bits": 2048}
-```
-
-Returns Tanimoto similarity.
-
-## Similarity Matrix
-
-Operation: `similarity-matrix`.
-
-```json
-{
-  "molecules": [
-    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
-    {"id": "ibuprofen", "smiles": "CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O"}
-  ],
-  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
-  "sanitize": true
-}
-```
-
-Returns `matrix` in input order and `ranked_pairs` sorted by descending
-Tanimoto similarity. Each ranked record is named, not index-based:
-
-```json
-{"a":"aspirin","b":"ibuprofen","similarity":0.195122}
-```
-
-Do not expect `i`, `j`, or `score` fields.
-
-## Substructure
-
-Operation: `substructure`.
-
-```json
-{"query_smarts": "c1ccccc1", "target_smiles": ["c1ccccc1", "CCO"]}
-```
-
-Limits: SMARTS max length 5000; target list size 1-500.
+# RDKit reference
+
+Call this tool only through `delta-cli science invoke`. Business responses are in the top-level
+CLI `data`; read only the fields described here and do not search recursively. This document
+records operation schemas and does not authorise direct HTTP access.
+
+Make only the calls needed to meet the request. To validate, canonicalise and calculate basic
+descriptors in one request, use `batch-parse-describe` with the `molecules:[{id,smiles}]` payload;
+do not split it into parse and descriptors calls. For all-pairs similarity across multiple
+molecules, use one `similarity-matrix` call. Its fixed ranking fields are `a`, `b` and
+`similarity`, not `i`, `j` or `score`.
+
+Report only descriptors actually present in the business response. When rendering a PNG, decode
+only the field specified in the documentation and verify that the bytes begin with
+`89 50 4e 47 0d 0a 1a 0a`; do not save a JSON envelope as an image.
+
+## Health
+
+Operation: `health`; no request body.
+
+## Parse
+
+Operation: `parse`.
+
+```json
+{"input": "CCO", "format": "smiles", "sanitize": true}
+```
+
+Formats: `smiles`, `inchi`, `molblock`.
+
+Key response fields in `data`: `valid`, `canonical_smiles`, `formula`,
+`molecular_weight`, `exact_molecular_weight`, `inchi_key`, `atom_count`,
+`heavy_atom_count`, `bond_count`, `warnings`, `error`.
+
+## Descriptors
+
+Operation: `descriptors`.
+
+```json
+{"smiles": "CCO", "descriptor_set": "basic", "sanitize": true}
+```
+
+`descriptor_set` currently supports `basic`. Descriptor keys include `Formula`,
+`MolWt`, `ExactMolWt`, `HeavyAtomMolWt`, `TPSA`, `MolLogP`, `NumHDonors`,
+`NumHAcceptors`, `NumRotatableBonds`, `RingCount`, `FractionCSP3`,
+`HeavyAtomCount`, `AtomCount`, and `BondCount`.
+
+## Batch Descriptors
+
+Operation: `batch-descriptors`.
+
+```json
+{"smiles": ["CCO", "c1ccccc1"], "descriptor_set": "basic", "sanitize": true}
+```
+
+Limits: 1-500 SMILES.
+
+## Batch Parse Describe
+
+Operation: `batch-parse-describe`.
+
+```json
+{
+  "molecules": [
+    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
+    {"id": "caffeine", "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C"}
+  ],
+  "descriptor_set": "basic",
+  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
+  "sanitize": true
+}
+```
+
+Limits: 1-500 molecules. Returns per-item `valid`, `canonical_smiles`, parse
+fields, `descriptors`, optional `fingerprint_metadata`, `on_bits`, `bit_count`,
+`warnings`, and `error`.
+
+## Render
+
+Operation: `render`.
+
+```json
+{"smiles": "CCO", "image_format": "svg", "width": 450, "height": 320}
+```
+
+Image formats: `svg`, `png`. SVG returns text; PNG returns base64.
+Width/height range: 150-2000.
+
+## Fingerprint
+
+Operation: `fingerprint`.
+
+```json
+{"smiles": "CCO", "radius": 2, "n_bits": 2048}
+```
+
+Morgan fingerprint parameters: `radius` 1-6, `n_bits` 128-8192.
+
+## Similarity
+
+Operation: `similarity`.
+
+```json
+{"query_smiles": "CCO", "target_smiles": "CCCO", "radius": 2, "n_bits": 2048}
+```
+
+Returns Tanimoto similarity.
+
+## Similarity Matrix
+
+Operation: `similarity-matrix`.
+
+```json
+{
+  "molecules": [
+    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
+    {"id": "ibuprofen", "smiles": "CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O"}
+  ],
+  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
+  "sanitize": true
+}
+```
+
+Returns `matrix` in input order and `ranked_pairs` sorted by descending
+Tanimoto similarity. Each ranked record is named, not index-based:
+
+```json
+{"a":"aspirin","b":"ibuprofen","similarity":0.195122}
+```
+
+Do not expect `i`, `j`, or `score` fields.
+
+## Substructure
+
+Operation: `substructure`.
+
+```json
+{"query_smarts": "c1ccccc1", "target_smiles": ["c1ccccc1", "CCO"]}
+```
+
+Limits: SMARTS max length 5000; target list size 1-500.

package/skills/delta-science/references/strbo.md

@@ -1,95 +1,95 @@
-# STRBO reference
-
-STRBO performs generative multi-objective optimisation for the server-fixed **KRAS G12D**
-target. The objective order is fixed as `[vina, activity]`: lower Vina is better and higher
-activity is better. `task` guides candidate generation but does not change the target; do not
-claim that user-defined receptors are supported.
-
-Use `tool="strbo"` for every call. Generation, suggestion, evaluation and job submission consume
-remote resources, so call them only when the user actually asks for the relevant research task.
-Do not retry if the outcome is unknown or the request times out.
-
-## Initialisation
-
-- Synchronous operation: `molecules-init`
-- Asynchronous operation: `molecules-init-job`
-- Validation-only operation: `molecules-init-validate`
-
-```json
-{
-  "task": "Generate candidate small molecules for KRAS G12D that balance binding and activity",
-  "num_initial": 3,
-  "seed": 42
-}
-```
-
-Use validate only when you need to check parameters. For a full run, do not validate before
-submitting; that would make an unnecessary call. A successful result should contain the same
-number of candidate SMILES as `num_initial`.
-
-## Suggest the next batch of candidates
-
-- Synchronous operation: `molecules-suggest`
-- Asynchronous operation: `molecules-suggest-job` (prefer it for heavy tasks)
-- Validation-only operation: `molecules-suggest-validate`
-
-```json
-{
-  "task": "Continue improving binding and activity for KRAS G12D",
-  "history_xs": ["CCO", "CCN", "CCC"],
-  "history_ys": [
-    [-6.8, 0.31],
-    [-7.1, 0.42],
-    [-6.5, 0.28]
-  ],
-  "num_suggestions": 2,
-  "seed": 42
-}
-```
-
-`history_xs` and `history_ys` must have the same length. Each `history_ys` item must contain two
-finite numbers in the exact order `[vina, activity]`. Do not present predictions as wet-lab results.
-
-## Evaluate candidates
-
-- Synchronous operation: `molecules-evaluate`
-- Asynchronous operation: `molecules-evaluate-job`
-- Validation-only operation: `molecules-evaluate-validate`
-
-```json
-{
-  "designs": ["CCO", "CCN"]
-}
-```
-
-The number of scores in a successful result must match the number of designs, with exactly two
-finite numbers per row. If any item explicitly fails, treat the entire run as failed; do not
-report only the successful subset.
-
-## Asynchronous jobs
-
-After submitting an asynchronous operation, read a non-empty `job_id` from the current business
-response, then poll:
-
-```text
-delta-cli science invoke --tool strbo --endpoint job-status --params JSON
-```
-
-Read the result only once the status changes to `succeeded`:
-
-```text
-delta-cli science invoke --tool strbo --endpoint job-result --params JSON
-```
-
-`queued` and `running` do not mean the job is complete; stop immediately on `failed`. Status
-queries may be repeated at intervals of about five seconds, but never repeat the submission
-operation. The total wait for one user task is limited to 15 minutes. If that limit is reached,
-report that the job is still incomplete and retain its `job_id`; do not claim it was cancelled
-remotely.
-
-## Complete research workflow
-
-When the user explicitly asks for a complete iteration, run `initialise → evaluate → suggest →
-evaluate` sequentially. Use only verified business responses from the current calls as inputs to
-the next step. If the user asks only for initial candidates or evaluation of supplied SMILES, do
-not expand the task into a full loop.
+# STRBO reference
+
+STRBO performs generative multi-objective optimisation for the server-fixed **KRAS G12D**
+target. The objective order is fixed as `[vina, activity]`: lower Vina is better and higher
+activity is better. `task` guides candidate generation but does not change the target; do not
+claim that user-defined receptors are supported.
+
+Use `tool="strbo"` for every call. Generation, suggestion, evaluation and job submission consume
+remote resources, so call them only when the user actually asks for the relevant research task.
+Do not retry if the outcome is unknown or the request times out.
+
+## Initialisation
+
+- Synchronous operation: `molecules-init`
+- Asynchronous operation: `molecules-init-job`
+- Validation-only operation: `molecules-init-validate`
+
+```json
+{
+  "task": "Generate candidate small molecules for KRAS G12D that balance binding and activity",
+  "num_initial": 3,
+  "seed": 42
+}
+```
+
+Use validate only when you need to check parameters. For a full run, do not validate before
+submitting; that would make an unnecessary call. A successful result should contain the same
+number of candidate SMILES as `num_initial`.
+
+## Suggest the next batch of candidates
+
+- Synchronous operation: `molecules-suggest`
+- Asynchronous operation: `molecules-suggest-job` (prefer it for heavy tasks)
+- Validation-only operation: `molecules-suggest-validate`
+
+```json
+{
+  "task": "Continue improving binding and activity for KRAS G12D",
+  "history_xs": ["CCO", "CCN", "CCC"],
+  "history_ys": [
+    [-6.8, 0.31],
+    [-7.1, 0.42],
+    [-6.5, 0.28]
+  ],
+  "num_suggestions": 2,
+  "seed": 42
+}
+```
+
+`history_xs` and `history_ys` must have the same length. Each `history_ys` item must contain two
+finite numbers in the exact order `[vina, activity]`. Do not present predictions as wet-lab results.
+
+## Evaluate candidates
+
+- Synchronous operation: `molecules-evaluate`
+- Asynchronous operation: `molecules-evaluate-job`
+- Validation-only operation: `molecules-evaluate-validate`
+
+```json
+{
+  "designs": ["CCO", "CCN"]
+}
+```
+
+The number of scores in a successful result must match the number of designs, with exactly two
+finite numbers per row. If any item explicitly fails, treat the entire run as failed; do not
+report only the successful subset.
+
+## Asynchronous jobs
+
+After submitting an asynchronous operation, read a non-empty `job_id` from the current business
+response, then poll:
+
+```text
+delta-cli science invoke --tool strbo --endpoint job-status --params JSON
+```
+
+Read the result only once the status changes to `succeeded`:
+
+```text
+delta-cli science invoke --tool strbo --endpoint job-result --params JSON
+```
+
+`queued` and `running` do not mean the job is complete; stop immediately on `failed`. Status
+queries may be repeated at intervals of about five seconds, but never repeat the submission
+operation. The total wait for one user task is limited to 15 minutes. If that limit is reached,
+report that the job is still incomplete and retain its `job_id`; do not claim it was cancelled
+remotely.
+
+## Complete research workflow
+
+When the user explicitly asks for a complete iteration, run `initialise → evaluate → suggest →
+evaluate` sequentially. Use only verified business responses from the current calls as inputs to
+the next step. If the user asks only for initial candidates or evaluation of supplied SMILES, do
+not expand the task into a full loop.