Merge branch 'postmerge-example-validation-docs'

Author: mitsenkov

README.md

@@ -21,6 +21,7 @@ A comprehensive toolkit for integrating structural models into the AlphaFold Dat
   - [Quick Start](#quick-start)
     - [Verify Installation](#verify-installation)
     - [Basic Usage Example](#basic-usage-example)
+    - [Validate Example Outputs](#validate-example-outputs)
   - [Usage](#usage)
     - [ModelCIF Generator](#modelcif-generator)
     - [CIF to BCIF Converter](#cif-to-bcif-converter)
@@ -274,6 +275,44 @@ uv run main.py run-dssp \
     -o output/AF-0000000000000001-model-v1.cif
 ```
 
+### Validate Example Outputs
+
+The committed end-to-end examples under [`examples/`](examples/README.md)
+can be validated directly from the repo root. Use `model-summary` for committed
+e2e `model_jsons/*.json`; the canonical `model` schema remains reserved for
+full model metadata entries and `AF-metadata-*-of-*.json` batches.
+
+```bash
+# Summary and provider metadata JSONs
+.venv/bin/python main.py run-schema-validation \
+  -i examples/colabfold_monomer_e2e/model_jsons/AF-0000000300000001.json \
+  -t model-summary
+.venv/bin/python main.py run-schema-validation \
+  -i examples/colabfold_monomer_e2e/config/provider.json \
+  -t provider
+
+# Score JSONs and confidence/PAE relationship
+.venv/bin/python main.py validate-plddt-file \
+  --file examples/colabfold_monomer_e2e/scores/AF-0000000300000001-confidence_v1.json
+.venv/bin/python main.py validate-pae-file \
+  --file examples/colabfold_monomer_e2e/scores/AF-0000000300000001-predicted_aligned_error_v1.json
+.venv/bin/python main.py validate-relationships-pair \
+  --plddt-file examples/colabfold_monomer_e2e/scores/AF-0000000300000001-confidence_v1.json \
+  --pae-file examples/colabfold_monomer_e2e/scores/AF-0000000300000001-predicted_aligned_error_v1.json
+
+# ModelCIF dictionary validation
+gemmi validate -p -d mmcif_ma.dic \
+  examples/colabfold_monomer_e2e/modelcif/AF-0000000300000001-model_v1.cif
+```
+
+For manual coordinate-file sanity checks, open representative PDB, ModelCIF,
+and BCIF files in the Mol* web viewer at https://molstar.org/viewer/. Drag and
+drop the files into the browser window, or use **Open Files** in the left
+panel. The structure should open correctly, no error messages should be shown
+in the viewer, and the structure should look structurally correct by eye. The
+same representative files can also be opened in ChimeraX or PyMOL; expect a
+clean import with no parser errors.
+
 ## Usage
 
 ### ColabFold conversion
@@ -420,11 +459,13 @@ Use these commands to sanity-check individual artifacts or entire datasets befor
 
 #### Schema Validation
 
-Validate metadata JSON files (`model` or `provider`) against the required JSON schemas to ensure data consistency and compliance.
+Validate metadata JSON files against the required JSON schemas to ensure data consistency and compliance.
 
 **Schemas:**
 
-* Model: `afdb_integration_kit/metadata/resources/model_schema.json`
+* Model: `afdb_integration_kit/metadata/resources/model_schema.json` for full model metadata entries and batches
+* Model summary: `afdb_integration_kit/metadata/resources/model_summary_schema.json` for e2e `model_jsons/*.json` and search summary documents
+* Collection doc: `afdb_integration_kit/metadata/resources/collection_doc_schema.json` for e2e `chain_jsons/*.json` and collection documents
 * Provider: `afdb_integration_kit/metadata/resources/provider_schema.json`
 
 **Command:**
@@ -436,12 +477,14 @@ uv run main.py run-schema-validation -i <metadata_json_file> -t <type>
 **Parameters:**
 
 * `-i, --input`: Path to the metadata JSON file to validate
-* `-t, --type`: Type of metadata to validate (`model` or `provider`)
+* `-t, --type`: Type of metadata to validate (`model`, `model-summary`, `collection-doc`, or `provider`)
 
 **Examples:**
 
 ```bash
 uv run main.py run-schema-validation -i model.json -t model
+uv run main.py run-schema-validation -i model_summary.json -t model-summary
+uv run main.py run-schema-validation -i collection_doc.json -t collection-doc
 uv run main.py run-schema-validation -i provider.json -t provider
 ```
 

afdb_integration_kit/metadata/resources/collection_doc_schema.json

@@ -0,0 +1,187 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "Collection Document Metadata Schema",
+  "type": "object",
+  "required": [
+    "uniqueId",
+    "toolUsed",
+    "modelCreatedDate",
+    "modelEntityId",
+    "isComplex",
+    "complexName",
+    "uniprotAccession",
+    "uniprotId",
+    "uniprotDescription",
+    "gene",
+    "taxId",
+    "organismScientificName",
+    "assemblyType",
+    "oligomericState",
+    "sequence",
+    "sequenceChecksum",
+    "sequenceVersionDate",
+    "sequenceStart",
+    "sequenceEnd",
+    "isIsoform",
+    "isFragment",
+    "isUniProt",
+    "isUniProtReferenceProteome",
+    "isUniProtReviewed",
+    "globalMetricValue",
+    "fractionPlddtVeryLow",
+    "fractionPlddtLow",
+    "fractionPlddtConfident",
+    "fractionPlddtVeryHigh",
+    "latestVersion",
+    "allVersions",
+    "providerId",
+    "entityType",
+    "isAMdata"
+  ],
+  "properties": {
+    "uniqueId": {
+      "type": "string",
+      "pattern": "^AF-[0-9]{16}_v[0-9]+_[A-Za-z0-9]+$"
+    },
+    "toolUsed": {
+      "type": "string"
+    },
+    "modelCreatedDate": {
+      "type": "string",
+      "format": "date-time"
+    },
+    "modelEntityId": {
+      "type": "string",
+      "pattern": "^AF-[0-9]{16}$"
+    },
+    "isComplex": {
+      "type": "boolean"
+    },
+    "complexName": {
+      "type": ["string", "null"]
+    },
+    "uniprotAccession": {
+      "type": ["string", "null"]
+    },
+    "uniprotId": {
+      "type": ["string", "null"]
+    },
+    "uniprotDescription": {
+      "type": ["string", "null"]
+    },
+    "gene": {
+      "type": ["string", "null"]
+    },
+    "geneSynonyms": {
+      "type": "array",
+      "items": { "type": "string" }
+    },
+    "taxId": {
+      "type": ["integer", "null"]
+    },
+    "organismScientificName": {
+      "type": ["string", "null"]
+    },
+    "organismScientificNameT": {
+      "type": ["string", "null"]
+    },
+    "organismCommonNames": {
+      "type": "array",
+      "items": { "type": "string" }
+    },
+    "organismSynonyms": {
+      "type": "array",
+      "items": { "type": "string" }
+    },
+    "assemblyType": {
+      "type": ["string", "null"],
+      "enum": ["Homo", "Hetero", null]
+    },
+    "oligomericState": {
+      "type": ["string", "null"]
+    },
+    "oligomericStateDescription": {
+      "type": ["string", "null"]
+    },
+    "sequence": {
+      "type": "string"
+    },
+    "sequenceChecksum": {
+      "type": "string",
+      "pattern": "^[a-fA-F0-9]{32}$"
+    },
+    "sequenceVersionDate": {
+      "type": ["string", "null"],
+      "format": "date-time"
+    },
+    "sequenceStart": {
+      "type": "integer",
+      "minimum": 1
+    },
+    "sequenceEnd": {
+      "type": "integer",
+      "minimum": 1
+    },
+    "isIsoform": {
+      "type": "boolean"
+    },
+    "isFragment": {
+      "type": "boolean"
+    },
+    "isUniProt": {
+      "type": "boolean"
+    },
+    "isUniProtReferenceProteome": {
+      "type": "boolean"
+    },
+    "isUniProtReviewed": {
+      "type": "boolean"
+    },
+    "globalMetricValue": {
+      "type": "number"
+    },
+    "fractionPlddtVeryLow": {
+      "type": "number"
+    },
+    "fractionPlddtLow": {
+      "type": "number"
+    },
+    "fractionPlddtConfident": {
+      "type": "number"
+    },
+    "fractionPlddtVeryHigh": {
+      "type": "number"
+    },
+    "latestVersion": {
+      "type": "integer",
+      "minimum": 1
+    },
+    "allVersions": {
+      "type": "array",
+      "items": { "type": "integer" },
+      "minItems": 1
+    },
+    "providerId": {
+      "type": "string"
+    },
+    "entityType": {
+      "type": "string"
+    },
+    "isAMdata": {
+      "type": "boolean"
+    },
+    "complexComposition": {
+      "type": ["string", "null"],
+      "pattern": "^[A-Za-z0-9-]+_[1-9][0-9]*(,[A-Za-z0-9-]+_[1-9][0-9]*)*$"
+    },
+    "_version_": {
+      "type": "integer"
+    }
+  },
+  "patternProperties": {
+    "^complexPredictionAccuracy_[A-Za-z0-9_]+$": {
+      "type": ["number", "null"]
+    }
+  },
+  "additionalProperties": false
+}