From 72e07c343c0d6336c9e423480ee1ed7b44f8f14e Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Tue, 27 Jan 2026 15:47:27 +0000 Subject: [PATCH 01/13] update fold spec --- source/_static/js/foldSpec.js | 68 ++++++++++++++++++----------------- 1 file changed, 35 insertions(+), 33 deletions(-) diff --git a/source/_static/js/foldSpec.js b/source/_static/js/foldSpec.js index 2ba4241..95fb9de 100644 --- a/source/_static/js/foldSpec.js +++ b/source/_static/js/foldSpec.js @@ -3933,7 +3933,7 @@ const foldSpec = { ], }, }, - "/api/v1/fold/{job_id}/{sequence}": { + "/api/v1/fold/{job_id}/{index}": { get: { tags: ["fold"], summary: "Retrieve protein structure", @@ -3950,12 +3950,12 @@ const foldSpec = { }, }, { - name: "sequence", + name: "index", in: "path", - description: "Sequence for which to retrieve result", + description: "Index of batch for which to retrieve result", required: true, schema: { - type: "string", + type: "number", }, }, { @@ -4065,11 +4065,11 @@ const foldSpec = { ], }, }, - "/api/v1/fold/{job_id}/complex": { + "/api/v1/fold/{job_id}/{index}/{extraKey}": { get: { tags: ["fold"], - summary: "Retrieve protein complex structure", - description: "Get protein complex structure for a submitted sequence", + summary: "Retrieve extra result", + description: "Get protein structure for a submitted sequence", parameters: [ { name: "job_id", @@ -4082,41 +4082,43 @@ const foldSpec = { }, }, { - name: "format", - in: "query", - description: - "Output format to retrieve the result in.\n\nDefaults to `pdb`. Note that requested format may not be supported for all jobs depending on when the job was created.\n", - required: false, + name: "index", + in: "path", + description: "Index of batch for which to retrieve result", + required: true, + schema: { + type: "number", + }, + }, + { + name: "extraKey", + in: "path", + description: "Extra key for extra result provided by fold model", + required: true, schema: { - title: "OutputFormat", - description: - "Output format of folded structure. Defaults to pdb.", type: "string", - enum: ["pdb", "mmcif"], - default: "pdb", + enum: [ + "pae", + "pde", + "plddt", + "ptm", + "confidence", + "affinity", + "score", + "metrics", + ], }, }, ], responses: { "200": { - description: "Result encoded in mmCIF/PDB.", + description: + "Extra result which could be a numpy array, or json, or csv.\n\npae, pde, plddt, ptm returns a .npy.\nconfidence, affinity returns a json.\nscore, metrics returns a csv.\n", content: { - "chemical/x-mmcif": { - schema: { - title: "CIFOutput", - description: "An output CIF structure file.", - type: "string", - example: - 'data_example\n#\n_entry.id example\n#\nloop_\n_entity.id\n_entity.type\n_entity.pdbx_description\n1 polymer "Example protein chain"\n#\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_entity_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\nATOM 1 N N MET A 1 1 12.011 13.456 14.789\nATOM 2 C CA MET A 1 1 13.123 14.567 15.890\nATOM 3 C C MET A 1 1 14.234 15.678 16.901\nATOM 4 O O MET A 1 1 15.345 16.789 17.012\n#\n', - }, - }, - "chemical/x-pdb": { + "application/octet-stream": { schema: { - title: "PDBOutput", - description: "An output pdb structure file.", - type: "string", - example: - "HEADER OXYGEN TRANSPORT 29-JUL-76 1HHO \nTITLE DEOXY HUMAN HEMOGLOBIN \nCOMPND MOL_ID: 1; MOLECULE: HEMOGLOBIN; CHAIN: A, B, C, D; \nSOURCE HUMAN (HOMO SAPIENS) \nKEYWDS OXYGEN TRANSPORT, HEME \nEXPDTA X-RAY DIFFRACTION \nAUTHOR F.PERUTZ,R.MATTHEWS \nREVDAT 1 24-FEB-09 1HHO 0 \nSEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR VAL LEU THR PRO GLU GLU \nSEQRES 2 A 141 LYS SER ALA GLY PHE LEU SER PRO GLU GLY ALA GLY\n", + type: "binary", + description: "Extra result as a file.", }, }, }, From e80f34b83f268ede93c0076c777dc2a9b6431fa0 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Tue, 27 Jan 2026 16:04:02 +0000 Subject: [PATCH 02/13] update design spec --- source/_static/js/designSpec.js | 372 ++++++++++++++++++++++++++++---- 1 file changed, 332 insertions(+), 40 deletions(-) diff --git a/source/_static/js/designSpec.js b/source/_static/js/designSpec.js index 78d3c97..e78553a 100644 --- a/source/_static/js/designSpec.js +++ b/source/_static/js/designSpec.js @@ -3,7 +3,7 @@ const designSpec = { info: { title: "OpenProtein Design", description: - "# Design API\nThe Design API provided by OpenProtein.ai builds on top of our predictive models to empower you to achieve your protein design goals easily. \n\nCurrently, we support the following design algorithms:\n- **Genetic Algorithm** - Evolutionary optimization for sequence design using trained `predictors`\n- **RFdiffusion** - Diffusion-based structure generation for motif scaffolding, binder design, and symmetric assemblies\n- **BoltzGen** - Advanced diffusion model for protein structure and sequence design, supporting protein-ligand complexes, multi-chain assemblies, and cyclic peptides\n", + "# Design API\nThe Design API provided by OpenProtein.ai builds on top of our predictive models to empower you to achieve your protein design goals easily. \n\nCurrently, we support the following design algorithms:\n- **Genetic Algorithm** - Evolutionary optimization for sequence design\n- **RFdiffusion** - Diffusion-based structure generation for motif scaffolding, binder design, and symmetric assemblies\n- **BoltzGen** - Advanced diffusion model for protein structure and sequence design, supporting protein-ligand complexes, multi-chain assemblies, and cyclic peptides\n", version: "1.0.0", }, paths: { @@ -1216,7 +1216,7 @@ const designSpec = { "/api/v1/designer/design/{job_id}": { get: { tags: ["design"], - summary: "Get design metadata", + summary: "Get sequence optimization design metadata", description: "Get design job metadata.\n\nThis endpoint will be used after a successful POST request.", operationId: "getDesign", @@ -1680,7 +1680,7 @@ const designSpec = { "/api/v1/designer/design/{job_id}/results": { get: { tags: ["design"], - summary: "Get design results", + summary: "Get sequence optimization design results", description: "Get design job with results if available.\n\nThis endpoint will be used after a successful POST request.", operationId: "getDesignResults", @@ -2105,7 +2105,7 @@ const designSpec = { schema: { title: "DesignRequestRFdiffusion", description: - "Request to design new structures using RFdiffusion.", + "Request to design new structures using RFdiffusion.\n\n`query_id` or `contigs` is required.\n", type: "object", properties: { n: { @@ -2117,6 +2117,13 @@ const designSpec = { example: 1, "x-order": 101, }, + query_id: { + title: "Query ID", + description: + "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or contigs should be specified.", + type: "string", + format: "uuid", + }, structure_text: { title: "Structure Text", description: "String contents of the input PDB file.", @@ -2250,6 +2257,10 @@ const designSpec = { }, }, examples: { + query: { + n: 1, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", + }, unconditional: { n: 3, contigs: "100-100", @@ -2260,8 +2271,8 @@ const designSpec = { }, }, example: { - n: 3, - contigs: "100-100", + n: 1, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", }, }, }, @@ -2512,9 +2523,9 @@ const designSpec = { "application/json": { schema: { title: "DesignRequestBoltzGen", - description: "Request to design new structures using BoltzGen.", + description: + "Request to design new structures using BoltzGen.\n\n`query_id` or `design_spec` is required.\n", type: "object", - required: ["design_spec"], properties: { n: { title: "Number of Designs", @@ -2524,11 +2535,63 @@ const designSpec = { example: 1, "x-order": 101, }, + query_id: { + title: "Query ID", + description: + "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or design_spec should be specified.", + type: "string", + format: "uuid", + }, design_spec: { - title: "Design Specification", + title: "BoltzGenDesignSpec", description: - "BoltzGen design specification defining entities and constraints.", - "x-order": 102, + "Complete BoltzGen design specification including entities and constraints.", + type: "object", + required: ["entities"], + properties: { + entities: { + title: "Entities", + description: + "List of entities in the design (proteins, ligands, or files).", + type: "array", + minItems: 1, + items: {}, + "x-order": 1, + }, + constraints: { + title: "Constraints", + description: "List of constraints for the design.", + type: "array", + nullable: true, + default: null, + items: {}, + "x-order": 2, + }, + }, + example: { + entities: [ + { + protein: { + id: "A", + sequence: "ACDEFGHIKLMNPQRSTVWY", + }, + }, + { + ligand: { + id: "B", + ccd: "ATP", + }, + }, + ], + constraints: [ + { + bond: { + atom1: ["A", 10, "CA"], + atom2: ["B", 1, "O"], + }, + }, + ], + }, }, structure_text: { title: "Structure Text", @@ -2575,6 +2638,10 @@ const designSpec = { }, }, examples: { + query: { + n: 1, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", + }, unconditional: { design_spec: { entities: [ @@ -2636,16 +2703,7 @@ const designSpec = { }, example: { n: 1, - design_spec: { - entities: [ - { - protein: { - id: "A", - sequence: "100", - }, - }, - ], - }, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", }, }, }, @@ -3042,6 +3100,124 @@ const designSpec = { ], }, }, + "/api/v1/design/{job_id}/results": { + get: { + tags: ["structure generation"], + summary: "Retrieve structure generation result", + description: "Get designed structure for a submitted design sequence", + parameters: [ + { + name: "job_id", + in: "path", + description: "Job ID to fetch", + required: true, + schema: { + type: "string", + format: "uuid", + }, + }, + { + name: "replicate", + in: "query", + description: + "Replicate index out of the `N` requested designs. Defaults to the first design.\n", + required: false, + schema: { + type: "number", + default: 0, + }, + }, + { + name: "format", + in: "query", + description: + "Output format to retrieve the result in.\n\nDefaults to `pdb`. Note that requested format may not be supported for all jobs depending on when the job was created.\n", + required: false, + schema: + ' \n\n OpenProtein API
', + }, + ], + responses: { + "200": { + description: "Result encoded in requested format.", + content: { + "chemical/x-mmcif": { + schema: + ' \n\n OpenProtein API
', + }, + "chemical/x-pdb": { + schema: + ' \n\n OpenProtein API
', + }, + }, + }, + "400": { + description: + "Result retrieval error. Contact support for assistance if persistent.", + content: { + "application/json": { + schema: { + title: "Error", + description: "A error object providing details of the error.", + required: ["detail"], + type: "object", + properties: { + detail: { + title: "Detail", + type: "string", + }, + }, + }, + }, + }, + }, + "401": { + description: + "Bad or expired token. This can happen if the token is revoked or expired. User should re-authenticate with their credentials.", + content: { + "application/json": { + schema: { + title: "Error", + description: "A error object providing details of the error.", + required: ["detail"], + type: "object", + properties: { + detail: { + title: "Detail", + type: "string", + }, + }, + }, + }, + }, + }, + "404": { + description: "Fold job not found.", + content: { + "application/json": { + schema: { + title: "Error", + description: "A error object providing details of the error.", + required: ["detail"], + type: "object", + properties: { + detail: { + title: "Detail", + type: "string", + }, + }, + }, + }, + }, + }, + }, + security: [ + { + oauth2: [], + }, + ], + }, + }, }, components: { securitySchemes: { @@ -3049,7 +3225,7 @@ const designSpec = { type: "oauth2", flows: { password: { - tokenUrl: "/api/v1/login/access-token", + tokenUrl: "/api/v1/auth/login", scopes: {}, }, }, @@ -4372,7 +4548,8 @@ const designSpec = { }, DesignRequestRFdiffusion: { title: "DesignRequestRFdiffusion", - description: "Request to design new structures using RFdiffusion.", + description: + "Request to design new structures using RFdiffusion.\n\n`query_id` or `contigs` is required.\n", type: "object", properties: { n: { @@ -4384,6 +4561,13 @@ const designSpec = { example: 1, "x-order": 101, }, + query_id: { + title: "Query ID", + description: + "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or contigs should be specified.", + type: "string", + format: "uuid", + }, structure_text: { title: "Structure Text", description: "String contents of the input PDB file.", @@ -4515,6 +4699,10 @@ const designSpec = { }, }, examples: { + query: { + n: 1, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", + }, unconditional: { n: 3, contigs: "100-100", @@ -4525,15 +4713,66 @@ const designSpec = { }, }, example: { - n: 3, - contigs: "100-100", + n: 1, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", + }, + }, + BoltzGenDesignSpec: { + title: "BoltzGenDesignSpec", + description: + "Complete BoltzGen design specification including entities and constraints.", + type: "object", + required: ["entities"], + properties: { + entities: { + title: "Entities", + description: + "List of entities in the design (proteins, ligands, or files).", + type: "array", + minItems: 1, + items: {}, + "x-order": 1, + }, + constraints: { + title: "Constraints", + description: "List of constraints for the design.", + type: "array", + nullable: true, + default: null, + items: {}, + "x-order": 2, + }, + }, + example: { + entities: [ + { + protein: { + id: "A", + sequence: "ACDEFGHIKLMNPQRSTVWY", + }, + }, + { + ligand: { + id: "B", + ccd: "ATP", + }, + }, + ], + constraints: [ + { + bond: { + atom1: ["A", 10, "CA"], + atom2: ["B", 1, "O"], + }, + }, + ], }, }, DesignRequestBoltzGen: { title: "DesignRequestBoltzGen", - description: "Request to design new structures using BoltzGen.", + description: + "Request to design new structures using BoltzGen.\n\n`query_id` or `design_spec` is required.\n", type: "object", - required: ["design_spec"], properties: { n: { title: "Number of Designs", @@ -4543,11 +4782,63 @@ const designSpec = { example: 1, "x-order": 101, }, + query_id: { + title: "Query ID", + description: + "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or design_spec should be specified.", + type: "string", + format: "uuid", + }, design_spec: { - title: "Design Specification", + title: "BoltzGenDesignSpec", description: - "BoltzGen design specification defining entities and constraints.", - "x-order": 102, + "Complete BoltzGen design specification including entities and constraints.", + type: "object", + required: ["entities"], + properties: { + entities: { + title: "Entities", + description: + "List of entities in the design (proteins, ligands, or files).", + type: "array", + minItems: 1, + items: {}, + "x-order": 1, + }, + constraints: { + title: "Constraints", + description: "List of constraints for the design.", + type: "array", + nullable: true, + default: null, + items: {}, + "x-order": 2, + }, + }, + example: { + entities: [ + { + protein: { + id: "A", + sequence: "ACDEFGHIKLMNPQRSTVWY", + }, + }, + { + ligand: { + id: "B", + ccd: "ATP", + }, + }, + ], + constraints: [ + { + bond: { + atom1: ["A", 10, "CA"], + atom2: ["B", 1, "O"], + }, + }, + ], + }, }, structure_text: { title: "Structure Text", @@ -4594,6 +4885,10 @@ const designSpec = { }, }, examples: { + query: { + n: 1, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", + }, unconditional: { design_spec: { entities: [ @@ -4655,16 +4950,7 @@ const designSpec = { }, example: { n: 1, - design_spec: { - entities: [ - { - protein: { - id: "A", - sequence: "100", - }, - }, - ], - }, + query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb", }, }, StructureGenerate: { @@ -4754,6 +5040,12 @@ const designSpec = { }, }, }, + OutputFormat: + ' \n\n OpenProtein API
', + CIFOutput: + ' \n\n OpenProtein API
', + PDBOutput: + ' \n\n OpenProtein API
', }, }, tags: [ From 17ad0ecccde405109354108fbcaa9a14f3e28bf7 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Wed, 28 Jan 2026 10:57:40 +0000 Subject: [PATCH 03/13] fix output for design results --- source/_static/js/designSpec.js | 36 +++++++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/source/_static/js/designSpec.js b/source/_static/js/designSpec.js index e78553a..81162e9 100644 --- a/source/_static/js/designSpec.js +++ b/source/_static/js/designSpec.js @@ -3142,12 +3142,22 @@ const designSpec = { description: "Result encoded in requested format.", content: { "chemical/x-mmcif": { - schema: - ' \n\n OpenProtein API
', + schema: { + title: "CIFOutput", + description: "An output CIF structure file.", + type: "string", + example: + 'data_example\n#\n_entry.id example\n#\nloop_\n_entity.id\n_entity.type\n_entity.pdbx_description\n1 polymer "Example protein chain"\n#\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_entity_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\nATOM 1 N N MET A 1 1 12.011 13.456 14.789\nATOM 2 C CA MET A 1 1 13.123 14.567 15.890\nATOM 3 C C MET A 1 1 14.234 15.678 16.901\nATOM 4 O O MET A 1 1 15.345 16.789 17.012\n#\n', + }, }, "chemical/x-pdb": { - schema: - ' \n\n OpenProtein API
', + schema: { + title: "PDBOutput", + description: "An output pdb structure file.", + type: "string", + example: + "HEADER OXYGEN TRANSPORT 29-JUL-76 1HHO \nTITLE DEOXY HUMAN HEMOGLOBIN \nCOMPND MOL_ID: 1; MOLECULE: HEMOGLOBIN; CHAIN: A, B, C, D; \nSOURCE HUMAN (HOMO SAPIENS) \nKEYWDS OXYGEN TRANSPORT, HEME \nEXPDTA X-RAY DIFFRACTION \nAUTHOR F.PERUTZ,R.MATTHEWS \nREVDAT 1 24-FEB-09 1HHO 0 \nSEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR VAL LEU THR PRO GLU GLU \nSEQRES 2 A 141 LYS SER ALA GLY PHE LEU SER PRO GLU GLY ALA GLY\n", + }, }, }, }, @@ -5042,10 +5052,20 @@ const designSpec = { }, OutputFormat: ' \n\n OpenProtein API
', - CIFOutput: - ' \n\n OpenProtein API
', - PDBOutput: - ' \n\n OpenProtein API
', + CIFOutput: { + title: "CIFOutput", + description: "An output CIF structure file.", + type: "string", + example: + 'data_example\n#\n_entry.id example\n#\nloop_\n_entity.id\n_entity.type\n_entity.pdbx_description\n1 polymer "Example protein chain"\n#\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_entity_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\nATOM 1 N N MET A 1 1 12.011 13.456 14.789\nATOM 2 C CA MET A 1 1 13.123 14.567 15.890\nATOM 3 C C MET A 1 1 14.234 15.678 16.901\nATOM 4 O O MET A 1 1 15.345 16.789 17.012\n#\n', + }, + PDBOutput: { + title: "PDBOutput", + description: "An output pdb structure file.", + type: "string", + example: + "HEADER OXYGEN TRANSPORT 29-JUL-76 1HHO \nTITLE DEOXY HUMAN HEMOGLOBIN \nCOMPND MOL_ID: 1; MOLECULE: HEMOGLOBIN; CHAIN: A, B, C, D; \nSOURCE HUMAN (HOMO SAPIENS) \nKEYWDS OXYGEN TRANSPORT, HEME \nEXPDTA X-RAY DIFFRACTION \nAUTHOR F.PERUTZ,R.MATTHEWS \nREVDAT 1 24-FEB-09 1HHO 0 \nSEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR VAL LEU THR PRO GLU GLU \nSEQRES 2 A 141 LYS SER ALA GLY PHE LEU SER PRO GLU GLY ALA GLY\n", + }, }, }, tags: [ From 43fcb0f7da0145b8f1923519fe56a8cc4df23e15 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Thu, 29 Jan 2026 11:46:01 +0000 Subject: [PATCH 04/13] fix output format --- source/_static/js/designSpec.js | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/source/_static/js/designSpec.js b/source/_static/js/designSpec.js index 81162e9..6dbfbde 100644 --- a/source/_static/js/designSpec.js +++ b/source/_static/js/designSpec.js @@ -3123,7 +3123,7 @@ const designSpec = { "Replicate index out of the `N` requested designs. Defaults to the first design.\n", required: false, schema: { - type: "number", + type: "integer", default: 0, }, }, @@ -3133,8 +3133,14 @@ const designSpec = { description: "Output format to retrieve the result in.\n\nDefaults to `pdb`. Note that requested format may not be supported for all jobs depending on when the job was created.\n", required: false, - schema: - ' \n\n OpenProtein API
', + schema: { + title: "OutputFormat", + description: + "Output format of folded structure. Defaults to pdb.", + type: "string", + enum: ["pdb", "mmcif"], + default: "pdb", + }, }, ], responses: { @@ -5050,8 +5056,13 @@ const designSpec = { }, }, }, - OutputFormat: - ' \n\n OpenProtein API
', + OutputFormat: { + title: "OutputFormat", + description: "Output format of folded structure. Defaults to pdb.", + type: "string", + enum: ["pdb", "mmcif"], + default: "pdb", + }, CIFOutput: { title: "CIFOutput", description: "An output CIF structure file.", From d165716e12f4c1e26ef96e9b1a3ab17c3f62b66e Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Fri, 30 Jan 2026 10:42:02 -0500 Subject: [PATCH 05/13] update rfdiffusion binder design tutorial to use templates --- pixi.lock | 321 ++++++++++++++++-- pyproject.toml | 2 +- ...otein_binder_design_with_RFdiffusion.ipynb | 41 ++- 3 files changed, 311 insertions(+), 53 deletions(-) diff --git a/pixi.lock b/pixi.lock index 266e66d..3722b20 100644 --- a/pixi.lock +++ b/pixi.lock @@ -591,7 +591,7 @@ environments: - pypi: https://files.pythonhosted.org/packages/b1/92/dfd892312d822f36c55366118b95d914e5f16de11044a27cf10a7d71bbbf/commonmark-0.9.1-py2.py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/04/5f/9ff93450ba96b09c7c2b3f81c94de31c89f92292f1380261bd7195bea4ea/contourpy-1.3.3-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl - 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pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl name: webencodings version: 0.5.1 @@ -3531,6 +3781,15 @@ packages: - pytest>=6.0.0 ; extra == 'test' - setuptools>=65 ; extra == 'test' requires_python: '>=3.8' +- pypi: https://files.pythonhosted.org/packages/87/22/b76d483683216dde3d67cba61fb2444be8d5be289bf628c13fc0fd90e5f9/wheel-0.46.3-py3-none-any.whl + name: wheel + version: 0.46.3 + sha256: 4b399d56c9d9338230118d705d9737a2a468ccca63d5e813e2a4fc7815d8bc4d + requires_dist: + - packaging>=24.0 + - pytest>=6.0.0 ; extra == 'test' + - setuptools>=77 ; extra == 'test' + requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7 md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829 diff --git a/pyproject.toml b/pyproject.toml index 834c1e9..6a5632b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ dev = [ nb = [ "molviewspec", "ipykernel", - # "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private.git@6e6214088bee247f20f72afe0bec4e8f686f08d9", + "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private.git@f2bd23a05b917c7e6edccd86a624f2f6cbb9f2a1", "seaborn", "scipy", ] diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb index 1ae9b9c..8dcf67a 100644 --- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb +++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb @@ -1312,18 +1312,14 @@ "\n", "Typically, to validate *in silico* binder designs, we predict the target-binder complex\n", "structure and check for consistency with the original designed structure and binding\n", - "interface. Because the structure of the target is known, but the binder structure is\n", + "interface. Because the structure of the target is known, but the binder structure is\n", "not, we usually run structure prediction in single sequence mode for both the binder and\n", "target sequences using only the target structure as a template. _Single sequence mode_\n", "means that no multiple sequence alignment is used for the binder. This is important to\n", "efficiently screen large numbers of binder designs where homology search is a bottleneck.\n", "\n", - "However, because we do support templates yet (coming soon!), in this tutorial we'll\n", - "use an MSA for the target instead of a template; this generally achieves the same\n", - "objective, allowing the model to accurately recapitulate the target's known structure.\n", - "\n", - "Below, we compute an MSA for the target, and use it to predict the structure of all\n", - "designed sequences; this generally takes about 50 minutes." + "Below, we apply this approach to predict the structures of all designed sequences; this\n", + "generally takes about 50 minutes." ] }, { @@ -1348,29 +1344,28 @@ } ], "source": [ - "# 1. Compute MSA for target to use for folding\n", - "target_msa = session.align.create_msa(target.sequence)\n", - "\n", - "# 2. Create the complexes to fold\n", + "# 1. Create the complexes to fold\n", "complexes_to_fold = []\n", "for i, generated_structure in enumerate(generated_structures): # for each structure\n", " for j in range(N_SEQS_PER_STRUCTURE):\n", " designed_binder_sequence = df.loc[(i, j)][\"sequence\"]\n", + " # 1a. Create the complex to fold, containing the target sequence and designed\n", + " # binder sequence\n", " complex = Complex(\n", " {\"A\": Protein(target.sequence), \"B\": Protein(designed_binder_sequence)}\n", " )\n", - " # set MSAs to use for structure prediction\n", - " # note that `binder.msa = Protein.single_sequence_mode` needs to be set\n", - " # explicitly when running structure prediction without MSAs\n", - " complex.get_protein(chain_id=\"A\").msa = target_msa\n", + " # 1b. Set both the target MSA and the binder MSA to single sequence mode\n", + " complex.get_protein(chain_id=\"A\").msa = Protein.single_sequence_mode\n", " complex.get_protein(chain_id=\"B\").msa = Protein.single_sequence_mode\n", + " # 1c. Set the known target structure as a template for the target only\n", + " complex.get_protein(chain_id=\"A\").templates = [target]\n", " complexes_to_fold.append(complex)\n", "\n", - "# 3. Create the job\n", + "# 2. Create the job\n", "fold_job = session.fold.boltz_2.fold(complexes_to_fold)\n", "print(fold_job)\n", "\n", - "# 4. Wait for the job to finish\n", + "# 3. Wait for the job to finish\n", "_ = fold_job.wait_until_done(verbose=True)" ] }, @@ -1945,7 +1940,7 @@ }, { "cell_type": "code", - "execution_count": 47, + "execution_count": null, "id": "3816751b", "metadata": {}, "outputs": [ @@ -1974,7 +1969,9 @@ ], "source": [ "# get predicted and generated structure of top design\n", - "design_idx, structure_idx = 263, 26\n", + "design_idx, structure_idx = df_selected.reset_index().iloc[0][\n", + " [\"design_idx\", \"structure_idx\"]\n", + "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", "# superimpose predicted structure on the generate structure\n", @@ -2016,7 +2013,7 @@ }, { "cell_type": "code", - "execution_count": 48, + "execution_count": null, "id": "87fde147", "metadata": {}, "outputs": [ @@ -2045,7 +2042,9 @@ ], "source": [ "# get predicted and generated structure of top sixth design\n", - "design_idx, structure_idx = 530, 53\n", + "design_idx, structure_idx = df_selected.reset_index().iloc[5][\n", + " [\"design_idx\", \"structure_idx\"]\n", + "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", "# superimpose predicted structure on the generate structure\n", From 8c77b5639ea6b765eed31fd771784130290dd267 Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Fri, 30 Jan 2026 10:44:57 -0500 Subject: [PATCH 06/13] update boltzgen binder design tutorial to use templates --- ...Nanobody_binder_design_with_BoltzGen.ipynb | 31 ++++++++----------- 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index c168d92..404fe46 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -890,23 +890,19 @@ "\n", "Typically, to validate *in silico* binder designs, we predict the target-binder complex\n", "structure and check for consistency with the original designed structure and binding\n", - "interface. Because the structure of the target is known, but the binder structure is\n", + "interface. Because the structure of the target is known, but the binder structure is\n", "not, we usually run structure prediction in single sequence mode for both the binder and\n", "target sequences using only the target structure as a template. _Single sequence mode_\n", "means that no multiple sequence alignment is used for the binder. This is important to\n", "efficiently screen large numbers of binder designs where homology search is a bottleneck.\n", "\n", - "However, because we do support templates yet (coming soon!), in this tutorial we'll\n", - "use an MSA for the target instead of a template; this generally achieves the same\n", - "objective, allowing the model to accurately recapitulate the target's known structure.\n", - "\n", - "Below, we compute an MSA for the target, and use it to predict the structure of all\n", - "designed sequences; this generally takes about 50 minutes." + "Below, we apply this approach to predict the structures of all designed sequences; this\n", + "generally takes about 50 minutes." ] }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "id": "78ea020d", "metadata": {}, "outputs": [ @@ -926,29 +922,28 @@ } ], "source": [ - "# 1. Compute MSA for target to use for folding\n", - "target_msa = session.align.create_msa(target.sequence)\n", - "\n", - "# 2. Create the complexes to fold\n", + "# 1. Create the complexes to fold\n", "complexes_to_fold = []\n", "for i, generated_structure in enumerate(generated_structures): # for each structure\n", " for j in range(N_SEQS_PER_STRUCTURE):\n", " designed_binder_sequence = df.loc[(i, j)][\"sequence\"]\n", + " # 1a. Create the complex to fold, containing the target sequence and designed\n", + " # binder sequence\n", " complex = Complex(\n", " {\"A\": Protein(target.sequence), \"B\": Protein(designed_binder_sequence)}\n", " )\n", - " # set MSAs to use for structure prediction\n", - " # note that `binder.msa = Protein.single_sequence_mode` needs to be set\n", - " # explicitly when running structure prediction without MSAs\n", - " complex.get_protein(chain_id=\"A\").msa = target_msa\n", + " # 1b. Set both the target MSA and the binder MSA to single sequence mode\n", + " complex.get_protein(chain_id=\"A\").msa = Protein.single_sequence_mode\n", " complex.get_protein(chain_id=\"B\").msa = Protein.single_sequence_mode\n", + " # 1c. Set the known target structure as a template for the target only\n", + " complex.get_protein(chain_id=\"A\").templates = [target]\n", " complexes_to_fold.append(complex)\n", "\n", - "# 3. Create the job\n", + "# 2. Create the job\n", "fold_job = session.fold.boltz_2.fold(complexes_to_fold)\n", "print(fold_job)\n", "\n", - "# 4. Wait for the job to finish\n", + "# 3. Wait for the job to finish\n", "_ = fold_job.wait_until_done(verbose=True)" ] }, From 3bac907c9fb99e976c0baa0a6d595151ea367f68 Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Fri, 30 Jan 2026 10:45:42 -0500 Subject: [PATCH 07/13] update minimum python version requirement in prereqs sections --- source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb | 2 +- .../Protein_protein_binder_design_with_RFdiffusion.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index 404fe46..48a3cba 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -33,7 +33,7 @@ "To run this tutorial, you'll need a Python environment containing the following\n", "packages:\n", "\n", - "- `openprotein_python>=0.10.1`\n", + "- `openprotein_python>=0.10.2`\n", "- `molviewspec` (for structure visualization)\n", "\n", "See the Python client [installation instructions](../python-api/installation.html) for more info.\n", diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb index 8dcf67a..48297c7 100644 --- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb +++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb @@ -38,7 +38,7 @@ "To run this tutorial, you'll need a Python environment containing the following\n", "packages:\n", "\n", - "- `openprotein_python>=0.10`\n", + "- `openprotein_python>=0.10.2`\n", "- `molviewspec` (for structure visualization)\n", "\n", "See the Python client [installation instructions](../python-api/installation.html) for more info.\n", From 24e74d8c1e171a9fb49bfe280d08a8aaf04adde4 Mon Sep 17 00:00:00 2001 From: Timothy Fei Truong Jr Date: Sat, 31 Jan 2026 11:18:44 -0500 Subject: [PATCH 08/13] update success rate when using template over msa --- .../Nanobody_binder_design_with_BoltzGen.ipynb | 8 ++++---- .../Protein_protein_binder_design_with_RFdiffusion.ipynb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index 48a3cba..8c47afa 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -1276,8 +1276,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "# designs passing filters 250\n", - "# unique structures passing filters 77\n" + "# designs passing filters 146\n", + "# unique structures passing filters 48\n" ] } ], @@ -1479,7 +1479,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", @@ -1544,7 +1544,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb index 48297c7..feb6305 100644 --- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb +++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb @@ -1715,8 +1715,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "# designs passing filters 279\n", - "# unique structures passing filters 65\n" + "# designs passing filters 253\n", + "# unique structures passing filters 58\n" ] } ], @@ -1974,7 +1974,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", @@ -2047,7 +2047,7 @@ "]\n", "predicted_structure = predicted_structures[design_idx]\n", "generated_structure = generated_structures[structure_idx]\n", - "# superimpose predicted structure on the generate structure\n", + "# superimpose predicted structure on the generated structure\n", "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n", "# visualize\n", "visualize_cif(\n", From ebf05ca02390e51bfee2b0a137173acc8155b0df Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Fri, 6 Feb 2026 01:27:25 +0000 Subject: [PATCH 09/13] Update required package version for tutorial --- source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb index 8c47afa..4a0764d 100644 --- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb +++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb @@ -33,7 +33,7 @@ "To run this tutorial, you'll need a Python environment containing the following\n", "packages:\n", "\n", - "- `openprotein_python>=0.10.2`\n", + "- `openprotein_python>=0.11.0`\n", "- `molviewspec` (for structure visualization)\n", "\n", "See the Python client [installation instructions](../python-api/installation.html) for more info.\n", From 5906d37bc532b8e6397ed933fd0ac89b865ae421 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Fri, 6 Feb 2026 01:28:28 +0000 Subject: [PATCH 10/13] Update openprotein-python version in pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6a5632b..5980e12 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ dependencies = [ "sphinx-notfound-page>=1.1.0,<1.2.0", "sphinx-design>=0.6.1,<0.7", # autodoc - "openprotein-python>=0.10.0,<0.11.0", + "openprotein-python>=0.11.0,<0.12.0", "ipython>=9.8.0,<10", ] From 1a5754515823162ce034cce834c420d27543897b Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Fri, 6 Feb 2026 01:37:52 +0000 Subject: [PATCH 11/13] update lock --- pixi.lock | 404 ++++++++++--------------------------------------- pyproject.toml | 16 +- 2 files changed, 90 insertions(+), 330 deletions(-) diff --git a/pixi.lock b/pixi.lock index 3722b20..335ba91 100644 --- a/pixi.lock +++ b/pixi.lock @@ -39,7 +39,7 @@ environments: - 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