From e58c978e0cbd6a104200080467170f29d49b80f0 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Fri, 15 Sep 2023 01:55:30 +0100 Subject: [PATCH] Avoid duplicate 0.3 .. as it is now archived at https://github.com/trefx/trefx.github.io/tree/main/trusted-wfrun-crate/0.3 --- 0.3/example-hutch/bag-info.txt | 1 - 0.3/example-hutch/bagit.txt | 2 - 0.3/example-hutch/data/hutch_cwl.wfex.stage | 24 - ...6-623e-492c-a135-8f247395d1df_workflow.cwl | 202 --- .../workflows/rquest-oneshot.cwl | 53 - .../workflows/sec-hutch.cwl | 202 --- .../containers/docker.io_node:slim.img | 3 - .../pszdldocker_rquest-oneshot:latest.img | 3 - .../results/outputs/_1683122029/output.json | 1 - .../data/results/ro-crate-metadata.json | 465 ------ .../data/results/ro-crate-preview.html | 191 --- 0.3/example-hutch/data/ro-crate-metadata.json | 456 ------ 0.3/example-hutch/data/ro-crate-preview.html | 1158 ------------- 0.3/example-hutch/data/rquest-query.json | 10 - 0.3/example-hutch/manifest-sha512.txt | 12 - 0.3/example-hutch/tagmanifest-sha512.txt | 3 - 0.3/example-request.bagit.zip | Bin 8831 -> 0 bytes 0.3/example-request/bag-info.txt | 1 - 0.3/example-request/bagit.txt | 2 - 0.3/example-request/data/index.html | 446 ----- 0.3/example-request/data/input1.txt | 3 - .../data/ro-crate-metadata.json | 160 -- .../data/ro-crate-preview.html | 446 ----- 0.3/example-request/manifest-sha512.txt | 4 - 0.3/example-request/tagmanifest-sha512.txt | 3 - 0.3/example-result.bagit.zip | Bin 73671 -> 0 bytes 0.3/example-result/bag-info.txt | 1 - 0.3/example-result/bagit.txt | 2 - 0.3/example-result/data/index.html | 1109 ------------- 0.3/example-result/data/input1.txt | 3 - .../data/outputs/diagrams/.keep | 0 0.3/example-result/data/outputs/qa.csv | 4 - .../data/ro-crate-metadata.json | 392 ----- 0.3/example-result/data/ro-crate-preview.html | 1109 ------------- .../data/workflow/289/README.md | 36 - 0.3/example-result/data/workflow/289/ions.pdb | 1 - .../data/workflow/289/ro-crate-metadata.json | 800 --------- .../data/workflow/289/ro-crate-preview.html | 977 ----------- .../data/workflow/289/structure.pdb | 1436 ----------------- ...458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg | 938 ----------- .../data/workflow/289/workflow.cwl | 359 ----- .../data/workflow/289/workflow_gather.cwl | 32 - .../289/workflow_input_descriptions.yml | 76 - .../data/workflow/289/workflow_list.cwl | 435 ----- 0.3/example-result/manifest-sha512.txt | 16 - 0.3/example-result/tagmanifest-sha512.txt | 3 - 0.3/index.html | 12 + 0.3/index.md | 755 --------- 0.3/ro-crate-metadata.json | 461 ------ 0.3/ro-crate-metadata.jsonld | 1 - 0.3/ro-crate-preview.html | 1312 --------------- 51 files changed, 12 insertions(+), 14109 deletions(-) delete mode 100644 0.3/example-hutch/bag-info.txt delete mode 100644 0.3/example-hutch/bagit.txt delete mode 100644 0.3/example-hutch/data/hutch_cwl.wfex.stage delete mode 100644 0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/2ef7f736-623e-492c-a135-8f247395d1df_workflow.cwl delete mode 100644 0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/rquest-oneshot.cwl delete mode 100644 0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl delete mode 100755 0.3/example-hutch/data/results/containers/docker.io_node:slim.img delete mode 100755 0.3/example-hutch/data/results/containers/pszdldocker_rquest-oneshot:latest.img delete mode 100644 0.3/example-hutch/data/results/outputs/_1683122029/output.json delete mode 100644 0.3/example-hutch/data/results/ro-crate-metadata.json delete mode 100644 0.3/example-hutch/data/results/ro-crate-preview.html delete mode 100644 0.3/example-hutch/data/ro-crate-metadata.json delete mode 100644 0.3/example-hutch/data/ro-crate-preview.html delete mode 100644 0.3/example-hutch/data/rquest-query.json delete mode 100644 0.3/example-hutch/manifest-sha512.txt delete mode 100644 0.3/example-hutch/tagmanifest-sha512.txt delete mode 100644 0.3/example-request.bagit.zip delete mode 100644 0.3/example-request/bag-info.txt delete mode 100644 0.3/example-request/bagit.txt delete mode 100644 0.3/example-request/data/index.html delete mode 100644 0.3/example-request/data/input1.txt delete mode 100644 0.3/example-request/data/ro-crate-metadata.json delete mode 100644 0.3/example-request/data/ro-crate-preview.html delete mode 100644 0.3/example-request/manifest-sha512.txt delete mode 100644 0.3/example-request/tagmanifest-sha512.txt delete mode 100644 0.3/example-result.bagit.zip delete mode 100644 0.3/example-result/bag-info.txt delete mode 100644 0.3/example-result/bagit.txt delete mode 100644 0.3/example-result/data/index.html delete mode 100644 0.3/example-result/data/input1.txt delete mode 100644 0.3/example-result/data/outputs/diagrams/.keep delete mode 100644 0.3/example-result/data/outputs/qa.csv delete mode 100644 0.3/example-result/data/ro-crate-metadata.json delete mode 100644 0.3/example-result/data/ro-crate-preview.html delete mode 100644 0.3/example-result/data/workflow/289/README.md delete mode 100644 0.3/example-result/data/workflow/289/ions.pdb delete mode 100644 0.3/example-result/data/workflow/289/ro-crate-metadata.json delete mode 100644 0.3/example-result/data/workflow/289/ro-crate-preview.html delete mode 100644 0.3/example-result/data/workflow/289/structure.pdb delete mode 100644 0.3/example-result/data/workflow/289/workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg delete mode 100644 0.3/example-result/data/workflow/289/workflow.cwl delete mode 100644 0.3/example-result/data/workflow/289/workflow_gather.cwl delete mode 100644 0.3/example-result/data/workflow/289/workflow_input_descriptions.yml delete mode 100644 0.3/example-result/data/workflow/289/workflow_list.cwl delete mode 100644 0.3/example-result/manifest-sha512.txt delete mode 100644 0.3/example-result/tagmanifest-sha512.txt create mode 100644 0.3/index.html delete mode 100644 0.3/index.md delete mode 100644 0.3/ro-crate-metadata.json delete mode 120000 0.3/ro-crate-metadata.jsonld delete mode 100644 0.3/ro-crate-preview.html diff --git a/0.3/example-hutch/bag-info.txt b/0.3/example-hutch/bag-info.txt deleted file mode 100644 index 2cda881..0000000 --- a/0.3/example-hutch/bag-info.txt +++ /dev/null @@ -1 +0,0 @@ -External-Identifier: urn:uuid:43b74460-cdec-4be4-aab5-1dd77ed61c50 diff --git a/0.3/example-hutch/bagit.txt b/0.3/example-hutch/bagit.txt deleted file mode 100644 index c679299..0000000 --- a/0.3/example-hutch/bagit.txt +++ /dev/null @@ -1,2 +0,0 @@ -BagIt-version: 1.0 -Tag-File-Character-Encoding: UTF-8 diff --git a/0.3/example-hutch/data/hutch_cwl.wfex.stage b/0.3/example-hutch/data/hutch_cwl.wfex.stage deleted file mode 100644 index 9df3d46..0000000 --- a/0.3/example-hutch/data/hutch_cwl.wfex.stage +++ /dev/null @@ -1,24 +0,0 @@ -workflow_id: https://raw.githubusercontent.com/HDRUK/hutch/main/workflows/sec-hutchx86.cwl -workflow_config: - container: 'docker' - secure: false -nickname: 'vas-workflow' -cacheDir: /tmp/wfexszn6siq2jtmpcache -crypt4gh: - key: cosifer_test1_cwl.wfex.stage.key - passphrase: mpel nite ified g - pub: cosifer_test1_cwl.wfex.stage.pub -outputs: - output_file: - c-l-a-s-s: File - glob: "output.json" -params: - body: - c-l-a-s-s: File - url: - - https://raw.githubusercontent.com/HDRUK/hutch/main/workflows/inputs/rquest-query.json - is_availability: true - db_host: "localhost" - db_name: "hutch" - db_user: "postgres" - db_password: "example" diff --git a/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/2ef7f736-623e-492c-a135-8f247395d1df_workflow.cwl b/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/2ef7f736-623e-492c-a135-8f247395d1df_workflow.cwl deleted file mode 100644 index 8c48d07..0000000 --- a/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/2ef7f736-623e-492c-a135-8f247395d1df_workflow.cwl +++ /dev/null @@ -1,202 +0,0 @@ -{ - "$graph": [ - { - "class": "CommandLineTool", - "id": "#rquest-oneshot.cwl", - "label": "rquest-oneshot", - "hints": [ - { - "dockerPull": "pszdldocker/rquest-oneshot:latest", - "class": "DockerRequirement" - } - ], - "requirements": [ - { - "envDef": [ - { - "envValue": "$(inputs.db_name)", - "envName": "DATASOURCE_DB_DATABASE" - }, - { - "envValue": "$(inputs.db_host)", - "envName": "DATASOURCE_DB_HOST" - }, - { - "envValue": "$(inputs.db_password)", - "envName": "DATASOURCE_DB_PASSWORD" - }, - { - "envValue": "$(inputs.db_user)", - "envName": "DATASOURCE_DB_USERNAME" - } - ], - "class": "EnvVarRequirement" - } - ], - "baseCommand": [ - "rquest-omop-agent" - ], - "inputs": [ - { - "type": "string", - "inputBinding": { - "position": 1, - "prefix": "--body" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/body" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_host" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_name" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_password" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_user" - }, - { - "type": "boolean", - "inputBinding": { - "position": 3, - "prefix": "-a" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/is_availability" - }, - { - "type": [ - "null", - "string" - ], - "inputBinding": { - "position": 2, - "prefix": "-m" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/result_modifiers" - }, - { - "type": [ - "null", - "string" - ], - "inputBinding": { - "position": 4, - "prefix": "-o" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/results" - } - ], - "outputs": [ - { - "type": "File", - "outputBinding": { - "glob": "output.json" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/output_file" - } - ] - }, - { - "class": "Workflow", - "id": "#main", - "label": "hutch-workflow", - "inputs": [ - { - "type": "string", - "id": "#main/body" - }, - { - "type": "string", - "id": "#main/db_host" - }, - { - "type": "string", - "id": "#main/db_name" - }, - { - "type": "string", - "id": "#main/db_password" - }, - { - "type": "string", - "id": "#main/db_user" - }, - { - "type": "boolean", - "id": "#main/is_availability" - }, - { - "type": [ - "null", - "string" - ], - "id": "#main/result_modifiers" - }, - { - "type": [ - "null", - "string" - ], - "id": "#main/results" - } - ], - "outputs": [ - { - "type": "File", - "outputSource": "#main/rquest_oneshot/output_file", - "id": "#main/output_file" - } - ], - "steps": [ - { - "run": "#rquest-oneshot.cwl", - "in": [ - { - "source": "#main/body", - "id": "#main/rquest_oneshot/body" - }, - { - "source": "#main/db_host", - "id": "#main/rquest_oneshot/db_host" - }, - { - "source": "#main/db_name", - "id": "#main/rquest_oneshot/db_name" - }, - { - "source": "#main/db_password", - "id": "#main/rquest_oneshot/db_password" - }, - { - "source": "#main/db_user", - "id": "#main/rquest_oneshot/db_user" - }, - { - "source": "#main/is_availability", - "id": "#main/rquest_oneshot/is_availability" - }, - { - "source": "#main/result_modifiers", - "id": "#main/rquest_oneshot/result_modifiers" - }, - { - "source": "#main/results", - "id": "#main/rquest_oneshot/results" - } - ], - "out": [ - "#main/rquest_oneshot/output_file" - ], - "id": "#main/rquest_oneshot" - } - ] - } - ], - "cwlVersion": "v1.0" -} diff --git a/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/rquest-oneshot.cwl b/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/rquest-oneshot.cwl deleted file mode 100644 index f4027f9..0000000 --- a/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/rquest-oneshot.cwl +++ /dev/null @@ -1,53 +0,0 @@ -cwlVersion: v1.0 -class: CommandLineTool -id: rquest-oneshot -label: rquest-oneshot - -hints: - DockerRequirement: - dockerPull: pszdldocker/rquest-oneshot:latest - -requirements: - EnvVarRequirement: - envDef: - DATASOURCE_DB_HOST: $(inputs.db_host) - DATASOURCE_DB_DATABASE: $(inputs.db_name) - DATASOURCE_DB_USERNAME: $(inputs.db_user) - DATASOURCE_DB_PASSWORD: $(inputs.db_password) - -baseCommand: [rquest-omop-agent] -inputs: - body: - type: string - inputBinding: - position: 1 - prefix: --body - result_modifiers: - type: string? - inputBinding: - position: 2 - prefix: -m - is_availability: - type: boolean - inputBinding: - position: 3 - prefix: -a - results: - type: string? - inputBinding: - position: 4 - prefix: -o - db_host: - type: string - db_name: - type: string - db_user: - type: string - db_password: - type: string - -outputs: - output_file: - type: File - outputBinding: - glob: "output.json" diff --git a/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl b/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl deleted file mode 100644 index 8c48d07..0000000 --- a/0.3/example-hutch/data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl +++ /dev/null @@ -1,202 +0,0 @@ -{ - "$graph": [ - { - "class": "CommandLineTool", - "id": "#rquest-oneshot.cwl", - "label": "rquest-oneshot", - "hints": [ - { - "dockerPull": "pszdldocker/rquest-oneshot:latest", - "class": "DockerRequirement" - } - ], - "requirements": [ - { - "envDef": [ - { - "envValue": "$(inputs.db_name)", - "envName": "DATASOURCE_DB_DATABASE" - }, - { - "envValue": "$(inputs.db_host)", - "envName": "DATASOURCE_DB_HOST" - }, - { - "envValue": "$(inputs.db_password)", - "envName": "DATASOURCE_DB_PASSWORD" - }, - { - "envValue": "$(inputs.db_user)", - "envName": "DATASOURCE_DB_USERNAME" - } - ], - "class": "EnvVarRequirement" - } - ], - "baseCommand": [ - "rquest-omop-agent" - ], - "inputs": [ - { - "type": "string", - "inputBinding": { - "position": 1, - "prefix": "--body" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/body" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_host" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_name" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_password" - }, - { - "type": "string", - "id": "#rquest-oneshot.cwl/rquest-oneshot/db_user" - }, - { - "type": "boolean", - "inputBinding": { - "position": 3, - "prefix": "-a" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/is_availability" - }, - { - "type": [ - "null", - "string" - ], - "inputBinding": { - "position": 2, - "prefix": "-m" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/result_modifiers" - }, - { - "type": [ - "null", - "string" - ], - "inputBinding": { - "position": 4, - "prefix": "-o" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/results" - } - ], - "outputs": [ - { - "type": "File", - "outputBinding": { - "glob": "output.json" - }, - "id": "#rquest-oneshot.cwl/rquest-oneshot/output_file" - } - ] - }, - { - "class": "Workflow", - "id": "#main", - "label": "hutch-workflow", - "inputs": [ - { - "type": "string", - "id": "#main/body" - }, - { - "type": "string", - "id": "#main/db_host" - }, - { - "type": "string", - "id": "#main/db_name" - }, - { - "type": "string", - "id": "#main/db_password" - }, - { - "type": "string", - "id": "#main/db_user" - }, - { - "type": "boolean", - "id": "#main/is_availability" - }, - { - "type": [ - "null", - "string" - ], - "id": "#main/result_modifiers" - }, - { - "type": [ - "null", - "string" - ], - "id": "#main/results" - } - ], - "outputs": [ - { - "type": "File", - "outputSource": "#main/rquest_oneshot/output_file", - "id": "#main/output_file" - } - ], - "steps": [ - { - "run": "#rquest-oneshot.cwl", - "in": [ - { - "source": "#main/body", - "id": "#main/rquest_oneshot/body" - }, - { - "source": "#main/db_host", - "id": "#main/rquest_oneshot/db_host" - }, - { - "source": "#main/db_name", - "id": "#main/rquest_oneshot/db_name" - }, - { - "source": "#main/db_password", - "id": "#main/rquest_oneshot/db_password" - }, - { - "source": "#main/db_user", - "id": "#main/rquest_oneshot/db_user" - }, - { - "source": "#main/is_availability", - "id": "#main/rquest_oneshot/is_availability" - }, - { - "source": "#main/result_modifiers", - "id": "#main/rquest_oneshot/result_modifiers" - }, - { - "source": "#main/results", - "id": "#main/rquest_oneshot/results" - } - ], - "out": [ - "#main/rquest_oneshot/output_file" - ], - "id": "#main/rquest_oneshot" - } - ] - } - ], - "cwlVersion": "v1.0" -} diff --git a/0.3/example-hutch/data/results/containers/docker.io_node:slim.img b/0.3/example-hutch/data/results/containers/docker.io_node:slim.img deleted file mode 100755 index c79bf6a..0000000 --- a/0.3/example-hutch/data/results/containers/docker.io_node:slim.img +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:a668dae09826000e6b99c2150fa5b66ad89210a5c64df58f2687520209397dd8 -size 68149248 diff --git a/0.3/example-hutch/data/results/containers/pszdldocker_rquest-oneshot:latest.img b/0.3/example-hutch/data/results/containers/pszdldocker_rquest-oneshot:latest.img deleted file mode 100755 index 9b22c4e..0000000 --- a/0.3/example-hutch/data/results/containers/pszdldocker_rquest-oneshot:latest.img +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:bbf3f03f36facc8a147dee8dc00d218e6ee3467aa912ff05ecd675ac38a7efe2 -size 340389888 diff --git a/0.3/example-hutch/data/results/outputs/_1683122029/output.json b/0.3/example-hutch/data/results/outputs/_1683122029/output.json deleted file mode 100644 index 78e5a9a..0000000 --- a/0.3/example-hutch/data/results/outputs/_1683122029/output.json +++ /dev/null @@ -1 +0,0 @@ -{"status": "ok", "protocolVersion": "v2", "uuid": "bf413750-21c5-4382-95f5-45c616b25013", "queryResult": {"count": 6272, "datasetCount": 0, "files": []}, "message": null, "collection_id": "RQ-CC-d3d61136-05bb-4388-8aa6-31c54e0c5735"} \ No newline at end of file diff --git a/0.3/example-hutch/data/results/ro-crate-metadata.json b/0.3/example-hutch/data/results/ro-crate-metadata.json deleted file mode 100644 index 82b5f3b..0000000 --- a/0.3/example-hutch/data/results/ro-crate-metadata.json +++ /dev/null @@ -1,465 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.1/context", - "@graph": [ - { - "@id": "ro-crate-preview.html", - "@type": "CreativeWork", - "about": { - "@id": "./" - } - }, - { - "@id": "./", - "@type": "Dataset", - "conformsTo": [ - { - "@id": "https://w3id.org/ro/wfrun/process/0.1" - }, - { - "@id": "https://w3id.org/ro/wfrun/workflow/0.1" - }, - { - "@id": "https://w3id.org/ro/wfrun/provenance/0.1" - }, - { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - } - ], - "datePublished": "2023-05-11T09:10:56+00:00", - "hasPart": [ - { - "@id": "b5b59d4f-9797-5179-a131-e7089e943988/2ef7f736-623e-492c-a135-8f247395d1df_workflow.cwl" - }, - { - "@id": "containers/pszdldocker_rquest-oneshot:latest.img" - }, - { - "@id": "containers/docker.io_node:slim.img" - }, - { - "@id": "b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl" - }, - { - "@id": "b5b59d4f-9797-5179-a131-e7089e943988/workflows/rquest-oneshot.cwl" - }, - { - "@id": "outputs/_1683122029/output.json" - } - ], - "mainEntity": { - 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- - \ No newline at end of file diff --git a/0.3/example-hutch/data/ro-crate-metadata.json b/0.3/example-hutch/data/ro-crate-metadata.json deleted file mode 100644 index e7e1b6e..0000000 --- a/0.3/example-hutch/data/ro-crate-metadata.json +++ /dev/null @@ -1,456 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context", - "@graph": [ - { - "@type": "CreativeWork", - "@id": "ro-crate-metadata.json", - "about": { - "@id": "./" - }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.2-DRAFT" - } - }, - { - "@id": "./", - "@type": "Dataset", - "conformsTo": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "datePublished": "2023-04-24T09:56:15+00:00", - "hasPart": [ - { - "@id": "https://workflowhub.eu/workflows/471?version=1" - }, - { - "@id": "rqeuest-query.json" - }, - { - "@id": "hutch_cwl.wfex.stage" - }, - { - "@id": "results/" - }, - { - "@id": "results/outputs/_1683122029/output.json" - } - ], - "mainEntity": { - "@id": "https://workflowhub.eu/workflows/471?version=1" - }, - "mentions": [ - { - "@id": "#execute-43a74be3-c175-4fe6-a13d-b9f0dca3c0fc" - }, - { - "@id": "#check-4445b5a3-38f0-47e1-b3bd-a2693743b071" - }, - { - "@id": "#validate-6e4298fe-a0fe-45f7-ac9a-bec41ec0643f" - }, - { - "@id": "#signoff-00863632-4a12-45ab-be86-f896a670db39" - }, - { - "@id": "#disclosure-7ce35566-28f3-4e8d-aa4e-e1ac7d1344af" - }, - { - "@id": "#bagit-7a89e9e1-ba5c-4fef-96f6-0a4d53aad0d8" - } - ], - "sourceOrganization": { - "@id": "#project-065c9577-dd40-4cb2-bbc7-354e34ef37de" - }, - "publisher": { - "@id": "https://trefx.example.com/" - }, - "licence": { - "@id": "http://spdx.org/licenses/MIT" - } - }, - { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3", - "@type": "Profile", - "name": "Trusted Workflow Run Crate profile" - }, - { - "@id": "https://spdx.org/licenses/MIT", - "@type": "CreativeWork", - "name": "MIT Licence", - "identifier": "MIT" - }, - { - "@id": "https://workflowhub.eu/workflows/471?version=1", - "@type": "Dataset", - "name": "hutch-workflow (x86)", - "conformsTo": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - }, - "distribution": { - "@id": "https://workflowhub.eu/workflows/471/ro_crate?version=1" - }, - "sameAs": { - "@id": "results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl" - } - }, - { - "@id": "results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl", - "@type": "File", - "isPartOf": { - "@id": "results/" - } - }, - { - "@id": "https://workflowhub.eu/workflows/471/ro_crate?version=1", - "@type": "DataDownload", - "conformsTo": { - "@id": "https://w3id.org/ro/crate" - }, - "encodingFormat": "application/zip" - }, - { - "@id": "#execute-43a74be3-c175-4fe6-a13d-b9f0dca3c0fc", - "@type": "CreateAction", - "actionStatus": "http://schema.org/CompleteActionStatus", - "startTime": "2023-05-03T13:53:49.012349+00:00", - "endTime": "2023-05-03T13:53:53.715480+00:00", - "agent": { - "@id": "https://orcid.org/0000-0002-4206-4024" - }, - "instrument": { - "@id": "https://workflowhub.eu/workflows/471?version=1" - }, - "name": "Execute rquest query", - "object": [ - { - "@id": "rquest-query.json" - }, - { - "@id": "#input_is_availability" - }, - { - "@id": "#input_db_host" - }, - { - "@id": "#input_db_name" - }, - { - "@id": "#input_db_user" - }, - { - "@id": "#input_db_password" - } - ], - "result": [ - { - "@id": "results/outputs/_1683122029/output.json" - } - ], - "sameAs": { - "@id": "results/ro-crate-metadata.json#30494e22-a2fd-4d3c-945b-35f1b458eda9" - } - }, - { - "@id": "results/ro-crate-metadata.json#30494e22-a2fd-4d3c-945b-35f1b458eda9", - "@type": "CreateAction", - "subjectOf": {"@id": "results/"} - }, - { - "@id": "#project-065c9577-dd40-4cb2-bbc7-354e34ef37de", - "@type": "Project", - "name": "vas-workflow", - "identifier": [ - { - "@id": "_:localid:trefx:vas-workflow" - } - ], - "member": [ - { - "@id": "https://ror.org/01ee9ar58" - } - ] - }, - { - "@id": "_:localid:trefx:vas-workflow", - "@type": "PropertyValue", - "name": "trefx", - "value": "vas-workflow" - }, - { - "@id": "rquest-query.json", - "@type": "File", - "name": "rquest-query", - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-inputs-body" - } - }, - { - "@id": "hutch_cwl.wfex.stage", - "@type": "File", - "name": "Generated WfExS Staging file" - }, - { - "@id": "#input_is_availability", - "@type": "PropertyValue", - "name": "is_availability", - "value": true, - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-inputs-is_availability" - } - }, - { - "@id": "#input_db_host", - "@type": "PropertyValue", - "name": "db_host", - "value": "localhost", - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-inputs-db_host" - } - }, - { - "@id": "#input_db_name", - "@type": "PropertyValue", - "name": "db_name", - "value": "hutch", - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-inputs-db_name" - } - }, - { - "@id": "#input_db_user", - "@type": "PropertyValue", - "name": "db_user", - "value": "postgres", - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-inputs-db_user" - } - }, - { - "@id": "#input_db_password", - "@type": "PropertyValue", - "name": "db_password", - "value": "example", - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-inputs-db_password" - } - }, - { - "@id": "#hutch_workflow__x86_-inputs-body", - "@type": "FormalParameter", - "name": "body", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "#hutch_workflow__x86_-inputs-is_availability", - "@type": "FormalParameter", - "name": "is_availability", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "#hutch_workflow__x86_-inputs-db_host", - "@type": "FormalParameter", - "name": "db_host", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "#hutch_workflow__x86_-inputs-db_name", - "@type": "FormalParameter", - "name": "db_name", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "#hutch_workflow__x86_-inputs-db_user", - "@type": "FormalParameter", - "name": "db_user", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "#hutch_workflow__x86_-inputs-db_password", - "@type": "FormalParameter", - "name": "db_password", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "#hutch_workflow__x86_-outputs-output_file", - "@type": "FormalParameter", - "name": "output_file", - "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/" - }, - { - "@id": "results/outputs/_1683122029/output.json", - "@type": "File", - "encodingFormat": "application/json", - "exampleOfWork": { - "@id": "#hutch_workflow__x86_-outputs-output_file" - } - }, - { - "@id": "results/", - "@type": "Dataset", - "name": "Workflow Run Results", - "about": [ - { - "@id": "#execute-43a74be3-c175-4fe6-a13d-b9f0dca3c0fc" - }, - { - "@id": "https://workflowhub.eu/workflows/471?version=1" - } - ], - "conformsTo": [ - { - "@id": "https://w3id.org/ro/wfrun/process/0.1" - }, - { - "@id": "https://w3id.org/ro/wfrun/workflow/0.1" - }, - { - "@id": "https://w3id.org/ro/wfrun/provenance/0.1" - }, - { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - } - ] - }, - { - "@id": "#check-4445b5a3-38f0-47e1-b3bd-a2693743b071", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#CheckValue" - }, - "name": "BagIt checksum of Crate: FAILED (missing)", - "endTime": "2023-05-1518:00:00+01:00", - "object": { - "@id": "./" - }, - "instrument": { - "@id": "https://www.iana.org/assignments/named-information#sha-512" - }, - "agent": { - "@id": "https://orcid.org/0000-0001-9842-9718" - }, - "actionStatus": "http://schema.org/FailedActionStatus" - }, - { - "@id": "#validate-6e4298fe-a0fe-45f7-ac9a-bec41ec0643f", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#ValidationCheck" - }, - "name": "Validation against Trusted Workflow Run Crate profile: pending", - "object": { - "@id": "./" - }, - "instrument": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "actionStatus": "http://schema.org/PotentialActionStatus" - }, - { - "@id": "#signoff-00863632-4a12-45ab-be86-f896a670db39", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#SignOff" - }, - "name": "Sign-off of execution: approved", - "endTime": "2023-04-19T17:15:12+01:00", - "object": [ - { - "@id": "./" - }, - { - "@id": "https://workflowhub.eu/workflows/471?version=1" - }, - { - "@id": "#project-065c9577-dd40-4cb2-bbc7-354e34ef37de" - } - ], - "agent": { - "@id": "https://orcid.org/0000-0002-4206-4024" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "#disclosure-7ce35566-28f3-4e8d-aa4e-e1ac7d1344af", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#DisclosureCheck" - }, - "name": "Disclosure check of workflow results: OK", - "startTime": "2023-04-25T16:00:00+01:00", - "object": { - "@id": "./" - }, - "agent": { - "@id": "https://orcid.org/0000-0002-4206-4024" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "#bagit-7a89e9e1-ba5c-4fef-96f6-0a4d53aad0d8", - "type": "UpdateAction", - "startTime": "2023-05-15T17:40:25+01:00", - "additionalType": { - "@id": "https://w3id.org/shp#GenerateCheckValue" - }, - "name": "BagIt manifests of Crate updated", - "object": { - "@id": "./" - }, - "instrument": { - "@id": "https://www.iana.org/assignments/named-information#sha-512" - }, - "agent": { - "@id": "https://orcid.org/0000-0001-9842-9718" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "https://orcid.org/0000-0002-4206-4024", - "@type": "Person", - "name": "Vasiliki Panagi", - "affiliation": { - "@id": "https://ror.org/01ee9ar58" - }, - "memberOf": [ - { - "@id": "#project-065c9577-dd40-4cb2-bbc7-354e34ef37de" - } - ] - }, - { - "@id": "https://ror.org/01ee9ar58", - "@type": "Organization", - "name": "University of Nottingham" - }, - { - "@id": "https://trefx.example.com/", - "@type": "Organization", - "name": "TRE-FX's pod in some TRE", - "parentOrganization": { - "@id": "https://ror.org/01ee9ar58" - } - }, - { - "@id": "https://www.iana.org/assignments/named-information#sha-512", - "@type": "DefinedTerm", - "name": "sha-512 algorithm" - }, - { - "@id": "https://orcid.org/0000-0001-9842-9718", - "@type": "Person", - "name": "Stian Soiland-Reyes", - "affiliation": { - "@id": "https://ror.org/027m9bs27" - }, - "memberOf": { - "@id": "https://trefx.uk/" - } - }, - { - "@id": "https://ror.org/027m9bs27", - "@type": "CollegeOrUniversity", - "name": "The University of Manchester", - "url": "https://www.manchester.ac.uk/" - } - ] -} \ No newline at end of file diff --git a/0.3/example-hutch/data/ro-crate-preview.html b/0.3/example-hutch/data/ro-crate-preview.html deleted file mode 100644 index 4f16f67..0000000 --- a/0.3/example-hutch/data/ro-crate-preview.html +++ /dev/null @@ -1,1158 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -
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- - -⬇️🏷️ Download all the metadata for in JSON-LD format - - -
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./

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Go to: Trusted Workflow Run Crate profile

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@idhttps://w3id.org/trusted-wfrun-crate/0.3
name [?]Trusted Workflow Run Crate profile
@typeProfile
Items that reference this one
conformsTo [?]./
instrument [?]Validation against Trusted Workflow Run Crate profile: pending
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Go to: hutch-workflow (x86)

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@idhttps://workflowhub.eu/workflows/471?version=1
name [?]hutch-workflow (x86)
@typeDataset
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/471/ro_crate?version=1
sameAs [?]results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl
Items that reference this one
hasPart [?]./
mainEntity [?]./
instrument [?]Execute rquest query
about [?]Workflow Run Results
object [?]Sign-off of execution: approved
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⬇️ Download: Generated WfExS Staging file

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@idhutch_cwl.wfex.stage
name [?]Generated WfExS Staging file
@typeFile
Items that reference this one
hasPart [?]./
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Workflow Run Results

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⬇️ Download: results/outputs/_1683122029/output.json

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@idresults/outputs/_1683122029/output.json
@typeFile
encodingFormat [?]application/json
exampleOfWork [?]output_file
Items that reference this one
hasPart [?]./
result [?]Execute rquest query
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Execute rquest query

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#execute-43a74be3-c175-4fe6-a13d-b9f0dca3c0fc
name [?]Execute rquest query
@typeCreateAction
actionStatus [?]http://schema.org/CompleteActionStatus
startTime [?]2023-05-03T13:53:49.012349+00:00
endTime [?]2023-05-03T13:53:53.715480+00:00
agent [?]Vasiliki Panagi
instrument [?]hutch-workflow (x86)
object [?]
    -
  • rquest-query
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  • is_availability: true
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  • db_host: localhost
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  • db_name: hutch
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  • db_password: example
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result [?]results/outputs/_1683122029/output.json
sameAs [?]results/ro-crate-metadata.json#30494e22-a2fd-4d3c-945b-35f1b458eda9
Items that reference this one
mentions [?]./
about [?]Workflow Run Results
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BagIt checksum of Crate: FAILED (missing)

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@id#check-4445b5a3-38f0-47e1-b3bd-a2693743b071
name [?]BagIt checksum of Crate: FAILED (missing)
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#CheckValue
endTime [?]2023-05-1518:00:00+01:00
object [?]./
instrument [?]sha-512 algorithm
agent [?]Stian Soiland-Reyes
actionStatus [?]http://schema.org/FailedActionStatus
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mentions [?]./
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Validation against Trusted Workflow Run Crate profile: pending

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@id#validate-6e4298fe-a0fe-45f7-ac9a-bec41ec0643f
name [?]Validation against Trusted Workflow Run Crate profile: pending
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#ValidationCheck
object [?]./
instrument [?]Trusted Workflow Run Crate profile
actionStatus [?]http://schema.org/PotentialActionStatus
Items that reference this one
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Sign-off of execution: approved

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@id#signoff-00863632-4a12-45ab-be86-f896a670db39
name [?]Sign-off of execution: approved
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#SignOff
endTime [?]2023-04-19T17:15:12+01:00
object [?]
agent [?]Vasiliki Panagi
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
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Disclosure check of workflow results: OK

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@id#disclosure-7ce35566-28f3-4e8d-aa4e-e1ac7d1344af
name [?]Disclosure check of workflow results: OK
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#DisclosureCheck
startTime [?]2023-04-25T16:00:00+01:00
object [?]./
agent [?]Vasiliki Panagi
actionStatus [?]http://schema.org/CompletedActionStatus
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mentions [?]./
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BagIt manifests of Crate updated

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@id#bagit-7a89e9e1-ba5c-4fef-96f6-0a4d53aad0d8
name [?]BagIt manifests of Crate updated
@typeThing
typeUpdateAction
startTime [?]2023-05-15T17:40:25+01:00
additionalType [?]https://w3id.org/shp#GenerateCheckValue
object [?]./
instrument [?]sha-512 algorithm
agent [?]Stian Soiland-Reyes
actionStatus [?]http://schema.org/CompletedActionStatus
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vas-workflow

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@id#project-065c9577-dd40-4cb2-bbc7-354e34ef37de
name [?]vas-workflow
@typeProject
identifier [?]trefx: vas-workflow
member [?]University of Nottingham
Items that reference this one
sourceOrganization [?]./
object [?]Sign-off of execution: approved
memberOf [?]Vasiliki Panagi
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Go to: TRE-FX's pod in some TRE

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@idhttps://trefx.example.com/
name [?]TRE-FX's pod in some TRE
@typeOrganization
parentOrganization [?]University of Nottingham
Items that reference this one
publisher [?]./
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- - - - - - - diff --git a/0.3/example-hutch/data/rquest-query.json b/0.3/example-hutch/data/rquest-query.json deleted file mode 100644 index c2a063c..0000000 --- a/0.3/example-hutch/data/rquest-query.json +++ /dev/null @@ -1,10 +0,0 @@ -{ "task_id" : "job-2023-01-13-14: 20: 38-project", -"project" : "project_id", "owner" : "user1","cohort" : { "groups" : [ - { "rules" : [ - { "varname" : "OMOP", "varcat": "Person", "type" : "TEXT", "oper" : "=", "value" : "8507" - } - ],"rules_oper" : "AND" - } - ], "groups_oper" : "OR" - }, "collection" : "collection_id","protocol_version" : "v2", "char_salt" : "salt","uuid" : "unique_id" -} diff --git a/0.3/example-hutch/manifest-sha512.txt b/0.3/example-hutch/manifest-sha512.txt deleted file mode 100644 index ba10f76..0000000 --- a/0.3/example-hutch/manifest-sha512.txt +++ /dev/null @@ -1,12 +0,0 @@ -d4e4fcb4465f03314d9c46e25d320924664cc27e9f90b06451caf09961166d6af6eb622133897bc9c1d13c41370fcc1a670d921e8bbddbc32695584f568c4a6d data/ro-crate-metadata.json -ec982962393d69eefbf53f4762a79660bc59cc38be303db3e41ee185d873167e33702735dc9e5bb859031317066fa1ac17091329ee93597debdcb90ce38aa03c data/results/ro-crate-metadata.json -acad27736530e16bdc4797939ec92d8169050adaf45839fa6fa7a077549f8d93b9b4bacf0f9cb283e03241197b6122b112d627f10407f590999a62ce09422f49 data/results/b5b59d4f-9797-5179-a131-e7089e943988/2ef7f736-623e-492c-a135-8f247395d1df_workflow.cwl -acad27736530e16bdc4797939ec92d8169050adaf45839fa6fa7a077549f8d93b9b4bacf0f9cb283e03241197b6122b112d627f10407f590999a62ce09422f49 data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/sec-hutch.cwl -16fd97599dc26da8986819be978826b1769f7a47dccb47374b185c63f00184e71054641d494d297175290090ca8099076964a5a39b20b5f1ef41e2bc62a3a992 data/results/b5b59d4f-9797-5179-a131-e7089e943988/workflows/rquest-oneshot.cwl -2192f93eacd3fcadfde17b4c4b5e4616daaac11fbc60d9528e0852a42aeebe722487b57f0282d0762a33358a4971a5ff01097c9b8676bfaddb73e81bb17f33c7 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b/0.3/example-request/bagit.txt deleted file mode 100644 index c679299..0000000 --- a/0.3/example-request/bagit.txt +++ /dev/null @@ -1,2 +0,0 @@ -BagIt-version: 1.0 -Tag-File-Character-Encoding: UTF-8 diff --git a/0.3/example-request/data/index.html b/0.3/example-request/data/index.html deleted file mode 100644 index 1d45f0d..0000000 --- a/0.3/example-request/data/index.html +++ /dev/null @@ -1,446 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -
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./

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@id./
@typeDataset
conformsTo [?]Trusted Workflow Run Crate profile
hasPart [?]
mainEntity [?]CWL Protein MD Setup tutorial with mutations
mentions [?]Execute query 12389 on workflow
sourceOrganization [?]Investigation of cancer (TRE72 project 81)
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about [?]ro-crate-metadata.json
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Go to: Trusted Workflow Run Crate profile

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@idhttps://w3id.org/trusted-wfrun-crate/0.3
name [?]Trusted Workflow Run Crate profile
@typeProfile
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Go to: CWL Protein MD Setup tutorial with mutations

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@idhttps://workflowhub.eu/workflows/289?version=1
name [?]CWL Protein MD Setup tutorial with mutations
@typeDataset
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
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hasPart [?]./
mainEntity [?]./
instrument [?]Execute query 12389 on workflow
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⬇️ Download: input1

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object [?]Execute query 12389 on workflow
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Execute query 12389 on workflow

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@id#query-37252371-c937-43bd-a0a7-3680b48c0538
name [?]Execute query 12389 on workflow
@typeCreateAction
actionStatus [?]http://schema.org/PotentialActionStatus
agent [?]Stian Soiland-Reyes
instrument [?]CWL Protein MD Setup tutorial with mutations
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Investigation of cancer (TRE72 project 81)

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@id#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70
name [?]Investigation of cancer (TRE72 project 81)
@typeProject
identifier [?]tre72: project81
funding [?]EOSC4Cancer
member [?]
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- - - - - - - diff --git a/0.3/example-request/data/input1.txt b/0.3/example-request/data/input1.txt deleted file mode 100644 index e4d100f..0000000 --- a/0.3/example-request/data/input1.txt +++ /dev/null @@ -1,3 +0,0 @@ - A:Gly4Lys - A:Leu8Met - A:Tyr20Gln \ No newline at end of file diff --git a/0.3/example-request/data/ro-crate-metadata.json b/0.3/example-request/data/ro-crate-metadata.json deleted file mode 100644 index e42ee77..0000000 --- a/0.3/example-request/data/ro-crate-metadata.json +++ /dev/null @@ -1,160 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context", - "@graph": [ - { - "@type": "CreativeWork", - "@id": "ro-crate-metadata.json", - "about": { - "@id": "./" - }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.2-DRAFT" - } - }, - { - "@id": "./", - "@type": "Dataset", - "conformsTo": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "hasPart": [ - { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - { - "@id": "input1.txt" - } - ], - "mainEntity": { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - "mentions": { - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538" - }, - "sourceOrganization": { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - } - }, - { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3", - "@type": "Profile", - "name": "Trusted Workflow Run Crate profile" - }, - { - "@id": "https://workflowhub.eu/workflows/289?version=1", - "@type": "Dataset", - "name": "CWL Protein MD Setup tutorial with mutations", - "conformsTo": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - }, - "distribution": { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1" - } - }, - { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1", - "@type": "DataDownload", - "conformsTo": { - "@id": "https://w3id.org/ro/crate" - }, - "encodingFormat": "application/zip" - }, - { - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538", - "@type": "CreateAction", - "actionStatus": "http://schema.org/PotentialActionStatus", - "agent": { - "@id": "https://orcid.org/0000-0001-9842-9718" - }, - "instrument": { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - "name": "Execute query 12389 on workflow ", - "object": [ - { - "@id": "input1.txt" - }, - { - "@id": "#enableFastMode" - } - ] - }, - { - "@id": "https://orcid.org/0000-0001-9842-9718", - "@type": "Person", - "name": "Stian Soiland-Reyes", - "affiliation": { - "@id": "https://ror.org/027m9bs27" - }, - "memberOf": [ - { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - } - ] - }, - { - "@id": "https://ror.org/027m9bs27", - "@type": "Organization", - "name": "The University of Manchester" - }, - { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70", - "@type": "Project", - "name": "Investigation of cancer (TRE72 project 81)", - "identifier": [ - { - "@id": "_:localid:tre72:project81" - } - ], - "funding": { - "@id": "https://gtr.ukri.org/projects?ref=10038961" - }, - "member": [ - { - "@id": "https://ror.org/027m9bs27" - }, - { - "@id": "https://ror.org/01ee9ar58" - } - ] - }, - { - "@id": "_:localid:tre72:project81", - "@type": "PropertyValue", - "name": "tre72", - "value": "project81" - }, - { - "@id": "https://gtr.ukri.org/projects?ref=10038961", - "@type": "Grant", - "name": "EOSC4Cancer" - }, - { - "@id": "input1.txt", - "@type": "File", - "name": "input1", - "exampleOfWork": { - "@id": "#sequence" - } - }, - { - "@id": "#enableFastMode", - "@type": "PropertyValue", - "name": "--fast-mode", - "value": "True", - "exampleOfWork": { - "@id": "#fast" - } - }, - { - "@id": "#sequence", - "@type": "FormalParameter", - "name": "input-sequence" - }, - { - "@id": "#fast", - "@type": "FormalParameter", - "name": "fast-mode" - } - ] -} \ No newline at end of file diff --git a/0.3/example-request/data/ro-crate-preview.html b/0.3/example-request/data/ro-crate-preview.html deleted file mode 100644 index 1d45f0d..0000000 --- a/0.3/example-request/data/ro-crate-preview.html +++ /dev/null @@ -1,446 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -
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./

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@id./
@typeDataset
conformsTo [?]Trusted Workflow Run Crate profile
hasPart [?]
mainEntity [?]CWL Protein MD Setup tutorial with mutations
mentions [?]Execute query 12389 on workflow
sourceOrganization [?]Investigation of cancer (TRE72 project 81)
Items that reference this one
about [?]ro-crate-metadata.json
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Go to: Trusted Workflow Run Crate profile

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@idhttps://w3id.org/trusted-wfrun-crate/0.3
name [?]Trusted Workflow Run Crate profile
@typeProfile
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conformsTo [?]./
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Go to: CWL Protein MD Setup tutorial with mutations

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@idhttps://workflowhub.eu/workflows/289?version=1
name [?]CWL Protein MD Setup tutorial with mutations
@typeDataset
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
Items that reference this one
hasPart [?]./
mainEntity [?]./
instrument [?]Execute query 12389 on workflow
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⬇️ Download: input1

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@idinput1.txt
name [?]input1
@typeFile
exampleOfWork [?]input-sequence
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hasPart [?]./
object [?]Execute query 12389 on workflow
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Execute query 12389 on workflow

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@id#query-37252371-c937-43bd-a0a7-3680b48c0538
name [?]Execute query 12389 on workflow
@typeCreateAction
actionStatus [?]http://schema.org/PotentialActionStatus
agent [?]Stian Soiland-Reyes
instrument [?]CWL Protein MD Setup tutorial with mutations
object [?]
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  • input1
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mentions [?]./
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Investigation of cancer (TRE72 project 81)

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@id#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70
name [?]Investigation of cancer (TRE72 project 81)
@typeProject
identifier [?]tre72: project81
funding [?]EOSC4Cancer
member [?]
Items that reference this one
sourceOrganization [?]./
memberOf [?]Stian Soiland-Reyes
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- - -⬇️🏷️ Download all the metadata for in JSON-LD format - - -
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./

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Go to: Trusted Workflow Run Crate profile

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@idhttps://w3id.org/trusted-wfrun-crate/0.3
name [?]Trusted Workflow Run Crate profile
@typeProfile
Items that reference this one
conformsTo [?]./
instrument [?]Validation against Trusted Workflow Run Crate profile: approved
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Go to: CWL Protein MD Setup tutorial with mutations

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@idhttps://workflowhub.eu/workflows/289?version=1
name [?]CWL Protein MD Setup tutorial with mutations
@typeDataset
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
Items that reference this one
hasPart [?]./
mainEntity [?]./
instrument [?]Execute query 12389 on workflow
sameAs [?]CWL Protein MD Setup tutorial with mutations
object [?]Sign-off of execution according to Agreement policy: approved
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⬇️ Download: input1

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@idinput1.txt
name [?]input1
@typeFile
exampleOfWork [?]input-sequence
Items that reference this one
hasPart [?]./
object [?]Execute query 12389 on workflow
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CWL Protein MD Setup tutorial with mutations

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@idworkflow/289/
name [?]CWL Protein MD Setup tutorial with mutations
@typeDataset
sameAs [?]CWL Protein MD Setup tutorial with mutations
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
Items that reference this one
hasPart [?]./
result [?]Downloaded workflow RO-Crate via proxy
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Execute query 12389 on workflow

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@id#query-37252371-c937-43bd-a0a7-3680b48c0538
name [?]Execute query 12389 on workflow
@typeCreateAction
actionStatus [?]http://schema.org/CompleteActionStatus
agent [?]Stian Soiland-Reyes
instrument [?]CWL Protein MD Setup tutorial with mutations
object [?]
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  • input1
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result [?]
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mentions [?]./
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BagIt checksum of Crate: OK

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@id#check-f33fe90c-0c22-4c72-b299-de509028410e
name [?]BagIt checksum of Crate: OK
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#CheckValue
endTime [?]2023-04-18T12:11:45+01:00
object [?]./
instrument [?]sha-512 algorithm
agent [?]#validator-a4a66c63-2fe0-4c57-830d-268a40718313
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Validation against Trusted Workflow Run Crate profile: approved

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@id#validate-1146f640-819e-4c86-b029-b763a0040896
name [?]Validation against Trusted Workflow Run Crate profile: approved
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#ValidationCheck
startTime [?]2023-04-18T12:11:46+01:00
endTime [?]2023-04-18T12:11:49+01:00
object [?]./
instrument [?]Trusted Workflow Run Crate profile
agent [?]#validator-a4a66c63-2fe0-4c57-830d-268a40718313
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
-
- -
-


-
-

Downloaded workflow RO-Crate via proxy

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#download-8b51bf57-6b29-44da-b24b-638c8df91639
name [?]Downloaded workflow RO-Crate via proxy
@typeThing
typeDownloadAction
startTime [?]2023-04-18T12:11:50+01:00
endTime [?]2023-04-18T12:11:52+01:00
object [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
result [?]CWL Protein MD Setup tutorial with mutations
agent [?]http://proxy.example.com/
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
-
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Sign-off of execution according to Agreement policy: approved

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#signoff-3b741265-cfef-49ea-8138-a2fa149bf2f0
name [?]Sign-off of execution according to Agreement policy: approved
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#SignOff
endTime [?]2023-04-19T17:15:12+01:00
object [?]
instrument [?]Agreement policy for TRE72 for project 81
agent [?]https://orcid.org/0000-0002-1825-0097
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Disclosure check of workflow results: pending (estimate: 1 week)

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#disclosure-b16c1f0a-ae7f-4582-9b28-7d9df3313e27
name [?]Disclosure check of workflow results: pending (estimate: 1 week)
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#DisclosureCheck
startTime [?]2023-04-25T16:00:00+01:00
object [?]./
agent [?]https://orcid.org/0000-0002-1825-0097
actionStatus [?]http://schema.org/PotentialActionStatus
Items that reference this one
mentions [?]./
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-
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BagIt manifests of Crate updated

- - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#bagit-ce785c0b-c988-4043-8cbd-1489dcebc14f
name [?]BagIt manifests of Crate updated
@typeThing
typeUpdateAction
startTime [?]2023-04-29T12:12:25+01:00
additionalType [?]https://w3id.org/shp#GenerateCheckValue
object [?]./
instrument [?]sha-512 algorithm
agent [?]#validator-a4a66c63-2fe0-4c57-830d-268a40718313
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Investigation of cancer (TRE72 project 81)

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70
name [?]Investigation of cancer (TRE72 project 81)
@typeProject
identifier [?]tre72: project81
funding [?]EOSC4Cancer
member [?]
Items that reference this one
sourceOrganization [?]./
object [?]Sign-off of execution according to Agreement policy: approved
grantee [?]#permissions-07b81e0f
memberOf [?]Stian Soiland-Reyes
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Go to: TRE 72 trusted research environment at The University of Manchester

- - - - -
- - - - - - - - - - - - - - - - - - - - - -
@idhttps://tre72.example.com/
name [?]TRE 72 trusted research environment at The University of Manchester
@typeOrganization
parentOrganization [?]The University of Manchester
Items that reference this one
publisher [?]./
provider [?]RO-Crate validator at TRE72
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- -
-




-
- - - - - - - diff --git a/0.3/example-result/data/input1.txt b/0.3/example-result/data/input1.txt deleted file mode 100644 index e4d100f..0000000 --- a/0.3/example-result/data/input1.txt +++ /dev/null @@ -1,3 +0,0 @@ - A:Gly4Lys - A:Leu8Met - A:Tyr20Gln \ No newline at end of file diff --git a/0.3/example-result/data/outputs/diagrams/.keep b/0.3/example-result/data/outputs/diagrams/.keep deleted file mode 100644 index e69de29..0000000 diff --git a/0.3/example-result/data/outputs/qa.csv b/0.3/example-result/data/outputs/qa.csv deleted file mode 100644 index 6adaa09..0000000 --- a/0.3/example-result/data/outputs/qa.csv +++ /dev/null @@ -1,4 +0,0 @@ -data,qa -a,0.12 -b,0.98 -c,0.01 diff --git a/0.3/example-result/data/ro-crate-metadata.json b/0.3/example-result/data/ro-crate-metadata.json deleted file mode 100644 index 87f47f7..0000000 --- a/0.3/example-result/data/ro-crate-metadata.json +++ /dev/null @@ -1,392 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context", - "@graph": [ - { - "@type": "CreativeWork", - "@id": "ro-crate-metadata.json", - "about": { - "@id": "./" - }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.2-DRAFT" - } - }, - { - "@id": "./", - "@type": "Dataset", - "conformsTo": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "hasPart": [ - { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - { - "@id": "input1.txt" - }, - { - "@id": "workflow/289/" - } - ], - "mainEntity": { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - "mentions": [ - { - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538" - }, - { - "@id": "#check-f33fe90c-0c22-4c72-b299-de509028410e" - }, - { - "@id": "#validate-1146f640-819e-4c86-b029-b763a0040896" - }, - { - "@id": "#download-8b51bf57-6b29-44da-b24b-638c8df91639" - }, - { - "@id": "#signoff-3b741265-cfef-49ea-8138-a2fa149bf2f0" - }, - { - "@id": "#disclosure-b16c1f0a-ae7f-4582-9b28-7d9df3313e27" - }, - { - "@id": "#bagit-ce785c0b-c988-4043-8cbd-1489dcebc14f" - } - ], - "sourceOrganization": { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - }, - "publisher": { - "@id": "https://tre72.example.com/" - }, - "licence": { - "@id": "http://spdx.org/licenses/CC-BY-4.0" - } - }, - { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3", - "@type": "Profile", - "name": "Trusted Workflow Run Crate profile" - }, - { - "@id": "https://spdx.org/licenses/CC-BY-4.0", - "@type": "CreativeWork", - "name": "Creative Commons Attribution 4.0 International", - "identifier": "CC-BY-4.0" - }, - { - "@id": "https://workflowhub.eu/workflows/289?version=1", - "@type": "Dataset", - "name": "CWL Protein MD Setup tutorial with mutations", - "conformsTo": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - }, - "distribution": { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1" - } - }, - { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1", - "@type": "DataDownload", - "conformsTo": { - "@id": "https://w3id.org/ro/crate" - }, - "encodingFormat": "application/zip" - }, - { - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538", - "@type": "CreateAction", - "actionStatus": "http://schema.org/CompleteActionStatus", - "agent": { - "@id": "https://orcid.org/0000-0001-9842-9718" - }, - "instrument": { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - "name": "Execute query 12389 on workflow ", - "object": [ - { - "@id": "input1.txt" - }, - { - "@id": "#enableFastMode" - } - ], - "result": [ - { - "@id": "outputs/table.csv" - }, - { - "@id": "outputs/diagrams/" - }, - { - "@id": "urn:uuid:07b81e0f-7ac4-5428-9940-878b241e2397" - } - ] - }, - { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70", - "@type": "Project", - "name": "Investigation of cancer (TRE72 project 81)", - "identifier": [ - { - "@id": "_:localid:tre72:project81" - } - ], - "funding": { - "@id": "https://gtr.ukri.org/projects?ref=10038961" - }, - "member": [ - { - "@id": "https://ror.org/027m9bs27" - }, - { - "@id": "https://ror.org/01ee9ar58" - } - ] - }, - { - "@id": "_:localid:tre72:project81", - "@type": "PropertyValue", - "name": "tre72", - "value": "project81" - }, - { - "@id": "input1.txt", - "@type": "File", - "name": "input1", - "exampleOfWork": { - "@id": "#sequence" - } - }, - { - "@id": "#enableFastMode", - "@type": "PropertyValue", - "name": "--fast-mode", - "value": "True", - "exampleOfWork": { - "@id": "#fast" - } - }, - { - "@id": "#sequence", - "@type": "FormalParameter", - "name": "input-sequence" - }, - { - "@id": "#fast", - "@type": "FormalParameter", - "name": "fast-mode" - }, - { - "@id": "outputs/qa.csv", - "@type": "File", - "encodingFormat": "text/csv", - "name": "Tabular listing of quality assessment" - }, - { - "@id": "outputs/diagrams/", - "@type": "Dataset", - "name": "Diagrams of regions of interest" - }, - { - "@id": "workflow/289/", - "sameAs": { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - "@type": "Dataset", - "name": "CWL Protein MD Setup tutorial with mutations", - "conformsTo": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - }, - "distribution": { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1" - } - }, - { - "@id": "#check-f33fe90c-0c22-4c72-b299-de509028410e", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#CheckValue" - }, - "name": "BagIt checksum of Crate: OK", - "endTime": "2023-04-18T12:11:45+01:00", - "object": { - "@id": "./" - }, - "instrument": { - "@id": "https://www.iana.org/assignments/named-information#sha-512" - }, - "agent": { - "@id": "#validator-a4a66c63-2fe0-4c57-830d-268a40718313" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "#validate-1146f640-819e-4c86-b029-b763a0040896", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#ValidationCheck" - }, - "name": "Validation against Trusted Workflow Run Crate profile: approved", - "startTime": "2023-04-18T12:11:46+01:00", - "endTime": "2023-04-18T12:11:49+01:00", - "object": { - "@id": "./" - }, - "instrument": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "agent": { - "@id": "#validator-a4a66c63-2fe0-4c57-830d-268a40718313" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "#download-8b51bf57-6b29-44da-b24b-638c8df91639", - "type": "DownloadAction", - "name": "Downloaded workflow RO-Crate via proxy", - "startTime": "2023-04-18T12:11:50+01:00", - "endTime": "2023-04-18T12:11:52+01:00", - "object": { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1" - }, - "result": { - "@id": "workflow/289/" - }, - "agent": { - "@id": "http://proxy.example.com/" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "#signoff-3b741265-cfef-49ea-8138-a2fa149bf2f0", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#SignOff" - }, - "name": "Sign-off of execution according to Agreement policy: approved", - "endTime": "2023-04-19T17:15:12+01:00", - "object": [ - { - "@id": "./" - }, - { - "@id": "https://workflowhub.eu/workflows/289?version=1" - }, - { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - } - ], - "instrument": { - "@id": "https://tre72.example.com/agreement-policy/81" - }, - "agent": { - "@id": "https://orcid.org/0000-0002-1825-0097" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "#disclosure-b16c1f0a-ae7f-4582-9b28-7d9df3313e27", - "type": "AssessAction", - "additionalType": { - "@id": "https://w3id.org/shp#DisclosureCheck" - }, - "name": "Disclosure check of workflow results: pending (estimate: 1 week)", - "startTime": "2023-04-25T16:00:00+01:00", - "object": { - "@id": "./" - }, - "agent": { - "@id": "https://orcid.org/0000-0002-1825-0097" - }, - "actionStatus": "http://schema.org/PotentialActionStatus" - }, - { - "@id": "#bagit-ce785c0b-c988-4043-8cbd-1489dcebc14f", - "type": "UpdateAction", - "startTime": "2023-04-29T12:12:25+01:00", - "additionalType": { - "@id": "https://w3id.org/shp#GenerateCheckValue" - }, - "name": "BagIt manifests of Crate updated", - "object": { - "@id": "./" - }, - "instrument": { - "@id": "https://www.iana.org/assignments/named-information#sha-512" - }, - "agent": { - "@id": "#validator-a4a66c63-2fe0-4c57-830d-268a40718313" - }, - "actionStatus": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "urn:uuid:07b81e0f-7ac4-5428-9940-878b241e2397", - "@type": "DigitalDocument", - "encodingFormat": "text/csv", - "name": "Patient measurement 07b81e0f-7ac4-5428-9940-878b241e2397", - "hasDigitalDocumentPermission": { - "@id": "#permissions-07b81e0f" - } - }, - { - "@id": "#permissions-07b81e0f", - "@type": "DigitalDocumentPermission", - "permissionType": "http://schema.org/ReadPermission", - "grantee": { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - } - }, - { - "@id": "https://orcid.org/0000-0001-9842-9718", - "@type": "Person", - "name": "Stian Soiland-Reyes", - "affiliation": { - "@id": "https://ror.org/027m9bs27" - }, - "memberOf": [ - { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - } - ] - }, - { - "@id": "https://ror.org/027m9bs27", - "@type": "Organization", - "name": "The University of Manchester" - }, - { - "@id": "https://gtr.ukri.org/projects?ref=10038961", - "@type": "Grant", - "name": "EOSC4Cancer" - }, - { - "@id": "https://tre72.example.com/", - "@type": "Organization", - "name": "TRE 72 trusted research environment at The University of Manchester", - "parentOrganization": { - "@id": "https://ror.org/027m9bs27" - } - }, - { - "@id": "https://tre72.example.com/#crate-validator", - "@type": "SoftwareApplication", - "name": "RO-Crate validator at TRE72", - "provider": { - "@id": "https://tre72.example.com/" - } - }, - { - "@id": "https://tre72.example.com/agreement-policy/81", - "@type": "CreativeWork", - "name": "Agreement policy for TRE72 for project 81" - }, - { - "@id": "https://www.iana.org/assignments/named-information#sha-512", - "@type": "DefinedTerm", - "name": "sha-512 algorithm" - } - ] -} \ No newline at end of file diff --git a/0.3/example-result/data/ro-crate-preview.html b/0.3/example-result/data/ro-crate-preview.html deleted file mode 100644 index 43bb1d5..0000000 --- a/0.3/example-result/data/ro-crate-preview.html +++ /dev/null @@ -1,1109 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -
-
-

-

- - -⬇️🏷️ Download all the metadata for in JSON-LD format - - -
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./

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Go to: Trusted Workflow Run Crate profile

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- - - - - - - - - - - - - - - - - - -
@idhttps://w3id.org/trusted-wfrun-crate/0.3
name [?]Trusted Workflow Run Crate profile
@typeProfile
Items that reference this one
conformsTo [?]./
instrument [?]Validation against Trusted Workflow Run Crate profile: approved
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Go to: CWL Protein MD Setup tutorial with mutations

- - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@idhttps://workflowhub.eu/workflows/289?version=1
name [?]CWL Protein MD Setup tutorial with mutations
@typeDataset
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
Items that reference this one
hasPart [?]./
mainEntity [?]./
instrument [?]Execute query 12389 on workflow
sameAs [?]CWL Protein MD Setup tutorial with mutations
object [?]Sign-off of execution according to Agreement policy: approved
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⬇️ Download: input1

- - - - -
- - - - - - - - - - - - - - - - - - - - - -
@idinput1.txt
name [?]input1
@typeFile
exampleOfWork [?]input-sequence
Items that reference this one
hasPart [?]./
object [?]Execute query 12389 on workflow
-
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-
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CWL Protein MD Setup tutorial with mutations

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- - - - - - - - - - - - - - - - - - - - - - - - - - - -
@idworkflow/289/
name [?]CWL Protein MD Setup tutorial with mutations
@typeDataset
sameAs [?]CWL Protein MD Setup tutorial with mutations
conformsTo [?]https://w3id.org/workflowhub/workflow-ro-crate/1.0
distribution [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
Items that reference this one
hasPart [?]./
result [?]Downloaded workflow RO-Crate via proxy
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Execute query 12389 on workflow

- - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#query-37252371-c937-43bd-a0a7-3680b48c0538
name [?]Execute query 12389 on workflow
@typeCreateAction
actionStatus [?]http://schema.org/CompleteActionStatus
agent [?]Stian Soiland-Reyes
instrument [?]CWL Protein MD Setup tutorial with mutations
object [?]
    -
  • input1
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  • --fast-mode: True
    • -
result [?]
Items that reference this one
mentions [?]./
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BagIt checksum of Crate: OK

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#check-f33fe90c-0c22-4c72-b299-de509028410e
name [?]BagIt checksum of Crate: OK
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#CheckValue
endTime [?]2023-04-18T12:11:45+01:00
object [?]./
instrument [?]sha-512 algorithm
agent [?]#validator-a4a66c63-2fe0-4c57-830d-268a40718313
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Validation against Trusted Workflow Run Crate profile: approved

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#validate-1146f640-819e-4c86-b029-b763a0040896
name [?]Validation against Trusted Workflow Run Crate profile: approved
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#ValidationCheck
startTime [?]2023-04-18T12:11:46+01:00
endTime [?]2023-04-18T12:11:49+01:00
object [?]./
instrument [?]Trusted Workflow Run Crate profile
agent [?]#validator-a4a66c63-2fe0-4c57-830d-268a40718313
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Downloaded workflow RO-Crate via proxy

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#download-8b51bf57-6b29-44da-b24b-638c8df91639
name [?]Downloaded workflow RO-Crate via proxy
@typeThing
typeDownloadAction
startTime [?]2023-04-18T12:11:50+01:00
endTime [?]2023-04-18T12:11:52+01:00
object [?]https://workflowhub.eu/workflows/289/ro_crate?version=1
result [?]CWL Protein MD Setup tutorial with mutations
agent [?]http://proxy.example.com/
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Sign-off of execution according to Agreement policy: approved

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@id#signoff-3b741265-cfef-49ea-8138-a2fa149bf2f0
name [?]Sign-off of execution according to Agreement policy: approved
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#SignOff
endTime [?]2023-04-19T17:15:12+01:00
object [?]
instrument [?]Agreement policy for TRE72 for project 81
agent [?]https://orcid.org/0000-0002-1825-0097
actionStatus [?]http://schema.org/CompletedActionStatus
Items that reference this one
mentions [?]./
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Disclosure check of workflow results: pending (estimate: 1 week)

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@id#disclosure-b16c1f0a-ae7f-4582-9b28-7d9df3313e27
name [?]Disclosure check of workflow results: pending (estimate: 1 week)
@typeThing
typeAssessAction
additionalType [?]https://w3id.org/shp#DisclosureCheck
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BagIt manifests of Crate updated

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Investigation of cancer (TRE72 project 81)

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Go to: TRE 72 trusted research environment at The University of Manchester

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- - - - - - - diff --git a/0.3/example-result/data/workflow/289/README.md b/0.3/example-result/data/workflow/289/README.md deleted file mode 100644 index 5ccf0ca..0000000 --- a/0.3/example-result/data/workflow/289/README.md +++ /dev/null @@ -1,36 +0,0 @@ -# Execute workflow through CWL script - -To execute the workflow through a CWL script, please follow the next steps: - -## Workflow files - -Below you can find the list of all the needed **files** for executing this workflow: - -* **workflow.cwl:** the CWL file with all the common steps to execute this workflow. -* **workflow_input_descriptions.yml:** the configuration file with the I/O dependencies and settings for each step of the workflow. -* **workflow_list.cwl:** the CWL file with all the steps to execute each mutation for this workflow. -* **workflow_gather.cwl:** the CWL file with code needed to wrap up the outcome of this workflow. - -## Requirements - -For executing a BioBB workflow in CWL, you should have [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git), [cwltool](https://github.com/common-workflow-language/cwltool#install) and [docker](https://docs.docker.com/engine/install/) installed in your computer. - -The [**biobb_adapters**](https://github.com/bioexcel/biobb_adapters) must be installed in your computer as well. Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers, **CWL** amongst them. Install biobb_adapters is very easy, just execute the following script somewhere in your computer: - - git clone git@github.com:bioexcel/biobb_adapters.git - -## Custom paths - -To run this workflow properly in your computer, you should open in a text/code editor the **workflow.cwl** file and replace all the occurrences of **/path/to/** with the absolute path to the folder where you have installed the **biobb_adapters**. - -## Run workflow - -After that, the only thing left is to run the workflow: - - cwltool workflow.cwl workflow_input_descriptions.yml - -Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a **few minutes** to **several hours**. The workflow progress will be shown in your terminal. - -## Get output results - -Once the workflow is finished, you will have all the files generated in every step in the same folder. diff --git a/0.3/example-result/data/workflow/289/ions.pdb b/0.3/example-result/data/workflow/289/ions.pdb deleted file mode 100644 index a6fc82e..0000000 --- a/0.3/example-result/data/workflow/289/ions.pdb +++ /dev/null @@ -1 +0,0 @@ -TER \ No newline at end of file diff --git a/0.3/example-result/data/workflow/289/ro-crate-metadata.json b/0.3/example-result/data/workflow/289/ro-crate-metadata.json deleted file mode 100644 index 2fb0fbb..0000000 --- a/0.3/example-result/data/workflow/289/ro-crate-metadata.json +++ /dev/null @@ -1,800 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.1/context", - "@graph": [ - { - "@id": "ro-crate-metadata.json", - "@type": "CreativeWork", - "about": { - "@id": "./" - }, - "conformsTo": [ - { - "@id": "https://w3id.org/ro/crate/1.1" - }, - { - "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/" - } - ] - }, - { - "@id": "ro-crate-preview.html", - "@type": "CreativeWork", - "about": { - "@id": "./" - } - }, - { - "@id": "./", - "@type": "Dataset", - "mainEntity": { - "@id": "workflow.cwl" - }, - "author": [ - { - "@id": "https://orcid.org/0000-0002-8291-8071" - }, - { - "@id": "https://orcid.org/0000-0003-0513-0288" - } - ], - "license": "Apache-2.0", - "identifier": "https://doi.org/10.48546/workflowhub.workflow.289.1", - "url": "https://workflowhub.eu/workflows/289/ro_crate?version=1", - "name": "Research Object Crate for CWL Protein MD Setup tutorial with mutations", - "description": "# Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)\r\n\r\n**Based on the official [GROMACS tutorial](http://www.mdtutorials.com/gmx/lysozyme/index.html).**\r\n\r\n***\r\n\r\nThis tutorial aims to illustrate the process of **setting up a simulation** system containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI).\r\n\r\n***\r\n\r\n## Copyright & Licensing\r\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\r\n\r\n* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)\r\n* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\r\n\r\nLicensed under the\r\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\r\n\r\n![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")", - "isBasedOn": "https://github.com/bioexcel/biobb_workflows/tree/master/biobb_wf_md_setup_mutations/cwl", - "sdDatePublished": "2023-05-15 16:40:27 +0100", - "creativeWorkStatus": "Stable", - "hasPart": [ - { - "@id": "workflow.cwl" - }, - { - "@id": "workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg" - }, - { - "@id": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/workflow_list.cwl" - }, - { - "@id": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/workflow_gather.cwl" - }, - { - "@id": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/README.md" - }, - { - "@id": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/workflow_input_descriptions.yml" - }, - { - "@id": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/ions.pdb" - }, - { - "@id": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/structure.pdb" - } - ] - }, - { - "@id": "workflow.cwl", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], - "url": "https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_md_setup_mutations/cwl/workflow.cwl", - "contentSize": 16985, - "programmingLanguage": { - "@id": "#cwl" - }, - "image": { - "@id": "workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg" - }, - "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", - "description": "# Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)\r\n\r\n**Based on the official [GROMACS tutorial](http://www.mdtutorials.com/gmx/lysozyme/index.html).**\r\n\r\n***\r\n\r\nThis tutorial aims to illustrate the process of **setting up a simulation** system containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI).\r\n\r\n***\r\n\r\n## Copyright & Licensing\r\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\r\n\r\n* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)\r\n* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\r\n\r\nLicensed under the\r\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\r\n\r\n![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")", - "name": "CWL Protein MD Setup tutorial with mutations", - "keywords": "", - "version": 1, - "license": "https://opensource.org/licenses/Apache-2.0", - 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- - - - - -
-

Research Object Crate for CWL Protein MD Setup tutorial with mutations

- - Original URL: https://workflowhub.eu/workflows/289/ro_crate?version=1 - - - - -

- # Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb) - -**Based on the official [GROMACS tutorial](http://www.mdtutorials.com/gmx/lysozyme/index.html).** - -*** - -This tutorial aims to illustrate the process of **setting up a simulation** system containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI). - -*** - -## Copyright & Licensing -This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). - -* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/) -* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) - -Licensed under the -[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. - -![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel") -

- -
- -
Author
-
Adam Hospital, Genís Bayarri
- - - - -
License
-
Apache-2.0
- -
- -

Contents

- -
- - diff --git a/0.3/example-result/data/workflow/289/structure.pdb b/0.3/example-result/data/workflow/289/structure.pdb deleted file mode 100644 index 5228267..0000000 --- a/0.3/example-result/data/workflow/289/structure.pdb +++ /dev/null @@ -1,1436 +0,0 @@ -HEADER HYDROLASE 19-MAY-97 1AKI -TITLE THE STRUCTURE OF THE ORTHORHOMBIC FORM OF HEN EGG-WHITE -TITLE 2 LYSOZYME AT 1.5 ANGSTROMS RESOLUTION -COMPND MOL_ID: 1; -COMPND 2 MOLECULE: LYSOZYME; -COMPND 3 CHAIN: A; -COMPND 4 EC: 3.2.1.17 -SOURCE MOL_ID: 1; -SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; -SOURCE 3 ORGANISM_COMMON: CHICKEN; -SOURCE 4 ORGANISM_TAXID: 9031; -SOURCE 5 CELL: EGG -KEYWDS HYDROLASE, GLYCOSIDASE -EXPDTA X-RAY DIFFRACTION -AUTHOR D.CARTER,J.HE,J.R.RUBLE,B.WRIGHT -REVDAT 2 24-FEB-09 1AKI 1 VERSN -REVDAT 1 19-NOV-97 1AKI 0 -JRNL AUTH P.J.ARTYMIUK,C.C.F.BLAKE,D.W.RICE,K.S.WILSON -JRNL TITL THE STRUCTURES OF THE MONOCLINIC AND ORTHORHOMBIC -JRNL TITL 2 FORMS OF HEN EGG-WHITE LYSOZYME AT 6 ANGSTROMS -JRNL TITL 3 RESOLUTION -JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 38 778 1982 -JRNL REFN ISSN 0108-7681 -REMARK 1 -REMARK 2 -REMARK 2 RESOLUTION. 1.50 ANGSTROMS. -REMARK 3 -REMARK 3 REFINEMENT. -REMARK 3 PROGRAM : GPRLSA, X-PLOR -REMARK 3 AUTHORS : FUREY -REMARK 3 -REMARK 3 DATA USED IN REFINEMENT. -REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 -REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 -REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 -REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 -REMARK 3 NUMBER OF REFLECTIONS : 16327 -REMARK 3 -REMARK 3 FIT TO DATA USED IN REFINEMENT. -REMARK 3 CROSS-VALIDATION METHOD : NULL -REMARK 3 FREE R VALUE TEST SET SELECTION : NULL -REMARK 3 R VALUE (WORKING + TEST SET) : NULL -REMARK 3 R VALUE (WORKING SET) : 0.212 -REMARK 3 FREE R VALUE : NULL -REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL -REMARK 3 FREE R VALUE TEST SET COUNT : NULL -REMARK 3 -REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. -REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL -REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL -REMARK 3 FREE R VALUE (NO CUTOFF) : NULL -REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL -REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL -REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL -REMARK 3 -REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. -REMARK 3 PROTEIN ATOMS : 1001 -REMARK 3 NUCLEIC ACID ATOMS : 0 -REMARK 3 HETEROGEN ATOMS : 0 -REMARK 3 SOLVENT ATOMS : 78 -REMARK 3 -REMARK 3 B VALUES. -REMARK 3 FROM WILSON PLOT (A**2) : NULL -REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL -REMARK 3 OVERALL ANISOTROPIC B VALUE. -REMARK 3 B11 (A**2) : NULL -REMARK 3 B22 (A**2) : NULL -REMARK 3 B33 (A**2) : NULL -REMARK 3 B12 (A**2) : NULL -REMARK 3 B13 (A**2) : NULL -REMARK 3 B23 (A**2) : NULL -REMARK 3 -REMARK 3 ESTIMATED COORDINATE ERROR. -REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL -REMARK 3 ESD FROM SIGMAA (A) : NULL -REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.00 -REMARK 3 -REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. -REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA -REMARK 3 BOND LENGTH (A) : 0.009 ; 0.010 -REMARK 3 ANGLE DISTANCE (A) : 0.003 ; 0.025 -REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.024 ; 0.020 -REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL -REMARK 3 -REMARK 3 PLANE RESTRAINT (A) : 0.033 ; 0.030 -REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.212 ; 0.200 -REMARK 3 -REMARK 3 NON-BONDED CONTACT RESTRAINTS. -REMARK 3 SINGLE TORSION (A) : 0.183 ; 0.300 -REMARK 3 MULTIPLE TORSION (A) : 0.159 ; 0.300 -REMARK 3 H-BOND (X...Y) (A) : 0.299 ; 0.300 -REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL -REMARK 3 -REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. -REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL -REMARK 3 PLANAR (DEGREES) : 7.900 ; 5.000 -REMARK 3 STAGGERED (DEGREES) : 17.800; 15.000 -REMARK 3 TRANSVERSE (DEGREES) : 18.900; 15.000 -REMARK 3 -REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA -REMARK 3 MAIN-CHAIN BOND (A**2) : 2.500 ; 3.000 -REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.900 ; 4.000 -REMARK 3 SIDE-CHAIN BOND (A**2) : 3.200 ; 4.000 -REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 3.000 -REMARK 3 -REMARK 3 OTHER REFINEMENT REMARKS: NULL -REMARK 4 -REMARK 4 1AKI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 -REMARK 100 -REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. -REMARK 200 -REMARK 200 EXPERIMENTAL DETAILS -REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION -REMARK 200 DATE OF DATA COLLECTION : NOV-95 -REMARK 200 TEMPERATURE (KELVIN) : 298 -REMARK 200 PH : 4.48 -REMARK 200 NUMBER OF CRYSTALS USED : 1 -REMARK 200 -REMARK 200 SYNCHROTRON (Y/N) : N -REMARK 200 RADIATION SOURCE : ROTATING ANODE -REMARK 200 BEAMLINE : NULL -REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R -REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M -REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 -REMARK 200 MONOCHROMATOR : GRAPHITE(002) -REMARK 200 OPTICS : NULL -REMARK 200 -REMARK 200 DETECTOR TYPE : IMAGE PLATE -REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC -REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU -REMARK 200 DATA SCALING SOFTWARE : BIOTEX -REMARK 200 -REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20571 -REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 -REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 -REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 -REMARK 200 -REMARK 200 OVERALL. -REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 -REMARK 200 DATA REDUNDANCY : 3.100 -REMARK 200 R MERGE (I) : 0.04400 -REMARK 200 R SYM (I) : NULL -REMARK 200 FOR THE DATA SET : 11.7000 -REMARK 200 -REMARK 200 IN THE HIGHEST RESOLUTION SHELL. -REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL -REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL -REMARK 200 COMPLETENESS FOR SHELL (%) : NULL -REMARK 200 DATA REDUNDANCY IN SHELL : NULL -REMARK 200 R MERGE FOR SHELL (I) : NULL -REMARK 200 R SYM FOR SHELL (I) : NULL -REMARK 200 FOR SHELL : NULL -REMARK 200 -REMARK 200 DIFFRACTION PROTOCOL: NULL -REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT -REMARK 200 SOFTWARE USED: X-PLOR -REMARK 200 STARTING MODEL: PDB ENTRY 2LZH -REMARK 200 -REMARK 200 REMARK: NULL -REMARK 280 -REMARK 280 CRYSTAL -REMARK 280 SOLVENT CONTENT, VS (%): 42.84 -REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 -REMARK 280 -REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.48 -REMARK 290 -REMARK 290 CRYSTALLOGRAPHIC SYMMETRY -REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 -REMARK 290 -REMARK 290 SYMOP SYMMETRY -REMARK 290 NNNMMM OPERATOR -REMARK 290 1555 X,Y,Z -REMARK 290 2555 -X+1/2,-Y,Z+1/2 -REMARK 290 3555 -X,Y+1/2,-Z+1/2 -REMARK 290 4555 X+1/2,-Y+1/2,-Z -REMARK 290 -REMARK 290 WHERE NNN -> OPERATOR NUMBER -REMARK 290 MMM -> TRANSLATION VECTOR -REMARK 290 -REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS -REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM -REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY -REMARK 290 RELATED MOLECULES. -REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.53100 -REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.25850 -REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.22550 -REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.25850 -REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.53100 -REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.22550 -REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 -REMARK 290 REMARK: NULL -REMARK 300 -REMARK 300 BIOMOLECULE: 1 -REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM -REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN -REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON -REMARK 300 BURIED SURFACE AREA. -REMARK 350 -REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN -REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE -REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS -REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND -REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. -REMARK 350 -REMARK 350 BIOMOLECULE: 1 -REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC -REMARK 350 APPLY THE FOLLOWING TO CHAINS: A -REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 -REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 -REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT -REMARK 500 -REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. -REMARK 500 -REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE -REMARK 500 NH2 ARG A 45 NH2 ARG A 68 2.16 -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: CLOSE CONTACTS -REMARK 500 -REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC -REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 -REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A -REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 -REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE -REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. -REMARK 500 -REMARK 500 DISTANCE CUTOFF: -REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS -REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS -REMARK 500 -REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE -REMARK 500 OD1 ASN A 19 ND2 ASN A 39 1556 2.09 -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: COVALENT BOND ANGLES -REMARK 500 -REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES -REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE -REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN -REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). -REMARK 500 -REMARK 500 STANDARD TABLE: -REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) -REMARK 500 -REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 -REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 -REMARK 500 -REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 -REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES -REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES -REMARK 500 ARG A 21 CD - NE - CZ ANGL. DEV. = 13.6 DEGREES -REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES -REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES -REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES -REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES -REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES -REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES -REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES -REMARK 500 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES -REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 8.6 DEGREES -REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES -REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES -REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: PLANAR GROUPS -REMARK 500 -REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL -REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE -REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN -REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS -REMARK 500 AN RMSD GREATER THAN THIS VALUE -REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; -REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). -REMARK 500 -REMARK 500 M RES CSSEQI RMS TYPE -REMARK 500 ARG A 14 0.12 SIDE_CHAIN -REMARK 500 ARG A 21 0.21 SIDE_CHAIN -REMARK 500 ARG A 68 0.15 SIDE_CHAIN -REMARK 500 ARG A 73 0.25 SIDE_CHAIN -REMARK 500 ARG A 112 0.15 SIDE_CHAIN -REMARK 500 ARG A 114 0.13 SIDE_CHAIN -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY -REMARK 500 -REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY -REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER -REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; -REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; -REMARK 500 I=INSERTION CODE). -REMARK 500 -REMARK 500 M RES CSSEQI ANGLE -REMARK 500 ARG A 128 10.17 -REMARK 500 -REMARK 500 REMARK: NULL -DBREF 1AKI A 1 129 UNP P00698 LYSC_CHICK 19 147 -SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS -SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY -SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN -SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP -SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN -SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE -SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER -SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY -SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY -SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU -FORMUL 2 HOH *78(H2 O) -HELIX 1 1 ARG A 5 ARG A 14 1 10 -HELIX 2 2 TYR A 20 GLY A 22 5 3 -HELIX 3 3 LEU A 25 SER A 36 1 12 -HELIX 4 4 CYS A 80 LEU A 84 5 5 -HELIX 5 5 THR A 89 ASP A 101 1 13 -HELIX 6 6 GLY A 104 ALA A 107 5 4 -HELIX 7 7 VAL A 109 ARG A 114 1 6 -HELIX 8 8 VAL A 120 TRP A 123 5 4 -SHEET 1 A 2 THR A 43 ARG A 45 0 -SHEET 2 A 2 THR A 51 TYR A 53 -1 N ASP A 52 O ASN A 44 -SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.97 -SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.00 -SSBOND 3 CYS A 64 CYS A 80 1555 1555 1.99 -SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 -CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 21 21 21 4 -ORIGX1 1.000000 0.000000 0.000000 0.00000 -ORIGX2 0.000000 1.000000 0.000000 0.00000 -ORIGX3 0.000000 0.000000 1.000000 0.00000 -SCALE1 0.016931 0.000000 0.000000 0.00000 -SCALE2 0.000000 0.014609 0.000000 0.00000 -SCALE3 0.000000 0.000000 0.032769 0.00000 -ATOM 1 N LYS A 1 35.365 22.342 -11.980 1.00 22.28 N -ATOM 2 CA LYS A 1 35.892 21.073 -11.427 1.00 21.12 C -ATOM 3 C LYS A 1 34.741 20.264 -10.844 1.00 16.85 C -ATOM 4 O LYS A 1 33.945 20.813 -10.081 1.00 18.94 O -ATOM 5 CB LYS A 1 36.872 21.435 -10.306 1.00 20.78 C -ATOM 6 CG LYS A 1 37.453 20.248 -9.565 1.00 18.47 C -ATOM 7 CD LYS A 1 38.688 20.649 -8.775 1.00 20.32 C -ATOM 8 CE LYS A 1 39.057 19.508 -7.837 1.00 24.76 C -ATOM 9 NZ LYS A 1 40.423 19.771 -7.299 1.00 28.27 N -ATOM 10 N VAL A 2 34.739 18.961 -11.042 1.00 19.96 N -ATOM 11 CA VAL A 2 33.903 17.998 -10.333 1.00 18.10 C -ATOM 12 C VAL A 2 34.800 17.312 -9.294 1.00 19.39 C -ATOM 13 O VAL A 2 35.759 16.605 -9.665 1.00 22.14 O -ATOM 14 CB VAL A 2 33.140 17.034 -11.232 1.00 16.81 C -ATOM 15 CG1 VAL A 2 32.251 16.084 -10.434 1.00 21.92 C -ATOM 16 CG2 VAL A 2 32.294 17.714 -12.290 1.00 19.46 C -ATOM 17 N PHE A 3 34.491 17.546 -8.038 1.00 19.89 N -ATOM 18 CA PHE A 3 35.185 16.903 -6.918 1.00 17.43 C -ATOM 19 C PHE A 3 34.742 15.441 -6.771 1.00 15.70 C -ATOM 20 O PHE A 3 33.525 15.162 -6.862 1.00 18.52 O -ATOM 21 CB PHE A 3 34.967 17.632 -5.594 1.00 17.94 C -ATOM 22 CG PHE A 3 35.944 18.737 -5.375 1.00 16.78 C -ATOM 23 CD1 PHE A 3 35.666 20.050 -5.798 1.00 15.97 C -ATOM 24 CD2 PHE A 3 37.000 18.557 -4.473 1.00 19.95 C -ATOM 25 CE1 PHE A 3 36.577 21.076 -5.568 1.00 17.32 C -ATOM 26 CE2 PHE A 3 37.869 19.589 -4.157 1.00 17.65 C -ATOM 27 CZ PHE A 3 37.636 20.873 -4.666 1.00 17.91 C -ATOM 28 N GLY A 4 35.724 14.639 -6.331 1.00 16.79 N -ATOM 29 CA GLY A 4 35.366 13.280 -5.870 1.00 16.34 C -ATOM 30 C GLY A 4 34.924 13.420 -4.415 1.00 11.91 C -ATOM 31 O GLY A 4 35.303 14.403 -3.781 1.00 16.23 O -ATOM 32 N ARG A 5 34.053 12.538 -3.973 1.00 14.65 N -ATOM 33 CA ARG A 5 33.565 12.538 -2.588 1.00 15.91 C -ATOM 34 C ARG A 5 34.665 12.734 -1.556 1.00 15.38 C -ATOM 35 O ARG A 5 34.669 13.651 -0.704 1.00 13.15 O -ATOM 36 CB ARG A 5 32.765 11.262 -2.331 1.00 17.38 C -ATOM 37 CG ARG A 5 32.213 11.203 -0.920 1.00 13.79 C -ATOM 38 CD ARG A 5 31.375 10.001 -0.722 1.00 15.84 C -ATOM 39 NE ARG A 5 32.059 8.749 -0.958 1.00 18.74 N -ATOM 40 CZ ARG A 5 32.733 8.011 -0.097 1.00 15.19 C -ATOM 41 NH1 ARG A 5 32.836 8.332 1.187 1.00 17.50 N -ATOM 42 NH2 ARG A 5 33.245 6.836 -0.526 1.00 23.44 N -ATOM 43 N CYS A 6 35.674 11.853 -1.612 1.00 14.07 N -ATOM 44 CA CYS A 6 36.781 11.870 -0.654 1.00 14.62 C -ATOM 45 C CYS A 6 37.747 13.050 -0.777 1.00 10.99 C -ATOM 46 O CYS A 6 38.148 13.609 0.264 1.00 16.34 O -ATOM 47 CB CYS A 6 37.491 10.532 -0.621 1.00 16.90 C -ATOM 48 SG CYS A 6 36.540 9.205 0.140 1.00 18.61 S -ATOM 49 N GLU A 7 37.861 13.481 -2.019 1.00 14.24 N -ATOM 50 CA GLU A 7 38.685 14.686 -2.311 1.00 13.83 C -ATOM 51 C GLU A 7 38.049 15.926 -1.658 1.00 14.86 C -ATOM 52 O GLU A 7 38.744 16.729 -1.011 1.00 15.01 O -ATOM 53 CB GLU A 7 38.784 14.846 -3.818 1.00 14.85 C -ATOM 54 CG GLU A 7 39.540 16.051 -4.379 1.00 18.50 C -ATOM 55 CD GLU A 7 39.576 16.242 -5.870 1.00 20.16 C -ATOM 56 OE1 GLU A 7 38.672 15.644 -6.491 1.00 26.20 O -ATOM 57 OE2 GLU A 7 40.415 16.953 -6.381 1.00 25.49 O -ATOM 58 N LEU A 8 36.743 16.049 -1.819 1.00 15.18 N -ATOM 59 CA LEU A 8 35.964 17.158 -1.255 1.00 12.72 C -ATOM 60 C LEU A 8 36.051 17.132 0.266 1.00 9.45 C -ATOM 61 O LEU A 8 36.159 18.166 0.920 1.00 13.45 O -ATOM 62 CB LEU A 8 34.528 17.172 -1.811 1.00 14.31 C -ATOM 63 CG LEU A 8 33.718 18.354 -1.305 1.00 15.95 C -ATOM 64 CD1 LEU A 8 34.297 19.656 -1.841 1.00 16.56 C -ATOM 65 CD2 LEU A 8 32.246 18.143 -1.596 1.00 15.88 C -ATOM 66 N ALA A 9 35.754 15.980 0.828 1.00 14.24 N -ATOM 67 CA ALA A 9 35.838 15.757 2.284 1.00 13.25 C -ATOM 68 C ALA A 9 37.144 16.314 2.840 1.00 12.89 C -ATOM 69 O ALA A 9 37.151 16.978 3.897 1.00 14.78 O -ATOM 70 CB ALA A 9 35.656 14.287 2.623 1.00 13.89 C -ATOM 71 N ALA A 10 38.272 15.983 2.204 1.00 12.54 N -ATOM 72 CA ALA A 10 39.610 16.431 2.616 1.00 16.58 C -ATOM 73 C ALA A 10 39.736 17.944 2.459 1.00 15.35 C -ATOM 74 O ALA A 10 40.193 18.499 3.469 1.00 17.40 O -ATOM 75 CB ALA A 10 40.708 15.706 1.842 1.00 15.49 C -ATOM 76 N ALA A 11 39.227 18.519 1.385 1.00 13.54 N -ATOM 77 CA ALA A 11 39.264 19.982 1.223 1.00 15.23 C -ATOM 78 C ALA A 11 38.491 20.702 2.321 1.00 15.68 C -ATOM 79 O ALA A 11 38.946 21.658 2.953 1.00 16.87 O -ATOM 80 CB ALA A 11 38.869 20.421 -0.175 1.00 14.12 C -ATOM 81 N MET A 12 37.288 20.214 2.590 1.00 15.47 N -ATOM 82 CA MET A 12 36.398 20.781 3.612 1.00 13.69 C -ATOM 83 C MET A 12 36.990 20.715 5.007 1.00 12.55 C -ATOM 84 O MET A 12 36.906 21.637 5.840 1.00 17.69 O -ATOM 85 CB MET A 12 34.993 20.213 3.515 1.00 11.18 C -ATOM 86 CG MET A 12 34.320 20.724 2.265 1.00 15.06 C -ATOM 87 SD MET A 12 32.634 19.986 2.235 1.00 17.81 S -ATOM 88 CE MET A 12 31.788 21.135 1.138 1.00 18.08 C -ATOM 89 N LYS A 13 37.688 19.628 5.314 1.00 12.42 N -ATOM 90 CA LYS A 13 38.387 19.385 6.579 1.00 14.58 C -ATOM 91 C LYS A 13 39.460 20.467 6.731 1.00 14.55 C -ATOM 92 O LYS A 13 39.507 21.137 7.776 1.00 16.49 O -ATOM 93 CB LYS A 13 38.934 17.952 6.572 1.00 15.36 C -ATOM 94 CG LYS A 13 39.742 17.555 7.798 1.00 20.46 C -ATOM 95 CD LYS A 13 38.973 16.777 8.834 1.00 23.53 C -ATOM 96 CE LYS A 13 39.293 15.305 8.751 1.00 26.37 C -ATOM 97 NZ LYS A 13 38.077 14.461 8.946 1.00 30.88 N -ATOM 98 N ARG A 14 40.267 20.629 5.688 1.00 18.91 N -ATOM 99 CA ARG A 14 41.387 21.577 5.713 1.00 17.66 C -ATOM 100 C ARG A 14 40.927 23.017 5.881 1.00 16.78 C -ATOM 101 O ARG A 14 41.557 23.834 6.584 1.00 20.06 O -ATOM 102 CB ARG A 14 42.388 21.351 4.601 1.00 20.89 C -ATOM 103 CG ARG A 14 42.173 22.079 3.289 1.00 25.07 C -ATOM 104 CD ARG A 14 43.444 22.075 2.490 1.00 23.98 C -ATOM 105 NE ARG A 14 43.687 20.710 2.012 1.00 31.92 N -ATOM 106 CZ ARG A 14 43.098 20.255 0.892 1.00 26.04 C -ATOM 107 NH1 ARG A 14 42.695 21.186 0.018 1.00 33.46 N -ATOM 108 NH2 ARG A 14 42.949 18.957 0.689 1.00 25.91 N -ATOM 109 N HIS A 15 39.681 23.247 5.463 1.00 17.84 N -ATOM 110 CA HIS A 15 39.075 24.591 5.526 1.00 15.99 C -ATOM 111 C HIS A 15 38.310 24.861 6.814 1.00 17.70 C -ATOM 112 O HIS A 15 37.608 25.875 6.952 1.00 22.68 O -ATOM 113 CB HIS A 15 38.223 24.918 4.285 1.00 19.19 C -ATOM 114 CG HIS A 15 39.085 25.388 3.171 1.00 20.14 C -ATOM 115 ND1 HIS A 15 39.457 24.635 2.091 1.00 24.53 N -ATOM 116 CD2 HIS A 15 39.739 26.570 2.993 1.00 24.44 C -ATOM 117 CE1 HIS A 15 40.211 25.312 1.258 1.00 20.68 C -ATOM 118 NE2 HIS A 15 40.524 26.419 1.889 1.00 27.34 N -ATOM 119 N GLY A 16 38.296 23.927 7.720 1.00 17.50 N -ATOM 120 CA GLY A 16 37.765 24.025 9.072 1.00 18.71 C -ATOM 121 C GLY A 16 36.264 23.799 9.210 1.00 18.40 C -ATOM 122 O GLY A 16 35.646 24.400 10.127 1.00 21.57 O -ATOM 123 N LEU A 17 35.665 23.073 8.274 1.00 17.56 N -ATOM 124 CA LEU A 17 34.238 22.795 8.298 1.00 15.38 C -ATOM 125 C LEU A 17 33.845 21.682 9.266 1.00 18.28 C -ATOM 126 O LEU A 17 32.643 21.594 9.552 1.00 18.24 O -ATOM 127 CB LEU A 17 33.648 22.647 6.901 1.00 15.02 C -ATOM 128 CG LEU A 17 33.451 23.889 6.060 1.00 16.08 C -ATOM 129 CD1 LEU A 17 32.933 23.420 4.705 1.00 13.83 C -ATOM 130 CD2 LEU A 17 32.556 24.946 6.679 1.00 18.60 C -ATOM 131 N ASP A 18 34.785 20.814 9.605 1.00 16.36 N -ATOM 132 CA ASP A 18 34.492 19.722 10.526 1.00 16.25 C -ATOM 133 C ASP A 18 34.015 20.222 11.901 1.00 17.32 C -ATOM 134 O ASP A 18 34.826 20.778 12.658 1.00 20.27 O -ATOM 135 CB ASP A 18 35.557 18.633 10.598 1.00 19.37 C -ATOM 136 CG ASP A 18 35.017 17.408 11.311 1.00 20.25 C -ATOM 137 OD1 ASP A 18 33.805 17.154 11.455 1.00 21.00 O -ATOM 138 OD2 ASP A 18 35.925 16.603 11.662 1.00 27.06 O -ATOM 139 N ASN A 19 32.746 19.990 12.205 1.00 18.55 N -ATOM 140 CA ASN A 19 32.123 20.431 13.448 1.00 17.19 C -ATOM 141 C ASN A 19 31.854 21.941 13.497 1.00 16.61 C -ATOM 142 O ASN A 19 31.426 22.398 14.573 1.00 18.56 O -ATOM 143 CB ASN A 19 32.767 20.004 14.770 1.00 18.92 C -ATOM 144 CG ASN A 19 32.162 20.512 16.064 1.00 24.64 C -ATOM 145 OD1 ASN A 19 30.967 20.273 16.355 1.00 32.53 O -ATOM 146 ND2 ASN A 19 32.847 21.361 16.852 1.00 24.14 N -ATOM 147 N TYR A 20 31.969 22.650 12.406 1.00 16.84 N -ATOM 148 CA TYR A 20 31.707 24.099 12.411 1.00 15.54 C -ATOM 149 C TYR A 20 30.231 24.343 12.759 1.00 15.81 C -ATOM 150 O TYR A 20 29.288 23.874 12.118 1.00 16.89 O -ATOM 151 CB TYR A 20 32.070 24.736 11.066 1.00 18.16 C -ATOM 152 CG TYR A 20 32.061 26.250 11.144 1.00 20.28 C -ATOM 153 CD1 TYR A 20 33.141 26.886 11.760 1.00 21.42 C -ATOM 154 CD2 TYR A 20 30.979 27.004 10.691 1.00 20.44 C -ATOM 155 CE1 TYR A 20 33.206 28.277 11.794 1.00 22.24 C -ATOM 156 CE2 TYR A 20 31.018 28.399 10.779 1.00 21.36 C -ATOM 157 CZ TYR A 20 32.102 29.017 11.383 1.00 19.38 C -ATOM 158 OH TYR A 20 32.136 30.371 11.525 1.00 26.77 O -ATOM 159 N ARG A 21 30.088 25.142 13.803 1.00 18.43 N -ATOM 160 CA ARG A 21 28.774 25.553 14.319 1.00 15.68 C -ATOM 161 C ARG A 21 27.964 24.312 14.623 1.00 15.17 C -ATOM 162 O ARG A 21 26.733 24.333 14.606 1.00 18.36 O -ATOM 163 CB ARG A 21 28.014 26.565 13.453 1.00 19.21 C -ATOM 164 CG ARG A 21 28.507 27.995 13.535 1.00 21.50 C -ATOM 165 CD ARG A 21 28.110 28.755 14.765 1.00 25.00 C -ATOM 166 NE ARG A 21 29.319 29.321 15.324 1.00 30.37 N -ATOM 167 CZ ARG A 21 30.215 30.234 14.978 1.00 29.02 C -ATOM 168 NH1 ARG A 21 31.501 29.856 14.846 1.00 29.04 N -ATOM 169 NH2 ARG A 21 29.938 31.437 14.495 1.00 31.89 N -ATOM 170 N GLY A 22 28.689 23.250 14.998 1.00 17.81 N -ATOM 171 CA GLY A 22 28.103 22.021 15.519 1.00 17.72 C -ATOM 172 C GLY A 22 27.748 21.018 14.436 1.00 18.89 C -ATOM 173 O GLY A 22 27.085 20.022 14.784 1.00 23.26 O -ATOM 174 N TYR A 23 28.209 21.230 13.216 1.00 18.20 N -ATOM 175 CA TYR A 23 27.887 20.318 12.111 1.00 15.42 C -ATOM 176 C TYR A 23 29.124 19.533 11.628 1.00 16.30 C -ATOM 177 O TYR A 23 30.045 20.191 11.139 1.00 16.66 O -ATOM 178 CB TYR A 23 27.351 21.107 10.913 1.00 15.82 C -ATOM 179 CG TYR A 23 26.001 21.745 11.127 1.00 15.96 C -ATOM 180 CD1 TYR A 23 24.846 20.962 11.139 1.00 14.81 C -ATOM 181 CD2 TYR A 23 25.897 23.096 11.458 1.00 16.60 C -ATOM 182 CE1 TYR A 23 23.600 21.518 11.422 1.00 17.08 C -ATOM 183 CE2 TYR A 23 24.647 23.673 11.726 1.00 19.34 C -ATOM 184 CZ TYR A 23 23.518 22.881 11.701 1.00 19.21 C -ATOM 185 OH TYR A 23 22.289 23.438 11.912 1.00 25.61 O -ATOM 186 N SER A 24 29.029 18.223 11.810 1.00 15.35 N -ATOM 187 CA SER A 24 30.143 17.347 11.414 1.00 16.89 C -ATOM 188 C SER A 24 30.359 17.379 9.895 1.00 15.61 C -ATOM 189 O SER A 24 29.442 17.687 9.139 1.00 13.88 O -ATOM 190 CB SER A 24 29.922 15.934 11.907 1.00 17.54 C -ATOM 191 OG SER A 24 28.799 15.336 11.308 1.00 19.85 O -ATOM 192 N LEU A 25 31.593 17.028 9.540 1.00 16.08 N -ATOM 193 CA LEU A 25 32.035 17.092 8.138 1.00 13.16 C -ATOM 194 C LEU A 25 31.030 16.437 7.183 1.00 13.39 C -ATOM 195 O LEU A 25 30.874 16.924 6.056 1.00 15.34 O -ATOM 196 CB LEU A 25 33.410 16.409 8.084 1.00 13.47 C -ATOM 197 CG LEU A 25 34.015 16.477 6.689 1.00 12.91 C -ATOM 198 CD1 LEU A 25 34.174 17.929 6.289 1.00 13.04 C -ATOM 199 CD2 LEU A 25 35.398 15.810 6.752 1.00 14.54 C -ATOM 200 N GLY A 26 30.501 15.280 7.576 1.00 13.10 N -ATOM 201 CA GLY A 26 29.539 14.561 6.756 1.00 13.88 C -ATOM 202 C GLY A 26 28.338 15.378 6.277 1.00 12.12 C -ATOM 203 O GLY A 26 27.886 15.250 5.120 1.00 13.13 O -ATOM 204 N ASN A 27 27.905 16.281 7.161 1.00 12.16 N -ATOM 205 CA ASN A 27 26.827 17.227 6.857 1.00 14.74 C -ATOM 206 C ASN A 27 27.164 18.015 5.597 1.00 15.43 C -ATOM 207 O ASN A 27 26.317 18.208 4.720 1.00 15.27 O -ATOM 208 CB ASN A 27 26.484 18.126 8.054 1.00 12.34 C -ATOM 209 CG ASN A 27 25.681 17.267 9.048 1.00 12.22 C -ATOM 210 OD1 ASN A 27 24.511 16.933 8.820 1.00 17.40 O -ATOM 211 ND2 ASN A 27 26.348 17.052 10.169 1.00 18.27 N -ATOM 212 N TRP A 28 28.344 18.591 5.583 1.00 16.78 N -ATOM 213 CA TRP A 28 28.831 19.475 4.513 1.00 16.49 C -ATOM 214 C TRP A 28 28.940 18.741 3.183 1.00 12.99 C -ATOM 215 O TRP A 28 28.742 19.321 2.090 1.00 13.97 O -ATOM 216 CB TRP A 28 30.104 20.145 5.023 1.00 14.55 C -ATOM 217 CG TRP A 28 29.941 20.978 6.251 1.00 11.93 C -ATOM 218 CD1 TRP A 28 30.176 20.624 7.546 1.00 14.42 C -ATOM 219 CD2 TRP A 28 29.319 22.284 6.287 1.00 13.11 C -ATOM 220 NE1 TRP A 28 29.924 21.690 8.365 1.00 16.94 N -ATOM 221 CE2 TRP A 28 29.337 22.679 7.641 1.00 14.07 C -ATOM 222 CE3 TRP A 28 28.894 23.168 5.295 1.00 15.97 C -ATOM 223 CZ2 TRP A 28 28.913 23.943 8.038 1.00 18.07 C -ATOM 224 CZ3 TRP A 28 28.398 24.404 5.682 1.00 18.26 C -ATOM 225 CH2 TRP A 28 28.431 24.766 7.025 1.00 17.18 C -ATOM 226 N VAL A 29 29.572 17.543 3.261 1.00 13.00 N -ATOM 227 CA VAL A 29 29.729 16.711 2.047 1.00 14.15 C -ATOM 228 C VAL A 29 28.379 16.340 1.429 1.00 10.43 C -ATOM 229 O VAL A 29 28.166 16.496 0.228 1.00 13.40 O -ATOM 230 CB VAL A 29 30.649 15.492 2.359 1.00 12.76 C -ATOM 231 CG1 VAL A 29 30.782 14.596 1.136 1.00 15.37 C -ATOM 232 CG2 VAL A 29 32.010 16.050 2.772 1.00 14.18 C -ATOM 233 N CYS A 30 27.501 15.906 2.299 1.00 15.32 N -ATOM 234 CA CYS A 30 26.115 15.567 1.991 1.00 15.59 C -ATOM 235 C CYS A 30 25.388 16.723 1.302 1.00 12.37 C -ATOM 236 O CYS A 30 24.894 16.516 0.172 1.00 14.44 O -ATOM 237 CB CYS A 30 25.343 15.046 3.172 1.00 14.99 C -ATOM 238 SG CYS A 30 23.719 14.376 2.695 1.00 17.71 S -ATOM 239 N ALA A 31 25.533 17.913 1.870 1.00 16.06 N -ATOM 240 CA ALA A 31 24.949 19.130 1.305 1.00 15.82 C -ATOM 241 C ALA A 31 25.487 19.354 -0.115 1.00 15.34 C -ATOM 242 O ALA A 31 24.675 19.686 -0.998 1.00 16.00 O -ATOM 243 CB ALA A 31 25.167 20.335 2.200 1.00 14.90 C -ATOM 244 N ALA A 32 26.807 19.354 -0.286 1.00 11.93 N -ATOM 245 CA ALA A 32 27.461 19.536 -1.579 1.00 13.08 C -ATOM 246 C ALA A 32 26.943 18.538 -2.620 1.00 12.38 C -ATOM 247 O ALA A 32 26.767 18.857 -3.789 1.00 13.89 O -ATOM 248 CB ALA A 32 28.982 19.476 -1.398 1.00 14.17 C -ATOM 249 N LYS A 33 26.731 17.303 -2.193 1.00 15.16 N -ATOM 250 CA LYS A 33 26.261 16.216 -3.037 1.00 16.16 C -ATOM 251 C LYS A 33 24.903 16.555 -3.658 1.00 15.04 C -ATOM 252 O LYS A 33 24.806 16.511 -4.890 1.00 15.00 O -ATOM 253 CB LYS A 33 26.221 14.860 -2.351 1.00 16.71 C -ATOM 254 CG LYS A 33 25.697 13.696 -3.185 1.00 19.51 C -ATOM 255 CD LYS A 33 26.498 13.400 -4.446 1.00 17.12 C -ATOM 256 CE LYS A 33 25.686 12.464 -5.331 1.00 24.06 C -ATOM 257 NZ LYS A 33 26.423 11.979 -6.525 1.00 26.78 N -ATOM 258 N PHE A 34 23.972 16.946 -2.817 1.00 16.81 N -ATOM 259 CA PHE A 34 22.569 17.125 -3.247 1.00 17.51 C -ATOM 260 C PHE A 34 22.346 18.506 -3.836 1.00 18.19 C -ATOM 261 O PHE A 34 21.504 18.692 -4.759 1.00 20.21 O -ATOM 262 CB PHE A 34 21.626 16.673 -2.130 1.00 18.58 C -ATOM 263 CG PHE A 34 21.644 15.172 -1.965 1.00 22.22 C -ATOM 264 CD1 PHE A 34 21.209 14.353 -3.007 1.00 20.24 C -ATOM 265 CD2 PHE A 34 22.272 14.627 -0.851 1.00 20.00 C -ATOM 266 CE1 PHE A 34 21.372 12.961 -2.910 1.00 22.03 C -ATOM 267 CE2 PHE A 34 22.443 13.245 -0.743 1.00 21.96 C -ATOM 268 CZ PHE A 34 21.923 12.406 -1.737 1.00 20.77 C -ATOM 269 N GLU A 35 23.251 19.415 -3.451 1.00 15.27 N -ATOM 270 CA GLU A 35 23.178 20.789 -3.996 1.00 15.45 C -ATOM 271 C GLU A 35 23.661 20.944 -5.423 1.00 17.45 C -ATOM 272 O GLU A 35 23.014 21.514 -6.310 1.00 17.91 O -ATOM 273 CB GLU A 35 23.698 21.892 -3.107 1.00 14.42 C -ATOM 274 CG GLU A 35 22.994 22.212 -1.809 1.00 11.08 C -ATOM 275 CD GLU A 35 21.631 22.846 -1.864 1.00 13.55 C -ATOM 276 OE1 GLU A 35 21.408 23.360 -2.981 1.00 20.77 O -ATOM 277 OE2 GLU A 35 20.947 23.032 -0.874 1.00 22.72 O -ATOM 278 N SER A 36 24.867 20.483 -5.674 1.00 15.66 N -ATOM 279 CA SER A 36 25.626 20.615 -6.903 1.00 17.79 C -ATOM 280 C SER A 36 26.139 19.341 -7.569 1.00 16.97 C -ATOM 281 O SER A 36 26.750 19.464 -8.642 1.00 21.78 O -ATOM 282 CB SER A 36 26.830 21.528 -6.654 1.00 18.12 C -ATOM 283 OG SER A 36 27.747 20.951 -5.748 1.00 15.16 O -ATOM 284 N ASN A 37 25.957 18.222 -6.927 1.00 20.15 N -ATOM 285 CA ASN A 37 26.628 16.968 -7.297 1.00 20.85 C -ATOM 286 C ASN A 37 28.149 17.091 -7.302 1.00 19.72 C -ATOM 287 O ASN A 37 28.813 16.627 -8.254 1.00 20.79 O -ATOM 288 CB ASN A 37 26.028 16.490 -8.617 1.00 20.82 C -ATOM 289 CG ASN A 37 26.156 14.980 -8.782 1.00 23.63 C -ATOM 290 OD1 ASN A 37 26.640 14.266 -7.885 1.00 28.05 O -ATOM 291 ND2 ASN A 37 25.867 14.506 -9.990 1.00 29.61 N -ATOM 292 N PHE A 38 28.691 17.882 -6.383 1.00 16.12 N -ATOM 293 CA PHE A 38 30.129 18.115 -6.279 1.00 14.75 C -ATOM 294 C PHE A 38 30.717 18.903 -7.448 1.00 13.86 C -ATOM 295 O PHE A 38 31.923 18.794 -7.702 1.00 16.66 O -ATOM 296 CB PHE A 38 30.914 16.823 -6.047 1.00 17.09 C -ATOM 297 CG PHE A 38 30.487 16.006 -4.863 1.00 15.96 C -ATOM 298 CD1 PHE A 38 30.100 16.572 -3.655 1.00 15.43 C -ATOM 299 CD2 PHE A 38 30.507 14.603 -4.993 1.00 17.66 C -ATOM 300 CE1 PHE A 38 29.766 15.808 -2.558 1.00 16.83 C -ATOM 301 CE2 PHE A 38 30.136 13.814 -3.891 1.00 15.86 C -ATOM 302 CZ PHE A 38 29.835 14.410 -2.646 1.00 18.90 C -ATOM 303 N ASN A 39 29.936 19.792 -8.033 1.00 17.63 N -ATOM 304 CA ASN A 39 30.341 20.573 -9.199 1.00 16.77 C -ATOM 305 C ASN A 39 30.543 22.034 -8.823 1.00 17.13 C -ATOM 306 O ASN A 39 29.544 22.649 -8.423 1.00 17.24 O -ATOM 307 CB ASN A 39 29.406 20.300 -10.366 1.00 17.40 C -ATOM 308 CG ASN A 39 29.876 20.771 -11.716 1.00 16.96 C -ATOM 309 OD1 ASN A 39 30.579 21.750 -11.956 1.00 23.22 O -ATOM 310 ND2 ASN A 39 29.578 19.864 -12.653 1.00 26.35 N -ATOM 311 N THR A 40 31.766 22.492 -8.928 1.00 14.88 N -ATOM 312 CA THR A 40 32.139 23.869 -8.657 1.00 16.08 C -ATOM 313 C THR A 40 31.504 24.890 -9.589 1.00 16.31 C -ATOM 314 O THR A 40 31.316 26.054 -9.213 1.00 17.50 O -ATOM 315 CB THR A 40 33.684 24.103 -8.422 1.00 17.07 C -ATOM 316 OG1 THR A 40 34.270 24.156 -9.775 1.00 23.76 O -ATOM 317 CG2 THR A 40 34.414 23.119 -7.491 1.00 16.46 C -ATOM 318 N GLN A 41 31.001 24.430 -10.706 1.00 16.39 N -ATOM 319 CA GLN A 41 30.524 25.291 -11.812 1.00 16.67 C -ATOM 320 C GLN A 41 28.993 25.381 -11.874 1.00 15.44 C -ATOM 321 O GLN A 41 28.504 26.019 -12.837 1.00 18.55 O -ATOM 322 CB GLN A 41 31.047 24.817 -13.168 1.00 19.65 C -ATOM 323 CG GLN A 41 32.549 25.004 -13.279 1.00 21.26 C -ATOM 324 CD GLN A 41 32.763 26.236 -14.129 1.00 26.23 C -ATOM 325 OE1 GLN A 41 32.356 26.308 -15.291 1.00 24.68 O -ATOM 326 NE2 GLN A 41 33.276 27.231 -13.420 1.00 25.96 N -ATOM 327 N ALA A 42 28.329 24.640 -11.012 1.00 15.95 N -ATOM 328 CA ALA A 42 26.859 24.579 -11.061 1.00 17.42 C -ATOM 329 C ALA A 42 26.257 25.969 -10.807 1.00 18.93 C -ATOM 330 O ALA A 42 26.645 26.686 -9.884 1.00 17.00 O -ATOM 331 CB ALA A 42 26.355 23.604 -9.998 1.00 22.79 C -ATOM 332 N THR A 43 25.276 26.293 -11.643 1.00 18.30 N -ATOM 333 CA THR A 43 24.441 27.490 -11.476 1.00 17.73 C -ATOM 334 C THR A 43 22.976 27.112 -11.714 1.00 19.61 C -ATOM 335 O THR A 43 22.715 26.271 -12.594 1.00 22.06 O -ATOM 336 CB THR A 43 24.814 28.728 -12.375 1.00 17.58 C -ATOM 337 OG1 THR A 43 24.555 28.321 -13.756 1.00 20.94 O -ATOM 338 CG2 THR A 43 26.247 29.213 -12.184 1.00 18.26 C -ATOM 339 N ASN A 44 22.088 27.742 -10.971 1.00 19.77 N -ATOM 340 CA ASN A 44 20.640 27.497 -11.108 1.00 19.51 C -ATOM 341 C ASN A 44 19.903 28.842 -10.963 1.00 14.85 C -ATOM 342 O ASN A 44 20.169 29.600 -10.033 1.00 19.43 O -ATOM 343 CB ASN A 44 20.155 26.480 -10.080 1.00 19.93 C -ATOM 344 CG ASN A 44 18.646 26.315 -10.115 1.00 22.01 C -ATOM 345 OD1 ASN A 44 18.128 25.720 -11.078 1.00 29.53 O -ATOM 346 ND2 ASN A 44 17.906 26.927 -9.188 1.00 22.94 N -ATOM 347 N ARG A 45 19.058 29.117 -11.924 1.00 16.90 N -ATOM 348 CA ARG A 45 18.303 30.363 -12.015 1.00 18.37 C -ATOM 349 C ARG A 45 16.955 30.163 -11.326 1.00 18.76 C -ATOM 350 O ARG A 45 16.396 29.062 -11.425 1.00 20.87 O -ATOM 351 CB ARG A 45 18.143 30.836 -13.462 1.00 19.30 C -ATOM 352 CG ARG A 45 17.012 31.859 -13.557 1.00 23.98 C -ATOM 353 CD ARG A 45 17.502 33.134 -12.930 1.00 23.36 C -ATOM 354 NE ARG A 45 18.311 33.758 -13.981 1.00 29.56 N -ATOM 355 CZ ARG A 45 17.620 34.271 -15.020 1.00 27.18 C -ATOM 356 NH1 ARG A 45 16.287 34.331 -15.098 1.00 31.99 N -ATOM 357 NH2 ARG A 45 18.374 34.698 -16.030 1.00 32.43 N -ATOM 358 N ASN A 46 16.553 31.171 -10.554 1.00 18.13 N -ATOM 359 CA ASN A 46 15.304 31.071 -9.782 1.00 20.10 C -ATOM 360 C ASN A 46 14.261 32.063 -10.313 1.00 17.35 C -ATOM 361 O ASN A 46 14.617 33.104 -10.880 1.00 19.15 O -ATOM 362 CB ASN A 46 15.576 31.229 -8.295 1.00 20.05 C -ATOM 363 CG ASN A 46 16.543 30.240 -7.679 1.00 20.12 C -ATOM 364 OD1 ASN A 46 17.659 30.661 -7.346 1.00 21.21 O -ATOM 365 ND2 ASN A 46 16.125 28.975 -7.600 1.00 19.44 N -ATOM 366 N THR A 47 13.027 31.834 -9.887 1.00 19.96 N -ATOM 367 CA THR A 47 11.871 32.654 -10.246 1.00 19.12 C -ATOM 368 C THR A 47 12.001 34.107 -9.810 1.00 19.44 C -ATOM 369 O THR A 47 11.600 34.969 -10.606 1.00 23.16 O -ATOM 370 CB THR A 47 10.499 32.017 -9.789 1.00 17.70 C -ATOM 371 OG1 THR A 47 10.507 32.195 -8.342 1.00 23.76 O -ATOM 372 CG2 THR A 47 10.331 30.554 -10.188 1.00 22.66 C -ATOM 373 N ASP A 48 12.625 34.377 -8.683 1.00 19.25 N -ATOM 374 CA ASP A 48 12.885 35.716 -8.168 1.00 17.33 C -ATOM 375 C ASP A 48 14.010 36.505 -8.823 1.00 17.71 C -ATOM 376 O ASP A 48 14.246 37.621 -8.309 1.00 23.04 O -ATOM 377 CB ASP A 48 13.023 35.735 -6.640 1.00 18.02 C -ATOM 378 CG ASP A 48 14.367 35.174 -6.168 1.00 17.88 C -ATOM 379 OD1 ASP A 48 15.104 34.602 -6.991 1.00 18.55 O -ATOM 380 OD2 ASP A 48 14.750 35.442 -5.013 1.00 22.86 O -ATOM 381 N GLY A 49 14.650 36.018 -9.862 1.00 17.62 N -ATOM 382 CA GLY A 49 15.744 36.702 -10.546 1.00 17.27 C -ATOM 383 C GLY A 49 17.147 36.315 -10.096 1.00 16.80 C -ATOM 384 O GLY A 49 18.168 36.688 -10.694 1.00 20.27 O -ATOM 385 N SER A 50 17.173 35.661 -8.930 1.00 19.61 N -ATOM 386 CA SER A 50 18.435 35.225 -8.279 1.00 14.28 C -ATOM 387 C SER A 50 18.977 33.963 -8.941 1.00 18.09 C -ATOM 388 O SER A 50 18.273 33.255 -9.697 1.00 16.76 O -ATOM 389 CB SER A 50 18.272 35.089 -6.781 1.00 17.64 C -ATOM 390 OG SER A 50 17.530 33.930 -6.463 1.00 17.54 O -ATOM 391 N THR A 51 20.271 33.766 -8.734 1.00 16.00 N -ATOM 392 CA THR A 51 20.970 32.557 -9.202 1.00 13.82 C -ATOM 393 C THR A 51 21.718 31.969 -8.000 1.00 14.58 C -ATOM 394 O THR A 51 22.160 32.712 -7.119 1.00 13.28 O -ATOM 395 CB THR A 51 21.904 32.908 -10.419 1.00 12.66 C -ATOM 396 OG1 THR A 51 21.099 33.576 -11.407 1.00 17.65 O -ATOM 397 CG2 THR A 51 22.686 31.699 -10.952 1.00 14.39 C -ATOM 398 N ASP A 52 21.708 30.650 -7.927 1.00 14.66 N -ATOM 399 CA ASP A 52 22.528 29.900 -6.959 1.00 13.43 C -ATOM 400 C ASP A 52 23.843 29.488 -7.635 1.00 12.35 C -ATOM 401 O ASP A 52 23.847 29.066 -8.805 1.00 15.18 O -ATOM 402 CB ASP A 52 21.765 28.649 -6.554 1.00 14.12 C -ATOM 403 CG ASP A 52 20.396 28.991 -6.002 1.00 20.03 C -ATOM 404 OD1 ASP A 52 20.220 29.928 -5.237 1.00 21.30 O -ATOM 405 OD2 ASP A 52 19.517 28.144 -6.222 1.00 20.92 O -ATOM 406 N TYR A 53 24.924 29.734 -6.905 1.00 14.56 N -ATOM 407 CA TYR A 53 26.278 29.604 -7.450 1.00 13.61 C -ATOM 408 C TYR A 53 27.161 28.595 -6.708 1.00 12.70 C -ATOM 409 O TYR A 53 27.289 28.606 -5.486 1.00 13.36 O -ATOM 410 CB TYR A 53 26.993 30.972 -7.489 1.00 12.10 C -ATOM 411 CG TYR A 53 26.437 31.959 -8.487 1.00 11.48 C -ATOM 412 CD1 TYR A 53 26.843 32.003 -9.821 1.00 17.21 C -ATOM 413 CD2 TYR A 53 25.510 32.907 -8.050 1.00 14.42 C -ATOM 414 CE1 TYR A 53 26.291 32.922 -10.717 1.00 17.40 C -ATOM 415 CE2 TYR A 53 24.907 33.803 -8.932 1.00 12.97 C -ATOM 416 CZ TYR A 53 25.357 33.847 -10.252 1.00 15.91 C -ATOM 417 OH TYR A 53 24.864 34.804 -11.094 1.00 19.31 O -ATOM 418 N GLY A 54 27.751 27.721 -7.493 1.00 16.54 N -ATOM 419 CA GLY A 54 28.845 26.832 -7.121 1.00 15.67 C -ATOM 420 C GLY A 54 28.499 25.601 -6.290 1.00 10.78 C -ATOM 421 O GLY A 54 27.339 25.155 -6.255 1.00 13.16 O -ATOM 422 N ILE A 55 29.560 25.088 -5.684 1.00 15.43 N -ATOM 423 CA ILE A 55 29.452 23.795 -4.994 1.00 14.01 C -ATOM 424 C ILE A 55 28.424 23.748 -3.872 1.00 12.26 C -ATOM 425 O ILE A 55 27.770 22.697 -3.693 1.00 16.92 O -ATOM 426 CB ILE A 55 30.891 23.340 -4.563 1.00 16.64 C -ATOM 427 CG1 ILE A 55 30.785 21.812 -4.319 1.00 17.00 C -ATOM 428 CG2 ILE A 55 31.396 24.210 -3.390 1.00 18.87 C -ATOM 429 CD1 ILE A 55 32.101 21.018 -4.339 1.00 20.60 C -ATOM 430 N LEU A 56 28.216 24.881 -3.236 1.00 12.85 N -ATOM 431 CA LEU A 56 27.173 24.998 -2.203 1.00 14.96 C -ATOM 432 C LEU A 56 25.981 25.838 -2.659 1.00 11.08 C -ATOM 433 O LEU A 56 25.161 26.111 -1.774 1.00 16.40 O -ATOM 434 CB LEU A 56 27.816 25.424 -0.877 1.00 14.44 C -ATOM 435 CG LEU A 56 28.692 24.348 -0.204 1.00 14.92 C -ATOM 436 CD1 LEU A 56 29.331 24.997 1.008 1.00 18.78 C -ATOM 437 CD2 LEU A 56 27.808 23.177 0.192 1.00 19.47 C -ATOM 438 N GLN A 57 25.865 26.104 -3.946 1.00 14.17 N -ATOM 439 CA GLN A 57 24.668 26.785 -4.465 1.00 11.55 C -ATOM 440 C GLN A 57 24.277 27.940 -3.558 1.00 15.09 C -ATOM 441 O GLN A 57 23.116 28.031 -3.094 1.00 15.28 O -ATOM 442 CB GLN A 57 23.521 25.765 -4.549 1.00 13.56 C -ATOM 443 CG GLN A 57 23.733 24.790 -5.699 1.00 12.45 C -ATOM 444 CD GLN A 57 23.684 25.440 -7.069 1.00 14.21 C -ATOM 445 OE1 GLN A 57 22.574 25.602 -7.591 1.00 18.18 O -ATOM 446 NE2 GLN A 57 24.813 25.805 -7.651 1.00 14.86 N -ATOM 447 N ILE A 58 25.164 28.910 -3.428 1.00 14.04 N -ATOM 448 CA ILE A 58 24.930 30.118 -2.649 1.00 16.09 C -ATOM 449 C ILE A 58 24.204 31.163 -3.504 1.00 11.19 C -ATOM 450 O ILE A 58 24.555 31.405 -4.667 1.00 14.34 O -ATOM 451 CB ILE A 58 26.301 30.665 -2.134 1.00 14.90 C -ATOM 452 CG1 ILE A 58 26.751 29.724 -0.985 1.00 13.85 C -ATOM 453 CG2 ILE A 58 26.178 32.135 -1.693 1.00 15.47 C -ATOM 454 CD1 ILE A 58 28.246 29.954 -0.641 1.00 16.12 C -ATOM 455 N ASN A 59 23.145 31.671 -2.905 1.00 14.23 N -ATOM 456 CA ASN A 59 22.146 32.510 -3.590 1.00 10.60 C -ATOM 457 C ASN A 59 22.550 33.974 -3.730 1.00 13.03 C -ATOM 458 O ASN A 59 22.917 34.607 -2.740 1.00 18.49 O -ATOM 459 CB ASN A 59 20.805 32.306 -2.884 1.00 15.76 C -ATOM 460 CG ASN A 59 19.650 32.986 -3.588 1.00 15.71 C -ATOM 461 OD1 ASN A 59 19.464 34.171 -3.244 1.00 18.79 O -ATOM 462 ND2 ASN A 59 19.155 32.320 -4.612 1.00 16.44 N -ATOM 463 N SER A 60 22.268 34.485 -4.941 1.00 11.71 N -ATOM 464 CA SER A 60 22.570 35.910 -5.255 1.00 13.81 C -ATOM 465 C SER A 60 21.687 36.993 -4.642 1.00 15.28 C -ATOM 466 O SER A 60 22.054 38.177 -4.774 1.00 17.67 O -ATOM 467 CB SER A 60 22.643 36.139 -6.750 1.00 14.62 C -ATOM 468 OG SER A 60 21.432 36.007 -7.444 1.00 14.30 O -ATOM 469 N ARG A 61 20.526 36.660 -4.138 1.00 15.88 N -ATOM 470 CA ARG A 61 19.691 37.653 -3.434 1.00 18.54 C -ATOM 471 C ARG A 61 20.277 38.108 -2.106 1.00 19.97 C -ATOM 472 O ARG A 61 20.282 39.333 -1.876 1.00 26.30 O -ATOM 473 CB ARG A 61 18.267 37.195 -3.250 1.00 18.00 C -ATOM 474 CG ARG A 61 17.315 38.350 -2.959 1.00 20.10 C -ATOM 475 CD ARG A 61 16.063 37.657 -2.503 1.00 26.00 C -ATOM 476 NE ARG A 61 15.101 38.653 -2.063 1.00 29.28 N -ATOM 477 CZ ARG A 61 13.794 38.351 -2.111 1.00 29.36 C -ATOM 478 NH1 ARG A 61 13.439 37.257 -2.784 1.00 26.50 N -ATOM 479 NH2 ARG A 61 12.925 39.249 -1.646 1.00 32.93 N -ATOM 480 N TRP A 62 20.773 37.202 -1.273 1.00 16.51 N -ATOM 481 CA TRP A 62 21.321 37.563 0.032 1.00 16.06 C -ATOM 482 C TRP A 62 22.848 37.643 0.101 1.00 15.55 C -ATOM 483 O TRP A 62 23.323 38.396 0.968 1.00 18.96 O -ATOM 484 CB TRP A 62 20.833 36.611 1.134 1.00 17.91 C -ATOM 485 CG TRP A 62 19.360 36.361 1.096 1.00 18.99 C -ATOM 486 CD1 TRP A 62 18.719 35.247 0.643 1.00 20.47 C -ATOM 487 CD2 TRP A 62 18.326 37.305 1.427 1.00 20.79 C -ATOM 488 NE1 TRP A 62 17.360 35.457 0.609 1.00 21.70 N -ATOM 489 CE2 TRP A 62 17.090 36.696 1.096 1.00 21.11 C -ATOM 490 CE3 TRP A 62 18.333 38.584 1.965 1.00 19.84 C -ATOM 491 CZ2 TRP A 62 15.875 37.327 1.307 1.00 22.57 C -ATOM 492 CZ3 TRP A 62 17.115 39.208 2.186 1.00 23.93 C -ATOM 493 CH2 TRP A 62 15.906 38.611 1.814 1.00 19.55 C -ATOM 494 N TRP A 63 23.537 36.731 -0.584 1.00 16.01 N -ATOM 495 CA TRP A 63 24.906 36.398 -0.276 1.00 15.21 C -ATOM 496 C TRP A 63 26.089 36.924 -1.052 1.00 15.84 C -ATOM 497 O TRP A 63 27.142 37.177 -0.432 1.00 19.13 O -ATOM 498 CB TRP A 63 25.068 34.919 0.112 1.00 15.47 C -ATOM 499 CG TRP A 63 24.036 34.428 1.068 1.00 12.46 C -ATOM 500 CD1 TRP A 63 22.959 33.620 0.777 1.00 16.95 C -ATOM 501 CD2 TRP A 63 23.919 34.728 2.450 1.00 13.27 C -ATOM 502 NE1 TRP A 63 22.243 33.344 1.899 1.00 17.64 N -ATOM 503 CE2 TRP A 63 22.761 34.067 2.931 1.00 17.28 C -ATOM 504 CE3 TRP A 63 24.694 35.480 3.323 1.00 15.25 C -ATOM 505 CZ2 TRP A 63 22.393 34.133 4.278 1.00 18.56 C -ATOM 506 CZ3 TRP A 63 24.302 35.586 4.648 1.00 18.76 C -ATOM 507 CH2 TRP A 63 23.179 34.910 5.117 1.00 19.36 C -ATOM 508 N CYS A 64 25.962 36.914 -2.353 1.00 17.00 N -ATOM 509 CA CYS A 64 26.985 37.433 -3.271 1.00 15.76 C -ATOM 510 C CYS A 64 26.324 38.355 -4.286 1.00 15.97 C -ATOM 511 O CYS A 64 25.102 38.314 -4.475 1.00 13.75 O -ATOM 512 CB CYS A 64 27.638 36.265 -3.988 1.00 16.64 C -ATOM 513 SG CYS A 64 26.562 35.233 -5.007 1.00 17.83 S -ATOM 514 N ASN A 65 27.157 39.165 -4.908 1.00 17.73 N -ATOM 515 CA ASN A 65 26.700 40.134 -5.920 1.00 16.46 C -ATOM 516 C ASN A 65 26.985 39.646 -7.342 1.00 13.16 C -ATOM 517 O ASN A 65 28.130 39.316 -7.647 1.00 15.95 O -ATOM 518 CB ASN A 65 27.381 41.492 -5.712 1.00 19.19 C -ATOM 519 CG ASN A 65 26.910 42.423 -6.824 1.00 19.59 C -ATOM 520 OD1 ASN A 65 25.736 42.559 -7.141 1.00 23.26 O -ATOM 521 ND2 ASN A 65 27.914 42.938 -7.527 1.00 25.56 N -ATOM 522 N ASP A 66 25.920 39.484 -8.116 1.00 15.60 N -ATOM 523 CA ASP A 66 26.102 39.180 -9.545 1.00 15.28 C -ATOM 524 C ASP A 66 25.664 40.317 -10.460 1.00 15.23 C -ATOM 525 O ASP A 66 25.719 40.143 -11.673 1.00 17.91 O -ATOM 526 CB ASP A 66 25.462 37.858 -9.894 1.00 14.84 C -ATOM 527 CG ASP A 66 23.951 37.903 -9.833 1.00 12.12 C -ATOM 528 OD1 ASP A 66 23.288 38.898 -9.542 1.00 16.56 O -ATOM 529 OD2 ASP A 66 23.455 36.769 -10.048 1.00 16.91 O -ATOM 530 N GLY A 67 25.234 41.408 -9.860 1.00 18.13 N -ATOM 531 CA GLY A 67 24.817 42.607 -10.577 1.00 19.40 C -ATOM 532 C GLY A 67 23.544 42.553 -11.401 1.00 20.37 C -ATOM 533 O GLY A 67 23.191 43.542 -12.055 1.00 18.23 O -ATOM 534 N ARG A 68 22.822 41.441 -11.348 1.00 18.79 N -ATOM 535 CA ARG A 68 21.560 41.308 -12.092 1.00 19.77 C -ATOM 536 C ARG A 68 20.424 40.765 -11.243 1.00 18.48 C -ATOM 537 O ARG A 68 19.385 40.383 -11.795 1.00 21.54 O -ATOM 538 CB ARG A 68 21.746 40.454 -13.339 1.00 18.97 C -ATOM 539 CG ARG A 68 22.197 39.048 -12.946 1.00 18.77 C -ATOM 540 CD ARG A 68 22.477 38.187 -14.122 1.00 23.25 C -ATOM 541 NE ARG A 68 21.439 37.201 -14.281 1.00 29.75 N -ATOM 542 CZ ARG A 68 20.242 37.255 -14.855 1.00 28.71 C -ATOM 543 NH1 ARG A 68 19.503 38.311 -15.145 1.00 32.34 N -ATOM 544 NH2 ARG A 68 19.897 36.127 -15.497 1.00 33.10 N -ATOM 545 N THR A 69 20.590 40.896 -9.952 1.00 18.68 N -ATOM 546 CA THR A 69 19.607 40.408 -8.973 1.00 20.02 C -ATOM 547 C THR A 69 18.994 41.597 -8.224 1.00 16.46 C -ATOM 548 O THR A 69 19.683 42.241 -7.425 1.00 23.13 O -ATOM 549 CB THR A 69 20.208 39.384 -7.910 1.00 19.66 C -ATOM 550 OG1 THR A 69 20.851 38.334 -8.715 1.00 19.19 O -ATOM 551 CG2 THR A 69 19.123 38.863 -6.955 1.00 18.58 C -ATOM 552 N PRO A 70 17.687 41.741 -8.418 1.00 20.50 N -ATOM 553 CA PRO A 70 16.953 42.824 -7.733 1.00 21.73 C -ATOM 554 C PRO A 70 16.955 42.520 -6.242 1.00 22.11 C -ATOM 555 O PRO A 70 16.739 41.356 -5.886 1.00 27.13 O -ATOM 556 CB PRO A 70 15.557 42.749 -8.333 1.00 23.50 C -ATOM 557 CG PRO A 70 15.759 42.092 -9.671 1.00 24.66 C -ATOM 558 CD PRO A 70 16.887 41.095 -9.463 1.00 21.80 C -ATOM 559 N GLY A 71 17.163 43.493 -5.401 1.00 21.67 N -ATOM 560 CA GLY A 71 17.135 43.383 -3.947 1.00 24.03 C -ATOM 561 C GLY A 71 18.328 42.710 -3.287 1.00 26.98 C -ATOM 562 O GLY A 71 18.257 42.257 -2.126 1.00 32.77 O -ATOM 563 N SER A 72 19.418 42.627 -4.018 1.00 26.40 N -ATOM 564 CA SER A 72 20.665 41.976 -3.588 1.00 26.94 C -ATOM 565 C SER A 72 21.139 42.582 -2.276 1.00 24.66 C -ATOM 566 O SER A 72 21.055 43.819 -2.125 1.00 29.91 O -ATOM 567 CB SER A 72 21.659 42.002 -4.737 1.00 25.16 C -ATOM 568 OG SER A 72 23.015 41.835 -4.343 1.00 32.21 O -ATOM 569 N ARG A 73 21.646 41.775 -1.369 1.00 22.51 N -ATOM 570 CA ARG A 73 22.254 42.196 -0.113 1.00 22.60 C -ATOM 571 C ARG A 73 23.774 42.058 0.029 1.00 22.33 C -ATOM 572 O ARG A 73 24.425 42.749 0.849 1.00 27.92 O -ATOM 573 CB ARG A 73 21.615 41.555 1.127 1.00 20.14 C -ATOM 574 CG ARG A 73 20.187 41.983 1.439 1.00 22.29 C -ATOM 575 CD ARG A 73 20.209 43.299 2.123 1.00 26.95 C -ATOM 576 NE ARG A 73 18.928 43.771 2.617 1.00 33.74 N -ATOM 577 CZ ARG A 73 17.980 44.302 1.823 1.00 33.76 C -ATOM 578 NH1 ARG A 73 17.841 43.934 0.544 1.00 35.78 N -ATOM 579 NH2 ARG A 73 17.571 45.545 2.146 1.00 33.83 N -ATOM 580 N ASN A 74 24.346 41.143 -0.705 1.00 17.74 N -ATOM 581 CA ASN A 74 25.780 40.833 -0.695 1.00 18.87 C -ATOM 582 C ASN A 74 26.315 40.718 0.731 1.00 16.22 C -ATOM 583 O ASN A 74 27.255 41.471 1.060 1.00 20.87 O -ATOM 584 CB ASN A 74 26.565 41.786 -1.589 1.00 19.51 C -ATOM 585 CG ASN A 74 27.982 41.328 -1.909 1.00 16.31 C -ATOM 586 OD1 ASN A 74 28.318 40.169 -1.652 1.00 18.61 O -ATOM 587 ND2 ASN A 74 28.838 42.192 -2.436 1.00 19.22 N -ATOM 588 N LEU A 75 25.723 39.860 1.544 1.00 15.25 N -ATOM 589 CA LEU A 75 26.153 39.690 2.930 1.00 14.82 C -ATOM 590 C LEU A 75 27.518 39.011 3.085 1.00 16.78 C -ATOM 591 O LEU A 75 28.167 39.197 4.141 1.00 22.00 O -ATOM 592 CB LEU A 75 25.009 39.055 3.733 1.00 16.64 C -ATOM 593 CG LEU A 75 23.815 39.998 3.979 1.00 17.08 C -ATOM 594 CD1 LEU A 75 22.574 39.193 4.336 1.00 25.82 C -ATOM 595 CD2 LEU A 75 24.156 40.969 5.110 1.00 20.95 C -ATOM 596 N CYS A 76 27.973 38.312 2.061 1.00 17.66 N -ATOM 597 CA CYS A 76 29.299 37.680 2.111 1.00 16.46 C -ATOM 598 C CYS A 76 30.390 38.598 1.589 1.00 15.66 C -ATOM 599 O CYS A 76 31.573 38.229 1.568 1.00 17.59 O -ATOM 600 CB CYS A 76 29.396 36.303 1.477 1.00 17.61 C -ATOM 601 SG CYS A 76 28.595 34.961 2.361 1.00 18.07 S -ATOM 602 N ASN A 77 29.964 39.681 0.971 1.00 18.55 N -ATOM 603 CA ASN A 77 30.827 40.725 0.395 1.00 19.18 C -ATOM 604 C ASN A 77 31.711 40.163 -0.702 1.00 16.58 C -ATOM 605 O ASN A 77 32.947 40.331 -0.689 1.00 21.61 O -ATOM 606 CB ASN A 77 31.589 41.488 1.483 1.00 17.72 C -ATOM 607 CG ASN A 77 32.126 42.812 0.957 1.00 20.20 C -ATOM 608 OD1 ASN A 77 31.351 43.589 0.396 1.00 28.77 O -ATOM 609 ND2 ASN A 77 33.430 43.012 1.047 1.00 27.05 N -ATOM 610 N ILE A 78 31.149 39.408 -1.616 1.00 18.88 N -ATOM 611 CA ILE A 78 31.904 38.780 -2.713 1.00 20.14 C -ATOM 612 C ILE A 78 31.099 38.850 -4.013 1.00 17.08 C -ATOM 613 O ILE A 78 29.864 38.688 -3.972 1.00 16.28 O -ATOM 614 CB ILE A 78 32.183 37.255 -2.384 1.00 19.93 C -ATOM 615 CG1 ILE A 78 30.882 36.639 -1.851 1.00 21.17 C -ATOM 616 CG2 ILE A 78 33.437 37.003 -1.524 1.00 24.25 C -ATOM 617 CD1 ILE A 78 30.936 35.120 -1.546 1.00 25.54 C -ATOM 618 N PRO A 79 31.828 38.795 -5.108 1.00 16.64 N -ATOM 619 CA PRO A 79 31.195 38.634 -6.421 1.00 19.12 C -ATOM 620 C PRO A 79 30.792 37.146 -6.446 1.00 14.71 C -ATOM 621 O PRO A 79 31.576 36.273 -6.005 1.00 17.48 O -ATOM 622 CB PRO A 79 32.261 38.967 -7.445 1.00 18.74 C -ATOM 623 CG PRO A 79 33.555 39.029 -6.710 1.00 18.97 C -ATOM 624 CD PRO A 79 33.276 39.023 -5.215 1.00 16.79 C -ATOM 625 N CYS A 80 29.629 36.908 -7.033 1.00 13.55 N -ATOM 626 CA CYS A 80 29.167 35.522 -7.236 1.00 14.33 C -ATOM 627 C CYS A 80 30.150 34.716 -8.073 1.00 13.92 C -ATOM 628 O CYS A 80 30.214 33.484 -7.880 1.00 16.74 O -ATOM 629 CB CYS A 80 27.749 35.338 -7.747 1.00 16.10 C -ATOM 630 SG CYS A 80 26.471 36.160 -6.762 1.00 16.97 S -ATOM 631 N SER A 81 30.769 35.294 -9.083 1.00 15.04 N -ATOM 632 CA SER A 81 31.775 34.671 -9.933 1.00 15.64 C -ATOM 633 C SER A 81 32.907 34.027 -9.109 1.00 14.90 C -ATOM 634 O SER A 81 33.338 32.939 -9.561 1.00 21.08 O -ATOM 635 CB SER A 81 32.381 35.643 -10.953 1.00 18.65 C -ATOM 636 OG SER A 81 33.035 36.681 -10.235 1.00 20.86 O -ATOM 637 N ALA A 82 33.226 34.572 -7.950 1.00 15.59 N -ATOM 638 CA ALA A 82 34.272 33.963 -7.107 1.00 18.01 C -ATOM 639 C ALA A 82 33.869 32.604 -6.540 1.00 18.75 C -ATOM 640 O ALA A 82 34.703 31.798 -6.081 1.00 19.60 O -ATOM 641 CB ALA A 82 34.722 34.930 -6.020 1.00 20.54 C -ATOM 642 N LEU A 83 32.571 32.338 -6.519 1.00 15.36 N -ATOM 643 CA LEU A 83 31.973 31.093 -6.042 1.00 18.66 C -ATOM 644 C LEU A 83 32.060 29.962 -7.049 1.00 17.84 C -ATOM 645 O LEU A 83 31.671 28.815 -6.739 1.00 21.50 O -ATOM 646 CB LEU A 83 30.618 31.424 -5.431 1.00 17.11 C -ATOM 647 CG LEU A 83 30.511 32.364 -4.244 1.00 16.65 C -ATOM 648 CD1 LEU A 83 29.040 32.573 -3.857 1.00 18.78 C -ATOM 649 CD2 LEU A 83 31.277 31.872 -3.020 1.00 20.62 C -ATOM 650 N LEU A 84 32.473 30.271 -8.267 1.00 17.31 N -ATOM 651 CA LEU A 84 32.610 29.295 -9.347 1.00 16.38 C -ATOM 652 C LEU A 84 34.047 28.841 -9.570 1.00 19.37 C -ATOM 653 O LEU A 84 34.334 28.243 -10.622 1.00 23.48 O -ATOM 654 CB LEU A 84 31.914 29.793 -10.614 1.00 20.87 C -ATOM 655 CG LEU A 84 30.446 30.183 -10.573 1.00 14.26 C -ATOM 656 CD1 LEU A 84 30.014 30.771 -11.916 1.00 21.15 C -ATOM 657 CD2 LEU A 84 29.597 28.942 -10.329 1.00 18.96 C -ATOM 658 N SER A 85 34.942 29.197 -8.676 1.00 21.00 N -ATOM 659 CA SER A 85 36.340 28.754 -8.727 1.00 20.86 C -ATOM 660 C SER A 85 36.474 27.245 -8.497 1.00 19.65 C -ATOM 661 O SER A 85 35.765 26.640 -7.681 1.00 20.62 O -ATOM 662 CB SER A 85 37.109 29.482 -7.633 1.00 20.91 C -ATOM 663 OG SER A 85 38.484 29.212 -7.834 1.00 26.88 O -ATOM 664 N SER A 86 37.619 26.742 -8.943 1.00 22.57 N -ATOM 665 CA SER A 86 38.008 25.343 -8.700 1.00 20.44 C -ATOM 666 C SER A 86 38.388 25.153 -7.233 1.00 19.98 C -ATOM 667 O SER A 86 38.314 24.055 -6.671 1.00 23.62 O -ATOM 668 CB SER A 86 39.107 24.868 -9.650 1.00 23.76 C -ATOM 669 OG SER A 86 38.401 24.215 -10.691 1.00 30.29 O -ATOM 670 N ASP A 87 38.846 26.244 -6.668 1.00 19.74 N -ATOM 671 CA ASP A 87 39.282 26.393 -5.271 1.00 18.72 C -ATOM 672 C ASP A 87 37.999 26.657 -4.471 1.00 17.93 C -ATOM 673 O ASP A 87 37.490 27.762 -4.712 1.00 20.06 O -ATOM 674 CB ASP A 87 40.221 27.607 -5.212 1.00 21.65 C -ATOM 675 CG ASP A 87 40.762 28.041 -3.869 1.00 23.98 C -ATOM 676 OD1 ASP A 87 40.335 27.702 -2.742 1.00 26.26 O -ATOM 677 OD2 ASP A 87 41.785 28.802 -3.933 1.00 32.04 O -ATOM 678 N ILE A 88 37.732 25.850 -3.461 1.00 15.96 N -ATOM 679 CA ILE A 88 36.515 26.089 -2.658 1.00 16.22 C -ATOM 680 C ILE A 88 36.582 27.142 -1.563 1.00 14.43 C -ATOM 681 O ILE A 88 35.600 27.315 -0.801 1.00 16.28 O -ATOM 682 CB ILE A 88 35.993 24.736 -2.046 1.00 16.45 C -ATOM 683 CG1 ILE A 88 36.920 24.200 -0.934 1.00 15.71 C -ATOM 684 CG2 ILE A 88 35.587 23.743 -3.163 1.00 19.87 C -ATOM 685 CD1 ILE A 88 36.363 23.226 0.137 1.00 17.47 C -ATOM 686 N THR A 89 37.742 27.786 -1.369 1.00 14.21 N -ATOM 687 CA THR A 89 37.913 28.772 -0.306 1.00 16.87 C -ATOM 688 C THR A 89 36.736 29.761 -0.161 1.00 11.06 C -ATOM 689 O THR A 89 36.341 29.983 1.000 1.00 13.83 O -ATOM 690 CB THR A 89 39.267 29.591 -0.423 1.00 18.61 C -ATOM 691 OG1 THR A 89 40.339 28.592 -0.514 1.00 20.24 O -ATOM 692 CG2 THR A 89 39.419 30.553 0.766 1.00 17.79 C -ATOM 693 N ALA A 90 36.507 30.482 -1.242 1.00 17.37 N -ATOM 694 CA ALA A 90 35.479 31.555 -1.244 1.00 16.63 C -ATOM 695 C ALA A 90 34.125 31.066 -0.735 1.00 14.09 C -ATOM 696 O ALA A 90 33.366 31.671 0.065 1.00 15.68 O -ATOM 697 CB ALA A 90 35.366 32.212 -2.617 1.00 17.13 C -ATOM 698 N SER A 91 33.746 29.919 -1.296 1.00 13.62 N -ATOM 699 CA SER A 91 32.494 29.220 -1.024 1.00 11.35 C -ATOM 700 C SER A 91 32.429 28.817 0.467 1.00 11.70 C -ATOM 701 O SER A 91 31.407 29.057 1.110 1.00 14.31 O -ATOM 702 CB SER A 91 32.282 28.035 -1.917 1.00 13.48 C -ATOM 703 OG SER A 91 32.020 28.335 -3.260 1.00 14.66 O -ATOM 704 N VAL A 92 33.502 28.211 0.953 1.00 13.17 N -ATOM 705 CA VAL A 92 33.595 27.846 2.381 1.00 13.44 C -ATOM 706 C VAL A 92 33.477 29.105 3.261 1.00 12.00 C -ATOM 707 O VAL A 92 32.716 29.020 4.244 1.00 13.83 O -ATOM 708 CB VAL A 92 34.890 27.038 2.650 1.00 11.69 C -ATOM 709 CG1 VAL A 92 35.125 26.987 4.151 1.00 16.05 C -ATOM 710 CG2 VAL A 92 34.776 25.672 2.013 1.00 15.64 C -ATOM 711 N ASN A 93 34.199 30.163 2.912 1.00 15.12 N -ATOM 712 CA ASN A 93 34.160 31.413 3.685 1.00 15.10 C -ATOM 713 C ASN A 93 32.747 32.034 3.803 1.00 9.80 C -ATOM 714 O ASN A 93 32.361 32.393 4.908 1.00 16.51 O -ATOM 715 CB ASN A 93 35.168 32.472 3.247 1.00 16.33 C -ATOM 716 CG ASN A 93 36.582 32.083 3.642 1.00 19.02 C -ATOM 717 OD1 ASN A 93 37.546 32.671 3.120 1.00 29.57 O -ATOM 718 ND2 ASN A 93 36.710 31.188 4.631 1.00 24.29 N -ATOM 719 N CYS A 94 32.096 31.996 2.670 1.00 15.72 N -ATOM 720 CA CYS A 94 30.695 32.449 2.633 1.00 13.58 C -ATOM 721 C CYS A 94 29.778 31.527 3.424 1.00 13.05 C -ATOM 722 O CYS A 94 28.973 32.025 4.236 1.00 16.42 O -ATOM 723 CB CYS A 94 30.291 32.704 1.185 1.00 12.05 C -ATOM 724 SG CYS A 94 28.644 33.431 1.046 1.00 15.81 S -ATOM 725 N ALA A 95 29.945 30.225 3.263 1.00 13.56 N -ATOM 726 CA ALA A 95 29.134 29.227 3.969 1.00 15.63 C -ATOM 727 C ALA A 95 29.236 29.330 5.491 1.00 10.80 C -ATOM 728 O ALA A 95 28.222 29.180 6.179 1.00 12.93 O -ATOM 729 CB ALA A 95 29.495 27.794 3.612 1.00 14.09 C -ATOM 730 N LYS A 96 30.424 29.628 5.987 1.00 11.19 N -ATOM 731 CA LYS A 96 30.627 29.912 7.419 1.00 13.27 C -ATOM 732 C LYS A 96 29.802 31.115 7.906 1.00 13.38 C -ATOM 733 O LYS A 96 29.296 31.011 9.027 1.00 15.75 O -ATOM 734 CB LYS A 96 32.100 30.112 7.775 1.00 12.67 C -ATOM 735 CG LYS A 96 32.874 28.792 7.697 1.00 11.93 C -ATOM 736 CD LYS A 96 34.358 29.071 7.879 1.00 15.55 C -ATOM 737 CE LYS A 96 35.205 27.816 7.938 1.00 18.03 C -ATOM 738 NZ LYS A 96 36.610 28.242 8.169 1.00 20.72 N -ATOM 739 N LYS A 97 29.660 32.101 7.049 1.00 12.90 N -ATOM 740 CA LYS A 97 28.811 33.263 7.379 1.00 16.43 C -ATOM 741 C LYS A 97 27.333 32.905 7.386 1.00 18.88 C -ATOM 742 O LYS A 97 26.570 33.318 8.272 1.00 19.20 O -ATOM 743 CB LYS A 97 29.087 34.456 6.470 1.00 18.97 C -ATOM 744 CG LYS A 97 30.537 34.927 6.563 1.00 19.81 C -ATOM 745 CD LYS A 97 30.841 36.073 5.610 1.00 22.00 C -ATOM 746 CE LYS A 97 32.340 36.293 5.510 1.00 23.71 C -ATOM 747 NZ LYS A 97 32.569 37.524 4.708 1.00 29.75 N -ATOM 748 N ILE A 98 26.897 32.127 6.416 1.00 15.72 N -ATOM 749 CA ILE A 98 25.520 31.693 6.266 1.00 16.36 C -ATOM 750 C ILE A 98 25.030 30.871 7.453 1.00 16.70 C -ATOM 751 O ILE A 98 24.059 31.254 8.126 1.00 18.80 O -ATOM 752 CB ILE A 98 25.307 30.997 4.896 1.00 15.14 C -ATOM 753 CG1 ILE A 98 25.643 31.910 3.702 1.00 13.63 C -ATOM 754 CG2 ILE A 98 23.887 30.386 4.817 1.00 15.62 C -ATOM 755 CD1 ILE A 98 25.620 31.204 2.321 1.00 17.82 C -ATOM 756 N VAL A 99 25.875 29.966 7.915 1.00 16.73 N -ATOM 757 CA VAL A 99 25.488 29.009 8.955 1.00 18.71 C -ATOM 758 C VAL A 99 25.431 29.697 10.316 1.00 20.36 C -ATOM 759 O VAL A 99 24.737 29.212 11.233 1.00 25.30 O -ATOM 760 CB VAL A 99 26.398 27.774 8.859 1.00 16.94 C -ATOM 761 CG1 VAL A 99 27.811 28.138 9.279 1.00 19.19 C -ATOM 762 CG2 VAL A 99 25.834 26.594 9.632 1.00 18.97 C -ATOM 763 N SER A 100 26.205 30.752 10.409 1.00 17.04 N -ATOM 764 CA SER A 100 26.297 31.529 11.650 1.00 23.81 C -ATOM 765 C SER A 100 25.124 32.495 11.765 1.00 24.03 C -ATOM 766 O SER A 100 24.995 33.131 12.820 1.00 28.66 O -ATOM 767 CB SER A 100 27.647 32.194 11.723 1.00 19.71 C -ATOM 768 OG SER A 100 28.714 31.264 11.818 1.00 25.04 O -ATOM 769 N ASP A 101 24.307 32.599 10.750 1.00 25.78 N -ATOM 770 CA ASP A 101 23.162 33.495 10.650 1.00 26.98 C -ATOM 771 C ASP A 101 21.924 33.183 11.481 1.00 28.34 C -ATOM 772 O ASP A 101 21.132 34.143 11.678 1.00 31.88 O -ATOM 773 CB ASP A 101 22.806 33.854 9.207 1.00 27.75 C -ATOM 774 CG ASP A 101 22.426 35.320 9.009 1.00 30.86 C -ATOM 775 OD1 ASP A 101 23.248 36.223 9.266 1.00 34.67 O -ATOM 776 OD2 ASP A 101 21.276 35.519 8.551 1.00 32.70 O -ATOM 777 N GLY A 102 21.723 31.942 11.887 1.00 28.87 N -ATOM 778 CA GLY A 102 20.622 31.656 12.823 1.00 30.67 C -ATOM 779 C GLY A 102 19.812 30.413 12.505 1.00 27.92 C -ATOM 780 O GLY A 102 19.195 29.898 13.458 1.00 30.42 O -ATOM 781 N ASN A 103 19.805 30.005 11.244 1.00 29.26 N -ATOM 782 CA ASN A 103 19.076 28.799 10.848 1.00 25.22 C -ATOM 783 C ASN A 103 19.990 27.600 10.597 1.00 22.06 C -ATOM 784 O ASN A 103 19.472 26.579 10.117 1.00 24.23 O -ATOM 785 CB ASN A 103 17.976 29.046 9.824 1.00 24.87 C -ATOM 786 CG ASN A 103 16.708 28.245 10.063 1.00 27.08 C -ATOM 787 OD1 ASN A 103 16.513 27.577 11.098 1.00 30.30 O -ATOM 788 ND2 ASN A 103 15.672 28.428 9.240 1.00 30.15 N -ATOM 789 N GLY A 104 21.240 27.711 10.997 1.00 23.20 N -ATOM 790 CA GLY A 104 22.177 26.567 10.860 1.00 19.51 C -ATOM 791 C GLY A 104 22.173 26.142 9.388 1.00 15.58 C -ATOM 792 O GLY A 104 22.151 27.040 8.541 1.00 22.50 O -ATOM 793 N MET A 105 22.185 24.847 9.115 1.00 17.51 N -ATOM 794 CA MET A 105 22.278 24.370 7.724 1.00 16.07 C -ATOM 795 C MET A 105 20.915 24.309 7.063 1.00 13.35 C -ATOM 796 O MET A 105 20.902 23.921 5.871 1.00 15.50 O -ATOM 797 CB MET A 105 23.036 23.048 7.632 1.00 19.32 C -ATOM 798 CG MET A 105 24.519 23.221 7.871 1.00 17.10 C -ATOM 799 SD MET A 105 25.379 21.660 7.491 1.00 20.27 S -ATOM 800 CE MET A 105 25.369 21.706 5.703 1.00 20.03 C -ATOM 801 N ASN A 106 19.896 24.839 7.735 1.00 14.64 N -ATOM 802 CA ASN A 106 18.557 24.898 7.103 1.00 18.58 C -ATOM 803 C ASN A 106 18.566 25.831 5.892 1.00 18.20 C -ATOM 804 O ASN A 106 17.678 25.748 5.021 1.00 22.14 O -ATOM 805 CB ASN A 106 17.420 25.150 8.084 1.00 19.18 C -ATOM 806 CG ASN A 106 17.207 23.938 8.967 1.00 19.21 C -ATOM 807 OD1 ASN A 106 16.836 22.867 8.443 1.00 24.65 O -ATOM 808 ND2 ASN A 106 17.542 24.047 10.255 1.00 25.28 N -ATOM 809 N ALA A 107 19.617 26.647 5.800 1.00 18.54 N -ATOM 810 CA ALA A 107 19.824 27.514 4.634 1.00 18.74 C -ATOM 811 C ALA A 107 20.007 26.744 3.329 1.00 16.80 C -ATOM 812 O ALA A 107 19.734 27.292 2.260 1.00 20.63 O -ATOM 813 CB ALA A 107 21.060 28.374 4.877 1.00 19.47 C -ATOM 814 N TRP A 108 20.371 25.465 3.434 1.00 16.46 N -ATOM 815 CA TRP A 108 20.532 24.624 2.241 1.00 14.68 C -ATOM 816 C TRP A 108 19.317 23.688 2.110 1.00 17.55 C -ATOM 817 O TRP A 108 19.240 22.816 2.993 1.00 20.05 O -ATOM 818 CB TRP A 108 21.840 23.826 2.338 1.00 16.18 C -ATOM 819 CG TRP A 108 23.000 24.736 2.026 1.00 15.50 C -ATOM 820 CD1 TRP A 108 23.360 25.234 0.803 1.00 15.45 C -ATOM 821 CD2 TRP A 108 23.798 25.437 2.991 1.00 15.57 C -ATOM 822 NE1 TRP A 108 24.414 26.102 0.952 1.00 17.40 N -ATOM 823 CE2 TRP A 108 24.711 26.237 2.272 1.00 15.78 C -ATOM 824 CE3 TRP A 108 23.833 25.426 4.379 1.00 12.79 C -ATOM 825 CZ2 TRP A 108 25.682 26.985 2.917 1.00 15.77 C -ATOM 826 CZ3 TRP A 108 24.773 26.200 5.033 1.00 16.28 C -ATOM 827 CH2 TRP A 108 25.691 26.960 4.298 1.00 16.65 C -ATOM 828 N VAL A 109 18.487 23.925 1.101 1.00 15.35 N -ATOM 829 CA VAL A 109 17.265 23.096 1.025 1.00 19.96 C -ATOM 830 C VAL A 109 17.573 21.611 0.884 1.00 17.16 C -ATOM 831 O VAL A 109 16.923 20.811 1.587 1.00 20.77 O -ATOM 832 CB VAL A 109 16.146 23.660 0.145 1.00 21.94 C -ATOM 833 CG1 VAL A 109 16.607 23.905 -1.285 1.00 27.84 C -ATOM 834 CG2 VAL A 109 14.901 22.783 0.136 1.00 21.22 C -ATOM 835 N ALA A 110 18.562 21.308 0.075 1.00 20.97 N -ATOM 836 CA ALA A 110 18.972 19.935 -0.237 1.00 18.78 C -ATOM 837 C ALA A 110 19.502 19.244 1.006 1.00 18.30 C -ATOM 838 O ALA A 110 19.197 18.046 1.174 1.00 18.47 O -ATOM 839 CB ALA A 110 19.857 19.777 -1.455 1.00 20.83 C -ATOM 840 N TRP A 111 20.121 19.983 1.892 1.00 16.62 N -ATOM 841 CA TRP A 111 20.551 19.500 3.202 1.00 15.74 C -ATOM 842 C TRP A 111 19.343 19.085 4.046 1.00 19.12 C -ATOM 843 O TRP A 111 19.284 17.986 4.643 1.00 16.20 O -ATOM 844 CB TRP A 111 21.486 20.451 3.925 1.00 14.63 C -ATOM 845 CG TRP A 111 21.858 19.904 5.252 1.00 14.87 C -ATOM 846 CD1 TRP A 111 22.856 18.975 5.486 1.00 18.11 C -ATOM 847 CD2 TRP A 111 21.199 20.093 6.504 1.00 16.63 C -ATOM 848 NE1 TRP A 111 22.848 18.592 6.808 1.00 17.16 N -ATOM 849 CE2 TRP A 111 21.798 19.221 7.435 1.00 16.77 C -ATOM 850 CE3 TRP A 111 20.182 20.959 6.908 1.00 15.16 C -ATOM 851 CZ2 TRP A 111 21.492 19.284 8.784 1.00 17.69 C -ATOM 852 CZ3 TRP A 111 19.818 20.954 8.240 1.00 16.88 C -ATOM 853 CH2 TRP A 111 20.443 20.110 9.162 1.00 19.73 C -ATOM 854 N ARG A 112 18.438 20.038 4.228 1.00 17.47 N -ATOM 855 CA ARG A 112 17.185 19.830 4.955 1.00 19.60 C -ATOM 856 C ARG A 112 16.472 18.593 4.391 1.00 17.68 C -ATOM 857 O ARG A 112 16.000 17.792 5.220 1.00 22.77 O -ATOM 858 CB ARG A 112 16.214 20.990 4.944 1.00 17.57 C -ATOM 859 CG ARG A 112 16.592 22.438 5.091 1.00 25.27 C -ATOM 860 CD ARG A 112 15.368 23.296 5.135 1.00 21.23 C -ATOM 861 NE ARG A 112 14.776 23.555 3.836 1.00 28.06 N -ATOM 862 CZ ARG A 112 14.785 24.695 3.143 1.00 27.89 C -ATOM 863 NH1 ARG A 112 15.596 25.721 3.383 1.00 30.12 N -ATOM 864 NH2 ARG A 112 13.717 25.008 2.398 1.00 30.39 N -ATOM 865 N ASN A 113 16.307 18.521 3.074 1.00 19.43 N -ATOM 866 CA ASN A 113 15.464 17.463 2.491 1.00 20.16 C -ATOM 867 C ASN A 113 16.111 16.083 2.586 1.00 21.26 C -ATOM 868 O ASN A 113 15.454 15.054 2.808 1.00 24.90 O -ATOM 869 CB ASN A 113 14.966 17.779 1.085 1.00 20.43 C -ATOM 870 CG ASN A 113 14.003 18.961 1.018 1.00 16.63 C -ATOM 871 OD1 ASN A 113 13.454 19.344 2.059 1.00 25.68 O -ATOM 872 ND2 ASN A 113 13.840 19.555 -0.159 1.00 22.00 N -ATOM 873 N ARG A 114 17.401 16.041 2.355 1.00 19.72 N -ATOM 874 CA ARG A 114 18.156 14.836 2.042 1.00 21.43 C -ATOM 875 C ARG A 114 19.258 14.440 2.991 1.00 22.71 C -ATOM 876 O ARG A 114 19.505 13.217 3.097 1.00 24.85 O -ATOM 877 CB ARG A 114 18.622 14.910 0.576 1.00 21.05 C -ATOM 878 CG ARG A 114 17.395 14.614 -0.300 1.00 26.59 C -ATOM 879 CD ARG A 114 17.729 14.399 -1.731 1.00 26.92 C -ATOM 880 NE ARG A 114 18.153 15.677 -2.301 1.00 33.46 N -ATOM 881 CZ ARG A 114 17.826 16.080 -3.535 1.00 32.00 C -ATOM 882 NH1 ARG A 114 17.378 15.225 -4.456 1.00 36.02 N -ATOM 883 NH2 ARG A 114 17.735 17.388 -3.796 1.00 36.05 N -ATOM 884 N CYS A 115 19.743 15.372 3.773 1.00 17.56 N -ATOM 885 CA CYS A 115 20.843 15.041 4.708 1.00 15.08 C -ATOM 886 C CYS A 115 20.448 14.933 6.159 1.00 16.64 C -ATOM 887 O CYS A 115 20.972 14.116 6.940 1.00 21.71 O -ATOM 888 CB CYS A 115 21.991 16.018 4.426 1.00 15.21 C -ATOM 889 SG CYS A 115 22.563 16.009 2.739 1.00 19.35 S -ATOM 890 N LYS A 116 19.714 15.918 6.619 1.00 18.76 N -ATOM 891 CA LYS A 116 19.332 16.085 8.025 1.00 19.14 C -ATOM 892 C LYS A 116 18.634 14.821 8.518 1.00 21.91 C -ATOM 893 O LYS A 116 17.819 14.234 7.785 1.00 24.78 O -ATOM 894 CB LYS A 116 18.492 17.363 8.126 1.00 21.01 C -ATOM 895 CG LYS A 116 17.930 17.512 9.547 1.00 21.28 C -ATOM 896 CD LYS A 116 16.745 18.481 9.554 1.00 25.86 C -ATOM 897 CE LYS A 116 16.658 19.147 10.918 1.00 25.58 C -ATOM 898 NZ LYS A 116 15.454 20.010 11.047 1.00 34.69 N -ATOM 899 N GLY A 117 19.152 14.318 9.635 1.00 26.39 N -ATOM 900 CA GLY A 117 18.558 13.126 10.267 1.00 29.06 C -ATOM 901 C GLY A 117 19.018 11.781 9.733 1.00 28.29 C -ATOM 902 O GLY A 117 18.499 10.733 10.164 1.00 31.90 O -ATOM 903 N THR A 118 19.892 11.802 8.740 1.00 26.88 N -ATOM 904 CA THR A 118 20.473 10.578 8.171 1.00 22.31 C -ATOM 905 C THR A 118 21.868 10.375 8.761 1.00 21.43 C -ATOM 906 O THR A 118 22.321 11.119 9.650 1.00 22.31 O -ATOM 907 CB THR A 118 20.440 10.571 6.598 1.00 18.59 C -ATOM 908 OG1 THR A 118 21.560 11.404 6.161 1.00 22.71 O -ATOM 909 CG2 THR A 118 19.095 11.104 6.074 1.00 21.13 C -ATOM 910 N ASP A 119 22.392 9.213 8.431 1.00 21.20 N -ATOM 911 CA ASP A 119 23.768 8.830 8.756 1.00 22.61 C -ATOM 912 C ASP A 119 24.713 9.543 7.779 1.00 20.13 C -ATOM 913 O ASP A 119 25.178 8.950 6.780 1.00 20.57 O -ATOM 914 CB ASP A 119 23.934 7.313 8.738 1.00 21.00 C -ATOM 915 CG ASP A 119 25.347 6.900 9.121 1.00 25.32 C -ATOM 916 OD1 ASP A 119 26.051 7.633 9.830 1.00 27.93 O -ATOM 917 OD2 ASP A 119 25.715 5.746 8.804 1.00 27.31 O -ATOM 918 N VAL A 120 24.988 10.793 8.094 1.00 23.41 N -ATOM 919 CA VAL A 120 25.886 11.637 7.306 1.00 20.10 C -ATOM 920 C VAL A 120 27.342 11.199 7.304 1.00 18.51 C -ATOM 921 O VAL A 120 28.099 11.604 6.406 1.00 19.95 O -ATOM 922 CB VAL A 120 25.721 13.134 7.630 1.00 19.91 C -ATOM 923 CG1 VAL A 120 24.356 13.655 7.183 1.00 23.59 C -ATOM 924 CG2 VAL A 120 26.088 13.478 9.055 1.00 20.79 C -ATOM 925 N GLN A 121 27.701 10.430 8.306 1.00 21.83 N -ATOM 926 CA GLN A 121 29.021 9.783 8.389 1.00 21.12 C -ATOM 927 C GLN A 121 29.317 8.861 7.207 1.00 20.78 C -ATOM 928 O GLN A 121 30.480 8.669 6.820 1.00 19.66 O -ATOM 929 CB GLN A 121 29.088 9.048 9.728 1.00 24.21 C -ATOM 930 CG GLN A 121 30.530 8.965 10.167 1.00 26.13 C -ATOM 931 CD GLN A 121 30.615 8.877 11.674 1.00 26.94 C -ATOM 932 OE1 GLN A 121 31.368 9.632 12.283 1.00 31.43 O -ATOM 933 NE2 GLN A 121 29.884 7.871 12.151 1.00 28.26 N -ATOM 934 N ALA A 122 28.300 8.271 6.576 1.00 17.62 N -ATOM 935 CA ALA A 122 28.390 7.548 5.311 1.00 19.46 C -ATOM 936 C ALA A 122 29.186 8.290 4.227 1.00 17.98 C -ATOM 937 O ALA A 122 30.031 7.710 3.523 1.00 21.35 O -ATOM 938 CB ALA A 122 26.999 7.244 4.783 1.00 18.29 C -ATOM 939 N TRP A 123 29.021 9.616 4.240 1.00 18.07 N -ATOM 940 CA TRP A 123 29.703 10.502 3.283 1.00 16.76 C -ATOM 941 C TRP A 123 31.218 10.581 3.392 1.00 16.76 C -ATOM 942 O TRP A 123 31.905 10.942 2.412 1.00 20.08 O -ATOM 943 CB TRP A 123 29.027 11.872 3.347 1.00 19.49 C -ATOM 944 CG TRP A 123 27.621 11.735 2.850 1.00 17.43 C -ATOM 945 CD1 TRP A 123 26.485 11.608 3.588 1.00 19.42 C -ATOM 946 CD2 TRP A 123 27.241 11.547 1.481 1.00 17.47 C -ATOM 947 NE1 TRP A 123 25.405 11.458 2.774 1.00 18.86 N -ATOM 948 CE2 TRP A 123 25.827 11.391 1.479 1.00 17.28 C -ATOM 949 CE3 TRP A 123 27.947 11.468 0.283 1.00 20.03 C -ATOM 950 CZ2 TRP A 123 25.111 11.184 0.311 1.00 18.33 C -ATOM 951 CZ3 TRP A 123 27.222 11.329 -0.886 1.00 20.85 C -ATOM 952 CH2 TRP A 123 25.835 11.127 -0.869 1.00 20.45 C -ATOM 953 N ILE A 124 31.741 10.269 4.554 1.00 14.19 N -ATOM 954 CA ILE A 124 33.186 10.292 4.801 1.00 16.82 C -ATOM 955 C ILE A 124 33.863 8.955 5.024 1.00 18.45 C -ATOM 956 O ILE A 124 35.100 8.892 5.134 1.00 21.02 O -ATOM 957 CB ILE A 124 33.504 11.403 5.863 1.00 17.69 C -ATOM 958 CG1 ILE A 124 32.956 10.984 7.234 1.00 18.86 C -ATOM 959 CG2 ILE A 124 33.024 12.804 5.387 1.00 21.01 C -ATOM 960 CD1 ILE A 124 33.729 11.437 8.488 1.00 22.81 C -ATOM 961 N ARG A 125 33.080 7.898 5.131 1.00 21.05 N -ATOM 962 CA ARG A 125 33.594 6.534 5.320 1.00 19.12 C -ATOM 963 C ARG A 125 34.311 6.113 4.036 1.00 17.52 C -ATOM 964 O ARG A 125 33.843 6.337 2.906 1.00 23.44 O -ATOM 965 CB ARG A 125 32.476 5.551 5.650 1.00 19.54 C -ATOM 966 CG ARG A 125 32.117 5.596 7.145 1.00 22.40 C -ATOM 967 CD ARG A 125 31.277 4.392 7.482 1.00 24.05 C -ATOM 968 NE ARG A 125 30.282 4.754 8.466 1.00 28.08 N -ATOM 969 CZ ARG A 125 28.984 4.993 8.331 1.00 23.40 C -ATOM 970 NH1 ARG A 125 28.334 4.690 7.207 1.00 23.69 N -ATOM 971 NH2 ARG A 125 28.392 5.549 9.392 1.00 23.77 N -ATOM 972 N GLY A 126 35.497 5.568 4.243 1.00 18.80 N -ATOM 973 CA GLY A 126 36.291 5.058 3.102 1.00 21.28 C -ATOM 974 C GLY A 126 37.334 6.066 2.658 1.00 22.50 C -ATOM 975 O GLY A 126 38.220 5.729 1.855 1.00 23.59 O -ATOM 976 N CYS A 127 37.335 7.221 3.297 1.00 19.05 N -ATOM 977 CA CYS A 127 38.234 8.333 2.961 1.00 19.13 C -ATOM 978 C CYS A 127 39.422 8.382 3.925 1.00 22.50 C -ATOM 979 O CYS A 127 39.206 8.267 5.138 1.00 21.64 O -ATOM 980 CB CYS A 127 37.453 9.628 2.990 1.00 18.75 C -ATOM 981 SG CYS A 127 36.010 9.816 1.936 1.00 19.93 S -ATOM 982 N ARG A 128 40.586 8.695 3.393 1.00 23.60 N -ATOM 983 CA ARG A 128 41.774 8.960 4.217 1.00 28.29 C -ATOM 984 C ARG A 128 41.820 10.438 4.578 1.00 25.64 C -ATOM 985 O ARG A 128 41.976 11.291 3.694 1.00 30.98 O -ATOM 986 CB ARG A 128 43.047 8.304 3.707 1.00 30.82 C -ATOM 987 CG ARG A 128 43.231 6.886 4.280 1.00 34.25 C -ATOM 988 CD ARG A 128 43.833 6.911 5.651 1.00 33.59 C -ATOM 989 NE ARG A 128 45.246 7.263 5.636 1.00 37.63 N -ATOM 990 CZ ARG A 128 45.862 8.258 6.281 1.00 38.37 C -ATOM 991 NH1 ARG A 128 45.241 9.069 7.151 1.00 38.97 N -ATOM 992 NH2 ARG A 128 47.134 8.554 5.973 1.00 40.22 N -ATOM 993 N LEU A 129 41.289 10.715 5.771 1.00 26.05 N -ATOM 994 CA LEU A 129 41.094 12.084 6.273 1.00 26.89 C -ATOM 995 C LEU A 129 42.119 12.382 7.370 1.00 29.58 C -ATOM 996 O LEU A 129 41.730 12.276 8.559 1.00 33.54 O -ATOM 997 CB LEU A 129 39.635 12.335 6.646 1.00 26.31 C -ATOM 998 CG LEU A 129 38.689 12.917 5.620 1.00 23.49 C -ATOM 999 CD1 LEU A 129 39.112 12.657 4.191 1.00 26.43 C -ATOM 1000 CD2 LEU A 129 37.310 12.325 5.886 1.00 25.15 C -ATOM 1001 OXT LEU A 129 43.232 12.675 6.905 1.00 34.20 O -TER 1002 LEU A 129 -HETATM 1003 O HOH A 130 23.434 40.063 -6.661 1.00 19.48 O -HETATM 1004 O HOH A 131 31.994 26.416 -6.047 0.90 22.43 O -HETATM 1005 O HOH A 132 30.250 13.337 9.787 0.98 20.93 O -HETATM 1006 O HOH A 133 22.384 42.331 -8.165 0.90 21.85 O -HETATM 1007 O HOH A 134 29.239 27.621 -3.670 1.00 17.47 O -HETATM 1008 O HOH A 135 29.464 37.761 -10.492 0.98 20.05 O -HETATM 1009 O HOH A 136 20.807 36.305 -11.082 1.00 18.47 O -HETATM 1010 O HOH A 137 41.318 17.849 -1.378 0.98 20.99 O -HETATM 1011 O HOH A 138 34.697 29.056 -4.039 0.89 22.31 O -HETATM 1012 O HOH A 139 26.871 17.298 13.496 1.00 20.31 O -HETATM 1013 O HOH A 140 32.131 11.050 -5.817 0.97 21.39 O -HETATM 1014 O HOH A 141 23.468 40.040 -2.372 0.91 23.40 O -HETATM 1015 O HOH A 142 21.390 45.524 -11.035 0.96 20.63 O -HETATM 1016 O HOH A 143 34.490 26.578 -5.741 0.75 22.11 O -HETATM 1017 O HOH A 144 16.422 34.139 -3.527 0.91 20.71 O -HETATM 1018 O HOH A 145 21.374 29.926 8.946 0.83 24.21 O -HETATM 1019 O HOH A 146 41.048 12.539 -0.011 0.70 22.71 O -HETATM 1020 O HOH A 147 32.794 35.686 2.558 0.78 20.71 O -HETATM 1021 O HOH A 148 49.648 8.964 6.343 0.83 21.93 O -HETATM 1022 O HOH A 149 14.452 34.901 -13.339 0.69 23.89 O -HETATM 1023 O HOH A 150 22.930 10.839 4.044 0.92 22.02 O -HETATM 1024 O HOH A 151 16.012 18.490 -2.200 0.85 24.37 O -HETATM 1025 O HOH A 152 12.130 21.587 3.044 0.78 24.35 O -HETATM 1026 O HOH A 153 15.684 38.922 -5.813 0.76 24.50 O -HETATM 1027 O HOH A 154 10.652 24.228 3.428 0.80 21.12 O -HETATM 1028 O HOH A 155 44.070 17.975 2.852 0.80 21.64 O -HETATM 1029 O HOH A 156 32.029 13.080 -8.110 0.85 20.63 O -HETATM 1030 O HOH A 157 36.425 19.613 15.174 0.56 23.44 O -HETATM 1031 O HOH A 158 37.941 30.505 -3.686 0.79 21.54 O -HETATM 1032 O HOH A 159 30.710 42.741 -6.289 0.72 22.79 O -HETATM 1033 O HOH A 160 23.922 44.367 -7.653 0.62 22.78 O -HETATM 1034 O HOH A 161 33.829 34.252 0.626 0.73 20.81 O -HETATM 1035 O HOH A 162 29.613 40.730 -9.602 0.78 22.12 O -HETATM 1036 O HOH A 163 23.563 7.995 4.406 0.58 22.93 O -HETATM 1037 O HOH A 164 31.511 42.362 -4.183 0.73 22.01 O -HETATM 1038 O HOH A 165 21.882 29.536 -15.013 0.81 22.04 O -HETATM 1039 O HOH A 166 37.763 20.913 9.782 0.86 21.57 O -HETATM 1040 O HOH A 167 42.338 17.481 5.165 0.65 22.17 O -HETATM 1041 O HOH A 168 23.344 39.739 -4.358 0.72 21.56 O -HETATM 1042 O HOH A 169 22.984 29.224 13.124 0.75 22.56 O -HETATM 1043 O HOH A 170 30.778 7.794 -3.514 0.65 21.58 O -HETATM 1044 O HOH A 171 42.965 14.657 4.991 0.63 23.91 O -HETATM 1045 O HOH A 172 36.927 17.948 -13.093 0.62 23.36 O -HETATM 1046 O HOH A 173 35.412 25.852 -11.575 0.58 23.42 O -HETATM 1047 O HOH A 174 37.428 32.540 -5.787 0.62 21.98 O -HETATM 1048 O HOH A 175 37.317 8.592 7.456 0.64 22.92 O -HETATM 1049 O HOH A 176 9.314 36.705 -11.546 0.69 23.77 O -HETATM 1050 O HOH A 177 39.972 23.760 -2.655 0.86 18.96 O -HETATM 1051 O HOH A 178 22.128 30.274 -0.543 0.76 18.78 O -HETATM 1052 O HOH A 179 22.244 15.813 10.000 0.68 19.66 O -HETATM 1053 O HOH A 180 40.729 9.223 0.292 0.64 20.15 O -HETATM 1054 O HOH A 181 12.500 15.267 4.097 0.56 20.12 O -HETATM 1055 O HOH A 182 20.372 28.618 -2.353 0.64 20.17 O -HETATM 1056 O HOH A 183 22.793 15.462 -6.673 0.63 20.60 O -HETATM 1057 O HOH A 184 23.138 31.809 15.121 0.55 20.90 O -HETATM 1058 O HOH A 185 22.671 38.691 8.245 0.48 21.16 O -HETATM 1059 O HOH A 186 33.966 33.112 6.837 0.59 19.45 O -HETATM 1060 O HOH A 187 19.572 25.423 -1.420 0.53 19.94 O -HETATM 1061 O HOH A 188 14.790 15.672 7.259 0.52 21.22 O -HETATM 1062 O HOH A 189 19.112 28.022 -14.647 0.49 19.83 O -HETATM 1063 O HOH A 190 17.302 39.059 -12.453 0.52 20.14 O -HETATM 1064 O HOH A 191 16.198 14.502 5.577 0.46 20.78 O -HETATM 1065 O HOH A 192 17.345 46.346 -7.080 0.50 18.13 O -HETATM 1066 O HOH A 193 14.992 31.300 -4.242 0.46 17.90 O -HETATM 1067 O HOH A 194 28.196 44.775 -3.148 0.44 18.15 O -HETATM 1068 O HOH A 195 29.479 13.863 -9.107 0.44 18.30 O -HETATM 1069 O HOH A 196 23.613 44.811 2.608 0.45 17.66 O -HETATM 1070 O HOH A 197 40.572 22.184 -6.358 0.42 18.06 O -HETATM 1071 O HOH A 198 12.475 31.860 -6.226 0.47 17.85 O -HETATM 1072 O HOH A 199 16.684 13.594 -5.832 0.31 18.51 O -HETATM 1073 O HOH A 200 27.534 38.059 -12.862 0.48 18.19 O -HETATM 1074 O HOH A 201 25.892 35.973 11.563 0.46 18.15 O -HETATM 1075 O HOH A 202 24.790 25.182 16.063 0.46 17.64 O -HETATM 1076 O HOH A 203 12.580 21.214 5.006 0.51 17.97 O -HETATM 1077 O HOH A 204 19.687 23.750 -4.851 0.37 18.08 O -HETATM 1078 O HOH A 205 27.098 35.956 -12.358 0.39 18.71 O -HETATM 1079 O HOH A 206 37.255 9.634 10.002 0.46 18.39 O -HETATM 1080 O HOH A 207 43.755 23.843 8.038 0.38 17.96 O -CONECT 48 981 -CONECT 238 889 -CONECT 513 630 -CONECT 601 724 -CONECT 630 513 -CONECT 724 601 -CONECT 889 238 -CONECT 981 48 -MASTER 290 0 0 8 2 0 0 6 1079 1 8 10 -END diff --git a/0.3/example-result/data/workflow/289/workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg b/0.3/example-result/data/workflow/289/workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg deleted file mode 100644 index b7c3f53..0000000 --- a/0.3/example-result/data/workflow/289/workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg +++ /dev/null @@ -1,938 +0,0 @@ - - - - - - -workflow - - -cluster_inputs - -Workflow Inputs - - -cluster_outputs - -Workflow Outputs - - - -mutations_list - -mutations_list - - - -subworkflow_mutate - -subworkflow_mutate - - - -mutations_list->subworkflow_mutate - - -mutation - - - -step0_reduce_remove_hydrogens_input_path - -step0_reduce_remove_hydrogens_input_path - - - -step0_reduce_remove_hydrogens - -ReduceRemoveHydrogens - - - -step0_reduce_remove_hydrogens_input_path->step0_reduce_remove_hydrogens - - -input_path - - - -step0_reduce_remove_hydrogens_output_path - -step0_reduce_remove_hydrogens_output_path - - - -step0_reduce_remove_hydrogens_output_path->step0_reduce_remove_hydrogens - - -output_path - - - -step1_extract_molecule_output_molecule_path - -step1_extract_molecule_output_molecule_path - - - -step1_extract_molecule - -ExtractMolecule - - - -step1_extract_molecule_output_molecule_path->step1_extract_molecule - - -output_molecule_path - - - -step00_cat_pdb_input_structure2 - -step00_cat_pdb_input_structure2 - - - -step00_cat_pdb - -CatPDB - - - -step00_cat_pdb_input_structure2->step00_cat_pdb - - -input_structure2 - - - -step00_cat_pdb_output_structure_path - -step00_cat_pdb_output_structure_path - - - -step00_cat_pdb_output_structure_path->step00_cat_pdb - - -output_structure_path - - - -step2_fix_side_chain_output_pdb_path - -step2_fix_side_chain_output_pdb_path - - - -step2_fix_side_chain - -FixSideChain - - - -step2_fix_side_chain_output_pdb_path->step2_fix_side_chain - - -output_pdb_path - - - -step3_mutate_output_pdb_path - -step3_mutate_output_pdb_path - - - -step3_mutate_output_pdb_path->subworkflow_mutate - - -step3_mutate_output_pdb_path - - - -step4_pdb2gmx_config - -step4_pdb2gmx_config - - - -step4_pdb2gmx_config->subworkflow_mutate - - -step4_pdb2gmx_config - - - -step4_pdb2gmx_output_gro_path - -step4_pdb2gmx_output_gro_path - - - -step4_pdb2gmx_output_gro_path->subworkflow_mutate - - -step4_pdb2gmx_output_gro_path - - - -step4_pdb2gmx_output_top_zip_path - -step4_pdb2gmx_output_top_zip_path - - - -step4_pdb2gmx_output_top_zip_path->subworkflow_mutate - - -step4_pdb2gmx_output_top_zip_path - - - -step5_editconf_config - -step5_editconf_config - - - -step5_editconf_config->subworkflow_mutate - - -step5_editconf_config - - - -step5_editconf_output_gro_path - -step5_editconf_output_gro_path - - - -step5_editconf_output_gro_path->subworkflow_mutate - - -step5_editconf_output_gro_path - - - -step6_solvate_output_gro_path - -step6_solvate_output_gro_path - - - -step6_solvate_output_gro_path->subworkflow_mutate - - -step6_solvate_output_gro_path - - - -step6_solvate_output_top_zip_path - -step6_solvate_output_top_zip_path - - - -step6_solvate_output_top_zip_path->subworkflow_mutate - - -step6_solvate_output_top_zip_path - - - -step7_grompp_genion_config - -step7_grompp_genion_config - - - -step7_grompp_genion_config->subworkflow_mutate - - -step7_grompp_genion_config - - - -step7_grompp_genion_output_tpr_path - -step7_grompp_genion_output_tpr_path - - - -step7_grompp_genion_output_tpr_path->subworkflow_mutate - - -step7_grompp_genion_output_tpr_path - - - -step8_genion_config - -step8_genion_config - - - -step8_genion_config->subworkflow_mutate - - -step8_genion_config - - - -step8_genion_output_gro_path - -step8_genion_output_gro_path - - - -step8_genion_output_gro_path->subworkflow_mutate - - -step8_genion_output_gro_path - - - -step8_genion_output_top_zip_path - -step8_genion_output_top_zip_path - - - -step8_genion_output_top_zip_path->subworkflow_mutate - - -step8_genion_output_top_zip_path - - - -step9_grompp_min_config - -step9_grompp_min_config - - - -step9_grompp_min_config->subworkflow_mutate - - -step9_grompp_min_config - - - -step9_grompp_min_output_tpr_path - -step9_grompp_min_output_tpr_path - - - -step9_grompp_min_output_tpr_path->subworkflow_mutate - - -step9_grompp_min_output_tpr_path - - - -step10_mdrun_min_output_trr_path - -step10_mdrun_min_output_trr_path - - - -step10_mdrun_min_output_trr_path->subworkflow_mutate - - -step10_mdrun_min_output_trr_path - - - -step10_mdrun_min_output_gro_path - -step10_mdrun_min_output_gro_path - - - -step10_mdrun_min_output_gro_path->subworkflow_mutate - - -step10_mdrun_min_output_gro_path - - - -step10_mdrun_min_output_edr_path - -step10_mdrun_min_output_edr_path - - - -step10_mdrun_min_output_edr_path->subworkflow_mutate - - -step10_mdrun_min_output_edr_path - - - -step10_mdrun_min_output_log_path - -step10_mdrun_min_output_log_path - - - -step10_mdrun_min_output_log_path->subworkflow_mutate - - -step10_mdrun_min_output_log_path - - - -step100_make_ndx_config - -step100_make_ndx_config - - - -step100_make_ndx_config->subworkflow_mutate - - -step100_make_ndx_config - - - -step100_make_ndx_output_ndx_path - -step100_make_ndx_output_ndx_path - - - -step100_make_ndx_output_ndx_path->subworkflow_mutate - - -step100_make_ndx_output_ndx_path - - - -step11_grompp_nvt_config - -step11_grompp_nvt_config - - - -step11_grompp_nvt_config->subworkflow_mutate - - -step11_grompp_nvt_config - - - -step11_grompp_nvt_output_tpr_path - -step11_grompp_nvt_output_tpr_path - - - -step11_grompp_nvt_output_tpr_path->subworkflow_mutate - - -step11_grompp_nvt_output_tpr_path - - - -step12_mdrun_nvt_output_trr_path - -step12_mdrun_nvt_output_trr_path - - - -step12_mdrun_nvt_output_trr_path->subworkflow_mutate - - -step12_mdrun_nvt_output_trr_path - - - -step12_mdrun_nvt_output_gro_path - -step12_mdrun_nvt_output_gro_path - - - -step12_mdrun_nvt_output_gro_path->subworkflow_mutate - - -step12_mdrun_nvt_output_gro_path - - - -step12_mdrun_nvt_output_edr_path - -step12_mdrun_nvt_output_edr_path - - - -step12_mdrun_nvt_output_edr_path->subworkflow_mutate - - -step12_mdrun_nvt_output_edr_path - - - -step12_mdrun_nvt_output_log_path - -step12_mdrun_nvt_output_log_path - - - -step12_mdrun_nvt_output_log_path->subworkflow_mutate - - -step12_mdrun_nvt_output_log_path - - - -step12_mdrun_nvt_output_cpt_path - -step12_mdrun_nvt_output_cpt_path - - - -step12_mdrun_nvt_output_cpt_path->subworkflow_mutate - - -step12_mdrun_nvt_output_cpt_path - - - -step13_grompp_npt_config - -step13_grompp_npt_config - - - -step13_grompp_npt_config->subworkflow_mutate - - -step13_grompp_npt_config - - - -step13_grompp_npt_output_tpr_path - -step13_grompp_npt_output_tpr_path - - - -step13_grompp_npt_output_tpr_path->subworkflow_mutate - - -step13_grompp_npt_output_tpr_path - - - -step14_mdrun_npt_output_trr_path - -step14_mdrun_npt_output_trr_path - - - -step14_mdrun_npt_output_trr_path->subworkflow_mutate - - -step14_mdrun_npt_output_trr_path - - - -step14_mdrun_npt_output_gro_path - -step14_mdrun_npt_output_gro_path - - - -step14_mdrun_npt_output_gro_path->subworkflow_mutate - - -step14_mdrun_npt_output_gro_path - - - -step14_mdrun_npt_output_edr_path - -step14_mdrun_npt_output_edr_path - - - -step14_mdrun_npt_output_edr_path->subworkflow_mutate - - -step14_mdrun_npt_output_edr_path - - - -step14_mdrun_npt_output_log_path - -step14_mdrun_npt_output_log_path - - - -step14_mdrun_npt_output_log_path->subworkflow_mutate - - -step14_mdrun_npt_output_log_path - - - -step14_mdrun_npt_output_cpt_path - -step14_mdrun_npt_output_cpt_path - - - -step14_mdrun_npt_output_cpt_path->subworkflow_mutate - - -step14_mdrun_npt_output_cpt_path - - - -step15_grompp_md_config - -step15_grompp_md_config - - - -step15_grompp_md_config->subworkflow_mutate - - -step15_grompp_md_config - - - -step15_grompp_md_output_tpr_path - -step15_grompp_md_output_tpr_path - - - -step15_grompp_md_output_tpr_path->subworkflow_mutate - - -step15_grompp_md_output_tpr_path - - - -step16_mdrun_md_output_trr_path - -step16_mdrun_md_output_trr_path - - - -step16_mdrun_md_output_trr_path->subworkflow_mutate - - -step16_mdrun_md_output_trr_path - - - -step16_mdrun_md_output_gro_path - -step16_mdrun_md_output_gro_path - - - -step16_mdrun_md_output_gro_path->subworkflow_mutate - - -step16_mdrun_md_output_gro_path - - - -step16_mdrun_md_output_edr_path - -step16_mdrun_md_output_edr_path - - - -step16_mdrun_md_output_edr_path->subworkflow_mutate - - -step16_mdrun_md_output_edr_path - - - -step16_mdrun_md_output_log_path - -step16_mdrun_md_output_log_path - - - -step16_mdrun_md_output_log_path->subworkflow_mutate - - -step16_mdrun_md_output_log_path - - - -step16_mdrun_md_output_cpt_path - -step16_mdrun_md_output_cpt_path - - - -step16_mdrun_md_output_cpt_path->subworkflow_mutate - - -step16_mdrun_md_output_cpt_path - - - -step17_gmx_image1_config - -step17_gmx_image1_config - - - -step17_gmx_image1_config->subworkflow_mutate - - -step17_gmx_image1_config - - - -step17_gmx_image1_output_traj_path - -step17_gmx_image1_output_traj_path - - - -step17_gmx_image1_output_traj_path->subworkflow_mutate - - -step17_gmx_image1_output_traj_path - - - -step18_gmx_image2_config - -step18_gmx_image2_config - - - -step18_gmx_image2_config->subworkflow_mutate - - -step18_gmx_image2_config - - - -step18_gmx_image2_output_traj_path - -step18_gmx_image2_output_traj_path - - - -step18_gmx_image2_output_traj_path->subworkflow_mutate - - -step18_gmx_image2_output_traj_path - - - -step19_gmx_trjconv_str_config - -step19_gmx_trjconv_str_config - - - -step19_gmx_trjconv_str_config->subworkflow_mutate - - -step19_gmx_trjconv_str_config - - - -step19_gmx_trjconv_str_output_str_path - -step19_gmx_trjconv_str_output_str_path - - - -step19_gmx_trjconv_str_output_str_path->subworkflow_mutate - - -step19_gmx_trjconv_str_output_str_path - - - -step20_gmx_energy_config - -step20_gmx_energy_config - - - -step20_gmx_energy_config->subworkflow_mutate - - -step20_gmx_energy_config - - - -step20_gmx_energy_output_xvg_path - -step20_gmx_energy_output_xvg_path - - - -step20_gmx_energy_output_xvg_path->subworkflow_mutate - - -step20_gmx_energy_output_xvg_path - - - -step21_gmx_rgyr_config - -step21_gmx_rgyr_config - - - -step21_gmx_rgyr_config->subworkflow_mutate - - -step21_gmx_rgyr_config - - - -step21_gmx_rgyr_output_xvg_path - -step21_gmx_rgyr_output_xvg_path - - - -step21_gmx_rgyr_output_xvg_path->subworkflow_mutate - - -step21_gmx_rgyr_output_xvg_path - - - -step22_rmsd_first_config - -step22_rmsd_first_config - - - -step22_rmsd_first_config->subworkflow_mutate - - -step22_rmsd_first_config - - - -step22_rmsd_first_output_xvg_path - -step22_rmsd_first_output_xvg_path - - - -step22_rmsd_first_output_xvg_path->subworkflow_mutate - - -step22_rmsd_first_output_xvg_path - - - -step23_rmsd_exp_config - -step23_rmsd_exp_config - - - -step23_rmsd_exp_config->subworkflow_mutate - - -step23_rmsd_exp_config - - - -step23_rmsd_exp_output_xvg_path - -step23_rmsd_exp_output_xvg_path - - - -step23_rmsd_exp_output_xvg_path->subworkflow_mutate - - -step23_rmsd_exp_output_xvg_path - - - -step24_grompp_md_config - -step24_grompp_md_config - - - -step24_grompp_md_config->subworkflow_mutate - - -step24_grompp_md_config - - - -step24_grompp_md_output_tpr_path - -step24_grompp_md_output_tpr_path - - - -step24_grompp_md_output_tpr_path->subworkflow_mutate - - -step24_grompp_md_output_tpr_path - - - -top_dir - -Collected Simulation Data - - - -step0_reduce_remove_hydrogens->step1_extract_molecule - - -input_structure_path - - - -step1_extract_molecule->step00_cat_pdb - - -input_structure1 - - - -step00_cat_pdb->step2_fix_side_chain - - -input_pdb_path - - - -step2_fix_side_chain->subworkflow_mutate - - -step2_output_pdb_path - - - -subworkflow_mutate->top_dir - - - - - diff --git a/0.3/example-result/data/workflow/289/workflow.cwl b/0.3/example-result/data/workflow/289/workflow.cwl deleted file mode 100644 index c6b94db..0000000 --- a/0.3/example-result/data/workflow/289/workflow.cwl +++ /dev/null @@ -1,359 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -class: Workflow -label: GROMACS Protein MD Setup with mutations -doc: |- - This workflow performs the process of setting up a simulation system containing a protein, step by step, using the GROMACS tools of the BioExcel Building Blocks library (biobb). Additionally, users can add mutations to the process. - -requirements: - SubworkflowFeatureRequirement: {} - ScatterFeatureRequirement: {} - -inputs: - mutations_list: - type: - type: array - items: string - step0_reduce_remove_hydrogens_input_path: File - step0_reduce_remove_hydrogens_output_path: string - step1_extract_molecule_output_molecule_path: string - step00_cat_pdb_input_structure2: File - step00_cat_pdb_output_structure_path: string - step2_fix_side_chain_output_pdb_path: string - step3_mutate_output_pdb_path: string - step4_pdb2gmx_config: string - step4_pdb2gmx_output_gro_path: string - step4_pdb2gmx_output_top_zip_path: string - step5_editconf_config: string - step5_editconf_output_gro_path: string - step6_solvate_output_gro_path: string - step6_solvate_output_top_zip_path: string - step7_grompp_genion_config: string - step7_grompp_genion_output_tpr_path: string - step8_genion_config: string - step8_genion_output_gro_path: string - step8_genion_output_top_zip_path: string - step9_grompp_min_config: string - step9_grompp_min_output_tpr_path: string - step10_mdrun_min_output_trr_path: string - step10_mdrun_min_output_gro_path: string - step10_mdrun_min_output_edr_path: string - step10_mdrun_min_output_log_path: string - step100_make_ndx_config: string - step100_make_ndx_output_ndx_path: string - step11_grompp_nvt_config: string - step11_grompp_nvt_output_tpr_path: string - step12_mdrun_nvt_output_trr_path: string - step12_mdrun_nvt_output_gro_path: string - step12_mdrun_nvt_output_edr_path: string - step12_mdrun_nvt_output_log_path: string - step12_mdrun_nvt_output_cpt_path: string - step13_grompp_npt_config: string - step13_grompp_npt_output_tpr_path: string - step14_mdrun_npt_output_trr_path: string - step14_mdrun_npt_output_gro_path: string - step14_mdrun_npt_output_edr_path: string - step14_mdrun_npt_output_log_path: string - step14_mdrun_npt_output_cpt_path: string - step15_grompp_md_config: string - step15_grompp_md_output_tpr_path: string - step16_mdrun_md_output_trr_path: string - step16_mdrun_md_output_gro_path: string - step16_mdrun_md_output_edr_path: string - step16_mdrun_md_output_log_path: string - step16_mdrun_md_output_cpt_path: string - step17_gmx_image1_config: string - step17_gmx_image1_output_traj_path: string - step18_gmx_image2_config: string - step18_gmx_image2_output_traj_path: string - step19_gmx_trjconv_str_config: string - step19_gmx_trjconv_str_output_str_path: string - step20_gmx_energy_config: string - step20_gmx_energy_output_xvg_path: string - step21_gmx_rgyr_config: string - step21_gmx_rgyr_output_xvg_path: string - step22_rmsd_first_config: string - step22_rmsd_first_output_xvg_path: string - step23_rmsd_exp_config: string - step23_rmsd_exp_output_xvg_path: string - step24_grompp_md_config: string - step24_grompp_md_output_tpr_path: string - -outputs: - top_dir: - label: Collected Simulation Data - doc: | - Assorted data files output by the workflow - type: - type: array - items: Directory - outputSource: subworkflow_mutate/outdir - -steps: - - step0_reduce_remove_hydrogens: - label: ReduceRemoveHydrogens - doc: |- - Removes hydrogen atoms to small molecules. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_chemistry/reduce_remove_hydrogens.cwl - in: - input_path: step0_reduce_remove_hydrogens_input_path - output_path: step0_reduce_remove_hydrogens_output_path - out: - - output_path - - step1_extract_molecule: - label: ExtractMolecule - doc: |- - This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_structure_utils/extract_molecule.cwl - in: - input_structure_path: step0_reduce_remove_hydrogens/output_path - output_molecule_path: step1_extract_molecule_output_molecule_path - out: - - output_molecule_path - - step00_cat_pdb: - label: CatPDB - doc: |- - Class to concat two PDB structures in a single PDB file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_structure_utils/cat_pdb.cwl - in: - input_structure1: step1_extract_molecule/output_molecule_path - input_structure2: step00_cat_pdb_input_structure2 - output_structure_path: step00_cat_pdb_output_structure_path - out: - - output_structure_path - - step2_fix_side_chain: - label: FixSideChain - doc: |- - Reconstructs the missing side chains and heavy atoms of the given PDB file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_model/fix_side_chain.cwl - in: - input_pdb_path: step00_cat_pdb/output_structure_path - output_pdb_path: step2_fix_side_chain_output_pdb_path - out: - - output_pdb_path - - subworkflow_mutate: - in: - step2_output_pdb_path: step2_fix_side_chain/output_pdb_path - mutation: mutations_list - step3_mutate_output_pdb_path: step3_mutate_output_pdb_path - step4_pdb2gmx_config: step4_pdb2gmx_config - step4_pdb2gmx_output_gro_path: step4_pdb2gmx_output_gro_path - step4_pdb2gmx_output_top_zip_path: step4_pdb2gmx_output_top_zip_path - step5_editconf_config: step5_editconf_config - step5_editconf_output_gro_path: step5_editconf_output_gro_path - step6_solvate_output_gro_path: step6_solvate_output_gro_path - step6_solvate_output_top_zip_path: step6_solvate_output_top_zip_path - step7_grompp_genion_config: step7_grompp_genion_config - step7_grompp_genion_output_tpr_path: step7_grompp_genion_output_tpr_path - step8_genion_config: step8_genion_config - step8_genion_output_gro_path: step8_genion_output_gro_path - step8_genion_output_top_zip_path: step8_genion_output_top_zip_path - step9_grompp_min_config: step9_grompp_min_config - step9_grompp_min_output_tpr_path: step9_grompp_min_output_tpr_path - step10_mdrun_min_output_trr_path: step10_mdrun_min_output_trr_path - step10_mdrun_min_output_gro_path: step10_mdrun_min_output_gro_path - step10_mdrun_min_output_edr_path: step10_mdrun_min_output_edr_path - step10_mdrun_min_output_log_path: step10_mdrun_min_output_log_path - step100_make_ndx_config: step100_make_ndx_config - step100_make_ndx_output_ndx_path: step100_make_ndx_output_ndx_path - step11_grompp_nvt_config: step11_grompp_nvt_config - step11_grompp_nvt_output_tpr_path: step11_grompp_nvt_output_tpr_path - step12_mdrun_nvt_output_trr_path: step12_mdrun_nvt_output_trr_path - step12_mdrun_nvt_output_gro_path: step12_mdrun_nvt_output_gro_path - step12_mdrun_nvt_output_edr_path: step12_mdrun_nvt_output_edr_path - step12_mdrun_nvt_output_log_path: step12_mdrun_nvt_output_log_path - step12_mdrun_nvt_output_cpt_path: step12_mdrun_nvt_output_cpt_path - step13_grompp_npt_config: step13_grompp_npt_config - step13_grompp_npt_output_tpr_path: step13_grompp_npt_output_tpr_path - step14_mdrun_npt_output_trr_path: step14_mdrun_npt_output_trr_path - step14_mdrun_npt_output_gro_path: step14_mdrun_npt_output_gro_path - step14_mdrun_npt_output_edr_path: step14_mdrun_npt_output_edr_path - step14_mdrun_npt_output_log_path: step14_mdrun_npt_output_log_path - step14_mdrun_npt_output_cpt_path: step14_mdrun_npt_output_cpt_path - step15_grompp_md_config: step15_grompp_md_config - step15_grompp_md_output_tpr_path: step15_grompp_md_output_tpr_path - step16_mdrun_md_output_trr_path: step16_mdrun_md_output_trr_path - step16_mdrun_md_output_gro_path: step16_mdrun_md_output_gro_path - step16_mdrun_md_output_edr_path: step16_mdrun_md_output_edr_path - step16_mdrun_md_output_log_path: step16_mdrun_md_output_log_path - step16_mdrun_md_output_cpt_path: step16_mdrun_md_output_cpt_path - step17_gmx_image1_config: step17_gmx_image1_config - step17_gmx_image1_output_traj_path: step17_gmx_image1_output_traj_path - step18_gmx_image2_config: step18_gmx_image2_config - step18_gmx_image2_output_traj_path: step18_gmx_image2_output_traj_path - step19_gmx_trjconv_str_config: step19_gmx_trjconv_str_config - step19_gmx_trjconv_str_output_str_path: step19_gmx_trjconv_str_output_str_path - step20_gmx_energy_config: step20_gmx_energy_config - step20_gmx_energy_output_xvg_path: step20_gmx_energy_output_xvg_path - step21_gmx_rgyr_config: step21_gmx_rgyr_config - step21_gmx_rgyr_output_xvg_path: step21_gmx_rgyr_output_xvg_path - step22_rmsd_first_config: step22_rmsd_first_config - step22_rmsd_first_output_xvg_path: step22_rmsd_first_output_xvg_path - step23_rmsd_exp_config: step23_rmsd_exp_config - step23_rmsd_exp_output_xvg_path: step23_rmsd_exp_output_xvg_path - step24_grompp_md_config: step24_grompp_md_config - step24_grompp_md_output_tpr_path: step24_grompp_md_output_tpr_path - - out: [outdir] - - scatter: mutation - run: - class: Workflow - inputs: - step2_output_pdb_path: File - mutation: string - step3_mutate_output_pdb_path: string - step4_pdb2gmx_config: string - step4_pdb2gmx_output_gro_path: string - step4_pdb2gmx_output_top_zip_path: string - step5_editconf_config: string - step5_editconf_output_gro_path: string - step6_solvate_output_gro_path: string - step6_solvate_output_top_zip_path: string - step7_grompp_genion_config: string - step7_grompp_genion_output_tpr_path: string - step8_genion_config: string - step8_genion_output_gro_path: string - step8_genion_output_top_zip_path: string - step9_grompp_min_config: string - step9_grompp_min_output_tpr_path: string - step10_mdrun_min_output_trr_path: string - step10_mdrun_min_output_gro_path: string - step10_mdrun_min_output_edr_path: string - step10_mdrun_min_output_log_path: string - step100_make_ndx_config: string - step100_make_ndx_output_ndx_path: string - step11_grompp_nvt_config: string - step11_grompp_nvt_output_tpr_path: string - step12_mdrun_nvt_output_trr_path: string - step12_mdrun_nvt_output_gro_path: string - step12_mdrun_nvt_output_edr_path: string - step12_mdrun_nvt_output_log_path: string - step12_mdrun_nvt_output_cpt_path: string - step13_grompp_npt_config: string - step13_grompp_npt_output_tpr_path: string - step14_mdrun_npt_output_trr_path: string - step14_mdrun_npt_output_gro_path: string - step14_mdrun_npt_output_edr_path: string - step14_mdrun_npt_output_log_path: string - step14_mdrun_npt_output_cpt_path: string - step15_grompp_md_config: string - step15_grompp_md_output_tpr_path: string - step16_mdrun_md_output_trr_path: string - step16_mdrun_md_output_gro_path: string - step16_mdrun_md_output_edr_path: string - step16_mdrun_md_output_log_path: string - step16_mdrun_md_output_cpt_path: string - step17_gmx_image1_config: string - step17_gmx_image1_output_traj_path: string - step18_gmx_image2_config: string - step18_gmx_image2_output_traj_path: string - step19_gmx_trjconv_str_config: string - step19_gmx_trjconv_str_output_str_path: string - step20_gmx_energy_config: string - step20_gmx_energy_output_xvg_path: string - step21_gmx_rgyr_config: string - step21_gmx_rgyr_output_xvg_path: string - step22_rmsd_first_config: string - step22_rmsd_first_output_xvg_path: string - step23_rmsd_exp_config: string - step23_rmsd_exp_output_xvg_path: string - step24_grompp_md_config: string - step24_grompp_md_output_tpr_path: string - - outputs: - outdir: - label: Simulation Data - type: Directory - outputSource: launch_workflow/dir - - steps: - - step3_mutate: - label: Mutate - doc: |- - Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_model/mutate.cwl - in: - config: mutation - input_pdb_path: step2_output_pdb_path - output_pdb_path: step3_mutate_output_pdb_path - out: - - output_pdb_path - - launch_workflow: - run: workflow_list.cwl - in: - mut: mutation - step3_mutate_output_pdb_path: - source: - - step3_mutate/output_pdb_path - pickValue: first_non_null - step4_pdb2gmx_config: step4_pdb2gmx_config - step4_pdb2gmx_output_gro_path: step4_pdb2gmx_output_gro_path - step4_pdb2gmx_output_top_zip_path: step4_pdb2gmx_output_top_zip_path - step5_editconf_config: step5_editconf_config - step5_editconf_output_gro_path: step5_editconf_output_gro_path - step6_solvate_output_gro_path: step6_solvate_output_gro_path - step6_solvate_output_top_zip_path: step6_solvate_output_top_zip_path - step7_grompp_genion_config: step7_grompp_genion_config - step7_grompp_genion_output_tpr_path: step7_grompp_genion_output_tpr_path - step8_genion_config: step8_genion_config - step8_genion_output_gro_path: step8_genion_output_gro_path - step8_genion_output_top_zip_path: step8_genion_output_top_zip_path - step9_grompp_min_config: step9_grompp_min_config - step9_grompp_min_output_tpr_path: step9_grompp_min_output_tpr_path - step10_mdrun_min_output_trr_path: step10_mdrun_min_output_trr_path - step10_mdrun_min_output_gro_path: step10_mdrun_min_output_gro_path - step10_mdrun_min_output_edr_path: step10_mdrun_min_output_edr_path - step10_mdrun_min_output_log_path: step10_mdrun_min_output_log_path - step100_make_ndx_config: step100_make_ndx_config - step100_make_ndx_output_ndx_path: step100_make_ndx_output_ndx_path - step11_grompp_nvt_config: step11_grompp_nvt_config - step11_grompp_nvt_output_tpr_path: step11_grompp_nvt_output_tpr_path - step12_mdrun_nvt_output_trr_path: step12_mdrun_nvt_output_trr_path - step12_mdrun_nvt_output_gro_path: step12_mdrun_nvt_output_gro_path - step12_mdrun_nvt_output_edr_path: step12_mdrun_nvt_output_edr_path - step12_mdrun_nvt_output_log_path: step12_mdrun_nvt_output_log_path - step12_mdrun_nvt_output_cpt_path: step12_mdrun_nvt_output_cpt_path - step13_grompp_npt_config: step13_grompp_npt_config - step13_grompp_npt_output_tpr_path: step13_grompp_npt_output_tpr_path - step14_mdrun_npt_output_trr_path: step14_mdrun_npt_output_trr_path - step14_mdrun_npt_output_gro_path: step14_mdrun_npt_output_gro_path - step14_mdrun_npt_output_edr_path: step14_mdrun_npt_output_edr_path - step14_mdrun_npt_output_log_path: step14_mdrun_npt_output_log_path - step14_mdrun_npt_output_cpt_path: step14_mdrun_npt_output_cpt_path - step15_grompp_md_config: step15_grompp_md_config - step15_grompp_md_output_tpr_path: step15_grompp_md_output_tpr_path - step16_mdrun_md_output_trr_path: step16_mdrun_md_output_trr_path - step16_mdrun_md_output_gro_path: step16_mdrun_md_output_gro_path - step16_mdrun_md_output_edr_path: step16_mdrun_md_output_edr_path - step16_mdrun_md_output_log_path: step16_mdrun_md_output_log_path - step16_mdrun_md_output_cpt_path: step16_mdrun_md_output_cpt_path - step17_gmx_image1_config: step17_gmx_image1_config - step17_gmx_image1_output_traj_path: step17_gmx_image1_output_traj_path - step18_gmx_image2_config: step18_gmx_image2_config - step18_gmx_image2_output_traj_path: step18_gmx_image2_output_traj_path - step19_gmx_trjconv_str_config: step19_gmx_trjconv_str_config - step19_gmx_trjconv_str_output_str_path: step19_gmx_trjconv_str_output_str_path - step20_gmx_energy_config: step20_gmx_energy_config - step20_gmx_energy_output_xvg_path: step20_gmx_energy_output_xvg_path - step21_gmx_rgyr_config: step21_gmx_rgyr_config - step21_gmx_rgyr_output_xvg_path: step21_gmx_rgyr_output_xvg_path - step22_rmsd_first_config: step22_rmsd_first_config - step22_rmsd_first_output_xvg_path: step22_rmsd_first_output_xvg_path - step23_rmsd_exp_config: step23_rmsd_exp_config - step23_rmsd_exp_output_xvg_path: step23_rmsd_exp_output_xvg_path - step24_grompp_md_config: step24_grompp_md_config - step24_grompp_md_output_tpr_path: step24_grompp_md_output_tpr_path - - out: [dir] - - - diff --git a/0.3/example-result/data/workflow/289/workflow_gather.cwl b/0.3/example-result/data/workflow/289/workflow_gather.cwl deleted file mode 100644 index cae2e0b..0000000 --- a/0.3/example-result/data/workflow/289/workflow_gather.cwl +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.1 -class: ExpressionTool - -doc: |- - This javascript takes two inputs: a list of files and a string. - It will create a directory named after the string, populate that - directory with the files in the list, and return the directory. -requirements: - InlineJavascriptRequirement: {} -inputs: - output_folder: string - external_files: File[] -outputs: - project_work_dir: - label: Output archive directory - doc: | - workflow output directory, containing required output files - type: Directory -expression: | - ${ - var myRegexp = new RegExp('{"mutation_list":"(.*)"}', "g"); - var match = myRegexp.exec(inputs.output_folder); - return { - "project_work_dir": { - "class": "Directory", - "basename": match[1], - "listing": inputs.external_files - } - }; - } diff --git a/0.3/example-result/data/workflow/289/workflow_input_descriptions.yml b/0.3/example-result/data/workflow/289/workflow_input_descriptions.yml deleted file mode 100644 index 86ae1fc..0000000 --- a/0.3/example-result/data/workflow/289/workflow_input_descriptions.yml +++ /dev/null @@ -1,76 +0,0 @@ -mutations_list: - - '{"mutation_list":"A:Gly4Lys"}' - - '{"mutation_list":"A:Leu8Met"}' - - '{"mutation_list":"A:Tyr20Gln"}' - -step0_reduce_remove_hydrogens_input_path: - class: File - path: structure.pdb - format: https://edamontology.org/format_1476 -step0_reduce_remove_hydrogens_output_path: structure.noH.pdb -step1_extract_molecule_output_molecule_path: protein.pdb -step00_cat_pdb_input_structure2: - class: File - path: ions.pdb - format: https://edamontology.org/format_1476 -step00_cat_pdb_output_structure_path: protein.ions.pdb -step2_fix_side_chain_output_pdb_path: fixsidechain.pdb -step3_mutate_output_pdb_path: mutate.pdb -step4_pdb2gmx_config: '{"force_field": "amber99sb", "water_type": "tip3p"}' -step4_pdb2gmx_output_gro_path: pdb2gmx.gro -step4_pdb2gmx_output_top_zip_path: pdb2gmx_top.zip -step5_editconf_config: '{"distance_to_molecule": 0.8, "box_type": "octahedron"}' -step5_editconf_output_gro_path: editconf.pdb -step6_solvate_output_gro_path: solvate.gro -step6_solvate_output_top_zip_path: solvate_top.zip -step7_grompp_genion_config: '{"simulation_type": "minimization", "maxwarn": 1, "mdp": {"nsteps": 5000}}' -step7_grompp_genion_output_tpr_path: gppion.tpr -step8_genion_config: '{"neutral": true, "concentration": 0.05}' -step8_genion_output_gro_path: genion.gro -step8_genion_output_top_zip_path: genion_top.zip -step9_grompp_min_config: '{"mdp": {"nsteps": 5000, "emtol": 500}, "simulation_type": "minimization"}' -step9_grompp_min_output_tpr_path: gppmin.tpr -step10_mdrun_min_output_trr_path: min.trr -step10_mdrun_min_output_gro_path: min.gro -step10_mdrun_min_output_edr_path: min.edr -step10_mdrun_min_output_log_path: min.log -step100_make_ndx_config: '{"selection": "System"}' -step100_make_ndx_output_ndx_path: str_index.ndx -step11_grompp_nvt_config: '{"mdp": {"nsteps": 50000, "dt": 0.002, "Define": "-DPOSRES", "tc-grps": "Protein Water_and_ions"}, "simulation_type": "nvt"}' -step11_grompp_nvt_output_tpr_path: gppnvt.tpr -step12_mdrun_nvt_output_trr_path: nvt.trr -step12_mdrun_nvt_output_gro_path: nvt.gro -step12_mdrun_nvt_output_edr_path: nvt.edr -step12_mdrun_nvt_output_log_path: nvt.log -step12_mdrun_nvt_output_cpt_path: nvt.cpt -step13_grompp_npt_config: '{"mdp": {"nsteps": 50000, "tc-grps": "Protein Water_and_ions"}, "simulation_type": "npt"}' -step13_grompp_npt_output_tpr_path: gppnpt.tpr -step14_mdrun_npt_output_trr_path: npt.trr -step14_mdrun_npt_output_gro_path: npt.gro -step14_mdrun_npt_output_edr_path: npt.edr -step14_mdrun_npt_output_log_path: npt.log -step14_mdrun_npt_output_cpt_path: npt.cpt -step15_grompp_md_config: '{"mdp": {"nsteps": 250000, "tc-grps": "Protein Water_and_ions"}, "simulation_type": "free"}' -step15_grompp_md_output_tpr_path: gppmd.tpr -step16_mdrun_md_output_trr_path: md.trr -step16_mdrun_md_output_gro_path: md.gro -step16_mdrun_md_output_edr_path: md.edr -step16_mdrun_md_output_log_path: md.log -step16_mdrun_md_output_cpt_path: md.cpt -step17_gmx_image1_config: '{"center_selection": "Protein", "output_selection": "System", "pbc": "mol", "center": true, "ur": "compact"}' -step17_gmx_image1_output_traj_path: md.imaged.trr -step18_gmx_image2_config: '{"fit_selection": "Protein", "output_selection": "System", "fit": "rot+trans"}' -step18_gmx_image2_output_traj_path: md.imaged.rot.xtc -step19_gmx_trjconv_str_config: '{"pbc": "mol", "selection": "System"}' -step19_gmx_trjconv_str_output_str_path: setup.top.pdb -step20_gmx_energy_config: '{"xvg": "xmgr", "terms": ["Potential", "Total-Energy"]}' -step20_gmx_energy_output_xvg_path: setup.energy.xvg -step21_gmx_rgyr_config: '{"xvg": "xmgr", "selection": "Protein-H"}' -step21_gmx_rgyr_output_xvg_path: setup.rgyr.xvg -step22_rmsd_first_config: '{"selection": "Protein-H"}' -step22_rmsd_first_output_xvg_path: setup.rmsd_first.xvg -step23_rmsd_exp_config: '{"selection": "Protein-H"}' -step23_rmsd_exp_output_xvg_path: setup.rmsd_exp.xvg -step24_grompp_md_config: '{"mdp": {"nsteps": 5000000, "dt": 0.002, "ref-t": "300 300", "nstxout": 100000, "nstxout-compresse -d": 500}, "simulation_type": "free"}' -step24_grompp_md_output_tpr_path: gppmdsim.tpr diff --git a/0.3/example-result/data/workflow/289/workflow_list.cwl b/0.3/example-result/data/workflow/289/workflow_list.cwl deleted file mode 100644 index 411e86d..0000000 --- a/0.3/example-result/data/workflow/289/workflow_list.cwl +++ /dev/null @@ -1,435 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -class: Workflow - -requirements: - MultipleInputFeatureRequirement: {} - -inputs: - mut: string - step3_mutate_output_pdb_path: - type: File - step4_pdb2gmx_config: string - step4_pdb2gmx_output_gro_path: string - step4_pdb2gmx_output_top_zip_path: string - step5_editconf_config: string - step5_editconf_output_gro_path: string - step6_solvate_output_gro_path: string - step6_solvate_output_top_zip_path: string - step7_grompp_genion_config: string - step7_grompp_genion_output_tpr_path: string - step8_genion_config: string - step8_genion_output_gro_path: string - step8_genion_output_top_zip_path: string - step9_grompp_min_config: string - step9_grompp_min_output_tpr_path: string - step10_mdrun_min_output_trr_path: string - step10_mdrun_min_output_gro_path: string - step10_mdrun_min_output_edr_path: string - step10_mdrun_min_output_log_path: string - step100_make_ndx_config: string - step100_make_ndx_output_ndx_path: string - step11_grompp_nvt_config: string - step11_grompp_nvt_output_tpr_path: string - step12_mdrun_nvt_output_trr_path: string - step12_mdrun_nvt_output_gro_path: string - step12_mdrun_nvt_output_edr_path: string - step12_mdrun_nvt_output_log_path: string - step12_mdrun_nvt_output_cpt_path: string - step13_grompp_npt_config: string - step13_grompp_npt_output_tpr_path: string - step14_mdrun_npt_output_trr_path: string - step14_mdrun_npt_output_gro_path: string - step14_mdrun_npt_output_edr_path: string - step14_mdrun_npt_output_log_path: string - step14_mdrun_npt_output_cpt_path: string - step15_grompp_md_config: string - step15_grompp_md_output_tpr_path: string - step16_mdrun_md_output_trr_path: string - step16_mdrun_md_output_gro_path: string - step16_mdrun_md_output_edr_path: string - step16_mdrun_md_output_log_path: string - step16_mdrun_md_output_cpt_path: string - step17_gmx_image1_config: string - step17_gmx_image1_output_traj_path: string - step18_gmx_image2_config: string - step18_gmx_image2_output_traj_path: string - step19_gmx_trjconv_str_config: string - step19_gmx_trjconv_str_output_str_path: string - step20_gmx_energy_config: string - step20_gmx_energy_output_xvg_path: string - step21_gmx_rgyr_config: string - step21_gmx_rgyr_output_xvg_path: string - step22_rmsd_first_config: string - step22_rmsd_first_output_xvg_path: string - step23_rmsd_exp_config: string - step23_rmsd_exp_output_xvg_path: string - step24_grompp_md_config: string - step24_grompp_md_output_tpr_path: string - -outputs: - dir: - label: Whole workflow output - type: Directory - outputSource: step25_gather_outputs/project_work_dir - -steps: - step4_pdb2gmx: - label: Pdb2gmx - doc: |- - Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/pdb2gmx.cwl - in: - config: step4_pdb2gmx_config - input_pdb_path: step3_mutate_output_pdb_path - output_gro_path: step4_pdb2gmx_output_gro_path - output_top_zip_path: step4_pdb2gmx_output_top_zip_path - out: - - output_gro_path - - output_top_zip_path - - step5_editconf: - label: Editconf - doc: |- - Creates a GROMACS structure file (GRO) adding the information of the solvent box to the input structure file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/editconf.cwl - in: - config: step5_editconf_config - input_gro_path: step4_pdb2gmx/output_gro_path - output_gro_path: step5_editconf_output_gro_path - out: - - output_gro_path - - step6_solvate: - label: Solvate - doc: |- - Creates a new compressed GROMACS topology file adding solvent molecules to a given input compressed GROMACS topology file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/solvate.cwl - in: - input_solute_gro_path: step5_editconf/output_gro_path - output_gro_path: step6_solvate_output_gro_path - input_top_zip_path: step4_pdb2gmx/output_top_zip_path - output_top_zip_path: step6_solvate_output_top_zip_path - out: - - output_gro_path - - output_top_zip_path - - step7_grompp_genion: - label: Grompp - doc: |- - Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/grompp.cwl - in: - config: step7_grompp_genion_config - input_gro_path: step6_solvate/output_gro_path - input_top_zip_path: step6_solvate/output_top_zip_path - output_tpr_path: step7_grompp_genion_output_tpr_path - out: - - output_tpr_path - - step8_genion: - label: Genion - doc: |- - Creates a new compressed GROMACS topology adding ions until reaching the desired concentration to the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/genion.cwl - in: - config: step8_genion_config - input_tpr_path: step7_grompp_genion/output_tpr_path - output_gro_path: step8_genion_output_gro_path - input_top_zip_path: step6_solvate/output_top_zip_path - output_top_zip_path: step8_genion_output_top_zip_path - out: - - output_gro_path - - output_top_zip_path - - step9_grompp_min: - label: Grompp - doc: |- - Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/grompp.cwl - in: - config: step9_grompp_min_config - input_gro_path: step8_genion/output_gro_path - input_top_zip_path: step8_genion/output_top_zip_path - output_tpr_path: step9_grompp_min_output_tpr_path - out: - - output_tpr_path - - step10_mdrun_min: - label: Mdrun - doc: |- - Performs molecular dynamics simulations from an input GROMACS TPR file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/mdrun.cwl - in: - input_tpr_path: step9_grompp_min/output_tpr_path - output_trr_path: step10_mdrun_min_output_trr_path - output_gro_path: step10_mdrun_min_output_gro_path - output_edr_path: step10_mdrun_min_output_edr_path - output_log_path: step10_mdrun_min_output_log_path - out: - - output_trr_path - - output_gro_path - - output_edr_path - - output_log_path - - step100_make_ndx: - label: MakeNdx - doc: |- - Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/make_ndx.cwl - in: - config: step100_make_ndx_config - input_structure_path: step10_mdrun_min/output_gro_path - output_ndx_path: step100_make_ndx_output_ndx_path - out: - - output_ndx_path - - step11_grompp_nvt: - label: Grompp - doc: |- - Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/grompp.cwl - in: - config: step11_grompp_nvt_config - input_gro_path: step10_mdrun_min/output_gro_path - input_ndx_path: step100_make_ndx/output_ndx_path - input_top_zip_path: step8_genion/output_top_zip_path - output_tpr_path: step11_grompp_nvt_output_tpr_path - out: - - output_tpr_path - - step12_mdrun_nvt: - label: Mdrun - doc: |- - Performs molecular dynamics simulations from an input GROMACS TPR file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/mdrun.cwl - in: - input_tpr_path: step11_grompp_nvt/output_tpr_path - output_trr_path: step12_mdrun_nvt_output_trr_path - output_gro_path: step12_mdrun_nvt_output_gro_path - output_edr_path: step12_mdrun_nvt_output_edr_path - output_log_path: step12_mdrun_nvt_output_log_path - output_cpt_path: step12_mdrun_nvt_output_cpt_path - out: - - output_trr_path - - output_gro_path - - output_edr_path - - output_log_path - - output_cpt_path - - step13_grompp_npt: - label: Grompp - doc: |- - Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/grompp.cwl - in: - config: step13_grompp_npt_config - input_gro_path: step12_mdrun_nvt/output_gro_path - input_ndx_path: step100_make_ndx/output_ndx_path - input_top_zip_path: step8_genion/output_top_zip_path - output_tpr_path: step13_grompp_npt_output_tpr_path - input_cpt_path: step12_mdrun_nvt/output_cpt_path - out: - - output_tpr_path - - step14_mdrun_npt: - label: Mdrun - doc: |- - Performs molecular dynamics simulations from an input GROMACS TPR file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/mdrun.cwl - in: - input_tpr_path: step13_grompp_npt/output_tpr_path - output_trr_path: step14_mdrun_npt_output_trr_path - output_gro_path: step14_mdrun_npt_output_gro_path - output_edr_path: step14_mdrun_npt_output_edr_path - output_log_path: step14_mdrun_npt_output_log_path - output_cpt_path: step14_mdrun_npt_output_cpt_path - out: - - output_trr_path - - output_gro_path - - output_edr_path - - output_log_path - - output_cpt_path - - step15_grompp_md: - label: Grompp - doc: |- - Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/grompp.cwl - in: - config: step15_grompp_md_config - input_gro_path: step14_mdrun_npt/output_gro_path - input_ndx_path: step100_make_ndx/output_ndx_path - input_top_zip_path: step8_genion/output_top_zip_path - output_tpr_path: step15_grompp_md_output_tpr_path - input_cpt_path: step14_mdrun_npt/output_cpt_path - out: - - output_tpr_path - - step16_mdrun_md: - label: Mdrun - doc: |- - Performs molecular dynamics simulations from an input GROMACS TPR file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/mdrun.cwl - in: - input_tpr_path: step15_grompp_md/output_tpr_path - output_trr_path: step16_mdrun_md_output_trr_path - output_gro_path: step16_mdrun_md_output_gro_path - output_edr_path: step16_mdrun_md_output_edr_path - output_log_path: step16_mdrun_md_output_log_path - output_cpt_path: step16_mdrun_md_output_cpt_path - out: - - output_trr_path - - output_gro_path - - output_edr_path - - output_log_path - - output_cpt_path - - step17_gmx_image1: - label: GMXImage - doc: |- - Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_image.cwl - in: - config: step17_gmx_image1_config - input_traj_path: step16_mdrun_md/output_trr_path - input_top_path: step9_grompp_min/output_tpr_path - input_index_path: step100_make_ndx/output_ndx_path - output_traj_path: step17_gmx_image1_output_traj_path - out: - - output_traj_path - - step18_gmx_image2: - label: GMXImage - doc: |- - Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_image.cwl - in: - config: step18_gmx_image2_config - input_traj_path: step17_gmx_image1/output_traj_path - input_top_path: step9_grompp_min/output_tpr_path - input_index_path: step100_make_ndx/output_ndx_path - output_traj_path: step18_gmx_image2_output_traj_path - out: - - output_traj_path - - step19_gmx_trjconv_str: - label: GMXTrjconvStr - doc: |- - Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_trjconv_str.cwl - in: - config: step19_gmx_trjconv_str_config - input_structure_path: step16_mdrun_md/output_gro_path - input_top_path: step9_grompp_min/output_tpr_path - input_index_path: step100_make_ndx/output_ndx_path - output_str_path: step19_gmx_trjconv_str_output_str_path - out: - - output_str_path - - step20_gmx_energy: - label: GMXEnergy - doc: |- - Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_energy.cwl - in: - config: step20_gmx_energy_config - input_energy_path: step16_mdrun_md/output_edr_path - output_xvg_path: step20_gmx_energy_output_xvg_path - out: - - output_xvg_path - - step21_gmx_rgyr: - label: GMXRgyr - doc: |- - Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_rgyr.cwl - in: - config: step21_gmx_rgyr_config - input_structure_path: step15_grompp_md/output_tpr_path - input_traj_path: step18_gmx_image2/output_traj_path - input_index_path: step100_make_ndx/output_ndx_path - output_xvg_path: step21_gmx_rgyr_output_xvg_path - out: - - output_xvg_path - - step22_rmsd_first: - label: GMXRms - doc: |- - Wrapper of the Ambertools GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_rms.cwl - in: - config: step22_rmsd_first_config - input_structure_path: step15_grompp_md/output_tpr_path - input_traj_path: step18_gmx_image2/output_traj_path - input_index_path: step100_make_ndx/output_ndx_path - output_xvg_path: step22_rmsd_first_output_xvg_path - out: - - output_xvg_path - - step23_rmsd_exp: - label: GMXRms - doc: |- - Wrapper of the Ambertools GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_analysis/gmx_rms.cwl - in: - config: step23_rmsd_exp_config - input_structure_path: step9_grompp_min/output_tpr_path - input_traj_path: step18_gmx_image2/output_traj_path - input_index_path: step100_make_ndx/output_ndx_path - output_xvg_path: step23_rmsd_exp_output_xvg_path - out: - - output_xvg_path - - step24_grompp_md: - label: Grompp - doc: |- - Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. - run: /path/to/biobb_adapters/biobb_adapters/cwl/biobb_md/grompp.cwl - in: - config: step24_grompp_md_config - input_gro_path: step16_mdrun_md/output_gro_path - input_top_zip_path: step8_genion/output_top_zip_path - output_tpr_path: step24_grompp_md_output_tpr_path - input_cpt_path: step16_mdrun_md/output_cpt_path - out: - - output_tpr_path - - step25_gather_outputs: - label: Archiving outputs to be returned to user - doc: > - This uses the local workflow_gather.cwl workflow to gather all desired output files. - A filter for missing files is applied (pickValue: all_non_null), which requires - using a runner which is compliant with v1.2.0, or later, CWL standards. - in: - output_folder: mut - external_files: - source: - - step8_genion/output_top_zip_path - - step15_grompp_md/output_tpr_path - - step16_mdrun_md/output_gro_path - - step16_mdrun_md/output_cpt_path - - step18_gmx_image2/output_traj_path - - step19_gmx_trjconv_str/output_str_path - - step20_gmx_energy/output_xvg_path - - step21_gmx_rgyr/output_xvg_path - - step22_rmsd_first/output_xvg_path - - step23_rmsd_exp/output_xvg_path - - step24_grompp_md/output_tpr_path - linkMerge: merge_flattened - pickValue: all_non_null - run: workflow_gather.cwl - out: [project_work_dir] - - - - - - - - - - - - diff --git a/0.3/example-result/manifest-sha512.txt b/0.3/example-result/manifest-sha512.txt deleted file mode 100644 index 5b0fde0..0000000 --- a/0.3/example-result/manifest-sha512.txt +++ /dev/null @@ -1,16 +0,0 @@ -c348d5d9846d9a00e9e59d5625a1abae70f0ab5e928904dfa9d94c645f8798f6eebbefc3627dd0ee90ce316863daf7cde7402f2c6e20c80136088d5a58ee341c data/index.html -93d7b4d1bf209f14ef5ded3e8bb598f2677f2caa4eaba6e024c0c9b1bf0f9cd09e7a517613ceb64ab65ec8e8da9f413449c364a82fe38581b9c06d57ecee1837 data/ro-crate-metadata.json -c348d5d9846d9a00e9e59d5625a1abae70f0ab5e928904dfa9d94c645f8798f6eebbefc3627dd0ee90ce316863daf7cde7402f2c6e20c80136088d5a58ee341c data/ro-crate-preview.html -a825e54ecdfebd0f38899d671216a20ca6a28e43e94828191ad52e9c5a05d96124ef54aee27450fb10b4136811f0c36cb1b405ceb7943271ab933bc4ccc1b9a7 data/workflow/289/ro-crate-metadata.json -b5144b746dccd3deb092daf3d9d86432f3a7b6a04b5c52ed195424831e0fa65e9b209f2965cf03e609748d808bd7a37e33defb1433c788d61a8f3e1379c21c51 data/workflow/289/workflow.cwl -4e8ee7f1dd4074b8c6ba884f6746ee307a2983d3d9e01bfa6417e4ad375ed703881c0d00bcf686accdbda06b1a18c11b44eb0cddb51d309ffabeeb5870eff542 data/workflow/289/ro-crate-preview.html -7be353d51fe42dfbb0fd84bcf99c545d9943ba0d913fb04b2206098788c8977505690a261055e89125fc9b26550cefdff9ce41356a178272d6ecf01ade4aad5d data/workflow/289/README.md -9ac846925bb587b71b05be55807c3187669b033640c9b98991d882aca95cbb5b6bf106079f981cc7ddd34e65a99816a7cf40e55b61135b270fcb94fe1cfc4120 data/workflow/289/workflow_list.cwl -b1421e5423874620a6a060f439884acb95f5a050b29fbb58798ddd9911b438080e1e01131414e6ce7a3169388b963ef9a6c070abbf1fbe4429730f32f125c80d data/workflow/289/workflow-289-70fda2af9a458dd693bce5aba2f0dd8e1a4ffd7c-diagram.svg -0811b70bfe092e9b0cb12f90b0a87fef362a1df4da9313be87374c117a7675df060483cad2914004ddb2a3f5480b55682c0fb29ed6f744477370c16b1a0fd916 data/workflow/289/workflow_gather.cwl -bb3f835459b0bb706e0daf28dd2ee8e6de9e9e3f5837157c38267178db04a52f90af57bd770f847c714c68ac8a87bd585cc4277176af9afcf3985eaeb63bf732 data/workflow/289/ions.pdb -7e4c51280e49ba93cf6555ac3aa73701c84f4737dc698b10188487025ea8eaf7b872fcf2c3da32b1771b98f3a9cf59f3506e3abce9db795504a3ceea748dd763 data/workflow/289/structure.pdb -6092d871f594b00e019b8377ced6f61375b2ea2b94953d8e8daa469eeab98ec95ddbce64ec4cb1d9ca498e55f8cb18a043509dde54102c52c0206f6ef1f04112 data/workflow/289/workflow_input_descriptions.yml -1bbf5899b38d2773976884f2f40257b2356940f6e43107216258b43998641cb8833a8ab0ac26bb41738951b3f95e423ccb3e71ef30711367f01c75c2935e6d8b data/input1.txt -a49c0f778f443d2ebf55b9d1054f064839f4925cabe3057a75bf0e84df194469d08bcddbe8c0142c3cbfa46b7895b45d19b9c5c01f9c189170bc398b3b454fb5 data/outputs/qa.csv -cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e data/outputs/diagrams/.keep diff --git a/0.3/example-result/tagmanifest-sha512.txt b/0.3/example-result/tagmanifest-sha512.txt deleted file mode 100644 index 355d8cb..0000000 --- a/0.3/example-result/tagmanifest-sha512.txt +++ /dev/null @@ -1,3 +0,0 @@ -0d645c3618bea9db3d530ff858d7773745cceec8bedea0866b66bb0c04fef7a7db2dc2e25c54e93bce6be5a07f2b55d1916e7d1b56352d545e39f50a773114ea bag-info.txt -2c7a3807b8b38d4ff447233220349d8e7fba7a8e4aa80df8b1163039c4053c7a3eea539fed4066c8653b86eaaba9274258892292e76cf087e1b56e37ab4eee64 bagit.txt -de82357ca12f92457afa0156028a90092a1340d5abb14e0a0eb14a2d655cfe0b9d8bf41c1f51fb974d7c1bade5ff37872784de8dee8990376e86e2ac93d9ad1c manifest-sha512.txt diff --git a/0.3/index.html b/0.3/index.html new file mode 100644 index 0000000..1924948 --- /dev/null +++ b/0.3/index.html @@ -0,0 +1,12 @@ + + + + + + Page moved + + +

Page moved

+ https://trefx.uk/trusted-wfrun-crate/0.3/ + + diff --git a/0.3/index.md b/0.3/index.md deleted file mode 100644 index 41c9bee..0000000 --- a/0.3/index.md +++ /dev/null @@ -1,755 +0,0 @@ - - -# Trusted Workflow Run Crate profile - -Authors: - -1. Stian Soiland-Reyes, The University of Manchester -2. Stuart Wheater - -* Permalink: -* Version: 0.3 -* Release notes: -* Published: 2023-05-16 -* Status: TRE-FX Candidate Recommendation -* Comments and suggestions: -* Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html) -* Specification: [trusted-wfrun-crate-0.3.0.pdf](https://github.com/trefx/trusted-wfrun-crate/releases/download/0.3.0/trusted-wfrun-crate-0.3.0.pdf) -* Example crate "Request": [example-request.bagit.zip](https://github.com/trefx/trusted-wfrun-crate/releases/download/0.3.0/example-request.bagit.zip) [ro-crate-metadata.json](example-request/data/ro-crate-metadata.json) [ro-crate-preview.html](example-request/data/ro-crate-preview.html) -* Example crate "Result": [example-result.bagit.zip](https://github.com/trefx/trusted-wfrun-crate/releases/download/0.3.0/example-result.bagit.zip) [ro-crate-metadata.json](example-result/data/ro-crate-metadata.json) [ro-crate-preview.html](example-result/data/ro-crate-preview.html) -* Example crate "Hutch": [example-hutch.bagit.zip](https://github.com/trefx/trusted-wfrun-crate/releases/download/0.3.0/example-hutch.bagit.zip) [ro-crate-metadata.json](example-hutch/data/ro-crate-metadata.json) [ro-crate-preview.html](example-hutch/data/ro-crate-preview.html) - -This document specifies a draft profile of [RO-Crate](https://w3id.org/ro/crate) for the purpose of [TRE-FX implementation](https://trefx.uk/implementation) of workflow execution in a distributed trusted research environment (TRE). - -_The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "NOT RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in BCP 14 [[RFC2119](https://doi.org/10.17487/RFC2119)] [[RFC8174](https://doi.org/10.17487/RFC8174)] when, and only when, they appear in all capitals, as shown here._ - - -**Note**: All references to schema.org types/properties/instances use the prefix `http://schema.org/` (not https) to correspond with their official JSON-LD context. - - -## Overview - -A Trusted Workflow Run Crate represents a unit of computational access to sensitive information which is managed in accordance with a set of principles conforming to the 5 safe framework. The aim is to enable trusted workflow execution in a Trusted Research Environment (TRE), from an authenticated workflow run request, through approval and review processes to a completed workflow execution. - -## Archive serialisation - -A compliant Trusted Workflow Run Crate SHOULD be stored and transferred as an [ZIP archive](http://www.pkware.com/documents/casestudies/APPNOTE.TXT) containing a single [BagIt directory](https://www.researchobject.org/ro-crate/1.1/appendix/implementation-notes.html#combining-with-other-packaging-schemes) (_bag_) of an arbitrary name, which payload folder `data/` contains the RO-Crate Metadata File `ro-crate-metadata.json` and any required data files (e.g. inputs). - -Internally a processing TRE MAY choose to unpack a ZIP file to a local file store, taking necessary security and performance precautions (see [Security considerations](#security-considerations)). - -The BagIt [payload manifest](https://www.rfc-editor.org/rfc/rfc8493.html#section-2.1.3) [[RFC8493](https://doi.org/10.17487/rfc8493)] MUST be present using sha-512 checksums, and the [tag manifest](https://www.rfc-editor.org/rfc/rfc8493.html#section-2.2.1) SHOULD be included as sha-512 [[FIPS 180-4](https://doi.org/10.6028/NIST.FIPS.180-4)]. Payload and tag manifests using other checksums MAY be included, taking care to exclude `tagmanifest-*` files from their checksums. - -Example: - -``` -query-12389/ - | bagit.txt # MUST indicate BagIt 1.0 or later - | bag-info.txt # As per BagIt specification - | manifest-sha512.txt # As per BagIt specification - | tagmanifest-sha512.txt # As per BagIt specification - | fetch.txt # Optional, per BagIt Specification - | data/ # Payload: RO-Crate root directory - | ro-crate-metadata.json # RO-Crate Metadata File MUST be present - | [payload files and directories] # 1 or more SHOULD be present -``` - -### BagIt expectations - -The [RO-Crate BagIt expectations](https://www.researchobject.org/ro-crate/1.1/appendix/implementation-notes.html#combining-with-other-packaging-schemes) for _Adding RO-Crate to Bagit_ MUST be followed. The `bag-info.txt` file MUST include a generated `External-Identifier:` field, which SHOULD be a UUID URN [[rfc4122](https://doi.org/10.17487/rfc4122)], e.g.: - -``` -External-Identifier: urn:uuid:9796155a-fe44-4614-89b8-71945f718ffb -``` - -The identifier of the `External-Identifier` represents this crate as a request and subsequent response, and SHOULD be freshly generated for each request. It is RECOMMENDED to _not_ modify this identifier as the Trusted Workflow Run Crate progresses through the distributed TRE processing, unless it is recognized as an previous execution. - -Note that as the ro-crate-metadata.json establishes payload directory data/ as the RO-Crate Root it can only reference files and directories there within, the RO-Crate MUST NOT reference tag files like `../fetch.txt` or other relative paths outside the Bag (see [Security considerations](#security-considerations)). - - -### Zip expectations - -The ZIP archive MUST only contain a single top-level entry for the bag directory, identified by the _bagit.txt_ marker. For interoperability in terms of ZIP features, implementations SHOULD follow [guidance for an OSF ZIP Container](https://www.w3.org/publishing/epub32/epub-ocf.html#sec-zip-container-zipreqs) (ignoring _OCF Abstract Container_ requirements). - - -## Metadata file expectations - -The RO-Crate Metadata File MUST conform to [RO-Crate 1.2](https://www.researchobject.org/ro-crate/1.2-DRAFT/) (or later minor version). - -For the purpose of this specification, this [Metadata file](https://www.researchobject.org/ro-crate/1.2-DRAFT/structure.html#ro-crate-metadata-file-ro-crate-metadatajson) skeleton is assumed, with all subsequent JSON elements shown added to the `@graph` array: - -```json -{ "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context", - "@graph": [ - - ] -} -``` - -The compliant RO-Crate version MUST be declared in the [metadata file descriptor](https://www.researchobject.org/ro-crate/1.2-DRAFT/root-data-entity.html#ro-crate-metadata-file-descriptor): - -```json -{ - "@type": "CreativeWork", - "@id": "ro-crate-metadata.json", - "about": {"@id": "./"}, - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"} -} -``` - -The [root data entity](https://www.researchobject.org/ro-crate/1.2-DRAFT/root-data-entity.html#direct-properties-of-the-root-data-entity) of a Trusted Workflow Run Crate MUST have the @id equal `"./"` (as it is stored within the BagIt ZIP archive). It MAY have an additional [`identifier`](https://www.researchobject.org/ro-crate/1.1/metadata.html#recommended-identifiers). - - -### Profile conformance - -Crates conforming to this profile specification SHOULD indicate this on the Root Data Entity dataset, using its own `conformsTo`: - -```json -{ - "@id": "./", - "@type": "Dataset", - "conformsTo": {"@id": "https://w3id.org/trusted-wfrun-crate/0.3"}, - "hasPart": [ - ], - "mainEntity": {"@id": "https://workflowhub.eu/workflows/289?version=1"}, - "mentions": {"@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538"}, - "sourceOrganization": - {"@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70"} -}, -{ - "@id": "https://w3id.org/trusted-wfrun-crate/0.3", - "@type": "Profile", - "name": "Trusted Workflow Run Crate profile" -} -``` - -Note that `licence` and `datePublished` is not required in a submitted crate, but SHOULD be included for a published crate (see [Publishing Phase](#publishing-phase)). - - -### Referencing a Workflow Crate - -The metadata file MUST reference a [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/1.0) `Dataset` as its `mainEntity`, indirectly indicating the workflow to execute. - -The identifier SHOULD be a permalink or versioned URL (e.g. [https://workflowhub.eu/workflows/289?version=1](https://workflowhub.eu/workflows/289?version=1)) or MAY be a nested directory within the BagIt payload directory (e.g. `"workflow289.1/"`). - -**Note**: unlike in the [Workflow Run profile](https://www.researchobject.org/workflow-run-crate/profiles/0.1/workflow_run_crate), the programming language of the workflow and its other metadata are not expressed in this RO-Crate, but within the referenced Workflow RO-Crate. The `programmingLanguage` inside the Workflow RO-Crate SHOULD be either [https://w3id.org/workflowhub/workflow-ro-crate#cwl](https://w3id.org/workflowhub/workflow-ro-crate#cwl) or [https://w3id.org/workflowhub/workflow-ro-crate#nextflow](https://w3id.org/workflowhub/workflow-ro-crate#nextflow). - -See [security considerations](#security-considerations) for workflow referencing and execution. - - -#### Finding the RO-Crate archive - -If the identifier is a URI, an URL to the downloadable Workflow RO-Crate ZIP archive SHOULD be included with `distribution`, otherwise clients SHOULD [use Signposting](https://signposting.org/adopters/#workflowhub) to find the link to the RO-Crate by looking for the link with `rel="item" type="application/zip" profile="https://w3id.org/ro/crate"` -- for instance: - -```bash -curl -I "https://workflowhub.eu/workflows/289?version=1" -``` - -```http -HTTP/1.1 200 OK -Content-Type: text/html; charset=UTF-8 -Link: ; - rel="item" ; - type="application/zip" ; - profile="https://w3id.org/ro/crate" -``` - - -#### Example: - - -```json -{ - "@id": "https://workflowhub.eu/workflows/289?version=1", - "@type": "Dataset", - "name": "CWL Protein MD Setup tutorial with mutations", - "conformsTo": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}, - "distribution": { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1" - } -}, -{ - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1", - "@type": "DataDownload", - "conformsTo": {"@id": "https://w3id.org/ro/crate"}, - "encodingFormat": "application/zip" -} -``` - -In the above example, the `mainEntity` points to a `Dataset` that conforms to the Workflow RO-Crate Profile and references the ZIP download URI using `distribution`, therefore the client can download the workflow directly without needing to follow Signposting headers. - - -### Requested Workflow Run - -The metadata file MUST include a [CreateAction](http://schema.org/CreateAction), which MUST be referenced from `mentions` of the root entity. The identifier SHOULD be based on a UUID (different from the BagIt `External-Identifier`). - -The CreateAction MUST reference the Workflow Crate using `instrument`. - - -#### Example: - -```json -{ - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538", - "@type": "CreateAction", - "actionStatus": "http://schema.org/PotentialActionStatus", - "agent": {"@id": "https://orcid.org/0000-0001-9842-9718"}, - "instrument": {"@id": "https://workflowhub.eu/workflows/289?version=1"}, - "name": "Execute query 12389 on workflow ", - "object": [ - {"@id": "input1.txt"} - ] -} -``` - -The [CreateAction’s actionStatus](#execution-states) will change during execution. - -### Requesting Agent - -The individual person who is requesting the run MUST be indicated as an `agent` from the `CreateAction`, which SHOULD have an `affiliation` to the organisation they are representing for access control purposes. - - -```json -{ - "@id": "https://orcid.org/0000-0001-9842-9718", - "@type": "Person", - "name": "Stian Soiland-Reyes", - "affiliation": { "@id": "https://ror.org/027m9bs27"}, - "memberOf": [ - {"@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70"} - ] -}, -{ - "@id": "https://ror.org/027m9bs27", - "@type": "Organization", - "name": "The University of Manchester" -} -``` - -**Note**: The organisation under `affiliation` is typically the employing organisation, e.g. a university or hospital. Virtual organisations such as research projects MAY additionally be listed using `memberOf` (see also [Responsible Project](#responsible-project) below). - - -### Responsible Project - -The project that the request is sent on behalf of, typically related to permission to use a TRE, MUST be indicated from the root dataset using `sourceOrganization` to a [`Project`](http://schema.org/Project). The responsible project SHOULD be referenced from the requesting agent’s `memberOf`. - -**Note**: The _responsible project_ is not necessarily a [ResearchProject](http://schema.org/ResearchProject) corresponding to a funded grant, but may be more specific studies within a funded project. Various TREs may have different granularity and identifiers for the responsible projects. A project `Grant` MAY be referenced using [funding](http://schema.org/funding) from the responsible project. - -It is RECOMMENDED to include TRE-specific ids under `identifier` (which MAY be an array). If the identifier is not globally unique (e.g. an integer rather than an UUID or URI), it is RECOMMENDED to add a [repository-specific identifier](https://www.researchobject.org/ro-crate/1.1/appendix/implementation-notes.html#repository-specific-identifiers) and provide the local identifier as `value` of a `PropertyValue` entity. Multiple repository-specific identifiers MAY be included for different TREs from a single Project entity. - -The project MAY indicate the `member` organisations, in which case one of them SHOULD match the `affiliation` of the _Requesting Agent_ with a `memberOf` to this project. - -#### Example - -```json -{ - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70", - "@type": "Project", - "name": "Investigation of cancer (TRE72 project 81)", - "identifier": [ - {"@id": "_:localid:tre72:project81"} - ], - "funding": { - "@id": "https://gtr.ukri.org/projects?ref=10038961" - }, - "member": [ - {"@id": "https://ror.org/027m9bs27"}, - {"@id": "https://ror.org/01ee9ar58"} - ] -}, -{ - "@id": "_:localid:tre72:project81", - "@type": "PropertyValue", - "name": "tre72", - "value": "project81" -}, -{ - "@id": "https://gtr.ukri.org/projects?ref=10038961", - "@type": "Grant", - "name": "EOSC4Cancer" -} -``` - - - -### Inputs - -Requested inputs SHOULD be set on the `CreateAction` using the `object` property: - -```json -{ - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538", - "@type": "CreateAction", - "object": [ - {"@id": "input1.txt"}, - {"@id": "#enableFastMode"} - ], - "…": {} -} -``` - -Each input MUST have a corresponding data entity, which SHOULD have a `exampleOfWork` reference to a corresponding `FormalParameter`: - -```json -{ - "@id": "input1.txt", - "@type": "File", - "name": "input1", - "exampleOfWork": { "@id": "#sequence"} -}, -{ - "@id": "#enableFastMode", - "@type": "PropertyValue", - "name": "--fast-mode", - "value": "True", - "exampleOfWork": {"@id": "#fast"} -}, -{ - "@id": "#sequence", - "@type": "FormalParameter", - "name": "input-sequence" -}, -{ - "@id": "#fast", - "@type": "FormalParameter", - "name": "fast-mode" -} -``` - -**Tip**: While the [FormalParameter](https://www.researchobject.org/ro-crate/1.1/workflows.html#describing-inputs-and-outputs) SHOULD match the definitions within the Workflow Crate referenced from `mainEntity`, the only requirement from this profile is that their `name` is programmatically recognized by the workflow engine for binding input parameters of the particular workflow. - - -### Outputs - - -If the workflow has successfully executed, that is the `CreateAction` has `actionStatus` set to `http://schema.org/CompletedActionStatus`, the output data entities SHOULD be referenced from the `results` array. - -Output entities MUST be described as in the [Workflow Run Crate profile](https://w3id.org/ro/wfrun/workflow/0.1), with type SHOULD be either `File`, `Dataset`, `Collection`, `DigitalDocument` or `PropertyValue`. - -Implementations MAY include the outputs within the Crate BagIt archive, in which case it is RECOMMENDED to use the folder `outputs/` to avoid conflict with other files in the crate. - - -```json -{ - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538", - "@type": "CreateAction", - "result": [ - {"@id": "outputs/table.csv"}, - {"@id": "outputs/diagrams/"} - ], - "…": {} -}, -{ - "@id": "outputs/qa.csv", - "@type": "File", - "encodingFormat": "text/csv", - "name": "Tabular listing of quality assessment" -}, -{ - "@id": "outputs/diagrams/", - "@type": "Dataset", - "name": "Diagrams of regions of interest" -} -``` - -**Tip**: Implementations may need to inspect the `FormalParameter` of the referenced Workflow Crate to propagate a human readable _name_ and _encodingFormat_ file format of the inputs and output in this crate. - - -#### Sensitive data - - -Outputs MAY include references to sensitive data that is only accessible from within the TRE or through URIs that require authentication. The requirement for permission SHOULD be indicated by typing the data entity as a [DigitalDocument](http://schema.org/DigitalDocument) that use `hasDigitalDocumentPermission` to reference the [DigitalDocumentPermission](http://schema.org/DigitalDocumentPermission) entity, typically assigning `http://schema.org/ReadPermission` with `grantee` to only to the _Responsible Project_. - - -```json -{ - "@id": "urn:uuid:07b81e0f-7ac4-5428-9940-878b241e2397", - "@type": "DigitalDocument", - "encodingFormat": "text/csv", - "name": "Patient measurement 07b81e0f-7ac4-5428-9940-878b241e2397", - "hasDigitalDocumentPermission": {"@id": "#permissions-07b81e0f"} -}, -{ - "@id": "#permissions-07b81e0f", - "@type": "DigitalDocumentPermission", - "permissionType": "http://schema.org/ReadPermission", - "grantee": { "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70"} -} -``` - - -### Review process - -The Trusted Workflow Run Crate may face several reviews both before and after workflow execution, automated and manual. To record that such review will or has taken place, a series of additional [`Action`](http://schema.org/docs/actions.html) contextual entities SHOULD be related to the root data entity using `mentions`. - -It is RECOMMENDED that the first step after authentication is a syntactic validation step that verifies the RO-Crate validity according to this profile and system expectations. This step SHOULD remove `mentions` references to any end-user-provided [AssessAction](http://schema.org/AssessAction) (as defined in this profile) from the submitted crate, in order to ensure only assessment endorsements by the particular TRE are considered in the subsequent internal processing. - -Assessment actions SHOULD indicate an [actionStatus](#heading=h.byrges19zp0h) to reflect the outcome or pending nature of the assessment. Each assessment SHOULD have the root data entity (typically `{"@id": "./"}`) listed under `object`, and MAY include additional entities that were assessed. - -The phase of the review process is indicated using subclasses of `Action` and more accurately with `additionalType` using terms from the Safe Haven Provenance ([SHP](https://w3id.org/shp)) ontology. - -The `name` of the action MUST provide a human readable name of the type of check and its outcome, but SHOULD NOT be consulted by software for decision making (rather they should check `actionStatus` and `additionalType`). - -Each completed action SHOULD have a timestamp using `endTime` that follow the ISO-8601 syntax of [RFC 3339](https://doi.org/10.17487/RFC3339) (including timezone or Z). `startTime` MAY be included for active, failed and completed actions. - -The main actor performing the assessment SHOULD be listed under _agent_ and refer to either a `Organization` (e.g. an TRE helpdesk), `Person` (manual check) or a [SoftwareApplication](http://schema.org/SoftwareApplication) (automated check). A `SoftwareApplication` acting on behalf of a TRE MUST include a reference to the TRE `Organization` using `provider`. There may be multiple actors appearing as `agent` for different actions, each of which should be listed as contextual entities with at least `name`. - - -```json -{ "@id": "https://tre72.example.com/#crate-validator", - "@type": "SoftwareApplication", - "name": "RO-Crate validator at TRE72", - "provider": {"@id": "https://tre72.example.com/"} -}, -{ "@id": "https://tre72.example.com/", - "@type": "Organization", - "name": "TRE 72 trusted research environment at The University of Manchester", - "parentOrganization": {"@id": "https://ror.org/027m9bs27"} -} -``` - - -#### Check phase - -Before any further processing, the content of a submitted crate SHOULD be checked for integrity and completeness against the BagIt payload manifest and tag manifest, considering at least the SHA-512 algorithm. This phase MAY also check any cryptographic signatures. - -Example: - -```json -{ - "@id": "#check-f33fe90c-0c22-4c72-b299-de509028410e", - "type": "AssessAction", - "additionalType": {"@id": "https://w3id.org/shp#CheckValue"}, - "name": "BagIt checksum of Crate: OK", - "endTime": "2023-04-18T12:11:45+01:00", - "object": {"@id": "./"}, - "instrument": { - "@id": "https://www.iana.org/assignments/named-information#sha-512"}, - "agent": {"@id": "#validator-a4a66c63-2fe0-4c57-830d-268a40718313"}, - "actionStatus": "http://schema.org/CompletedActionStatus" -}, -{ - "@id": "https://www.iana.org/assignments/named-information#sha-512", - "@type": "DefinedTerm", - "name": "sha-512 algorithm" -} -``` - -**Note** that subsequent modifications to the submitted crate by the TRE will necessarily mean checksums become out of date. It is RECOMMENDED to update the BagIt manifest following crate modifications if further TRE phases require checksum (e.g. after network transfer), however any subsequent internal checksum validations SHOULD NOT be recorded as an AssessAction. Checksums of the final crate MUST be updated by the [Publishing phase](#publishing-phase) and recorded accordingly. - -The check phase MAY perform any additional file-level security checks required by the particular TRE, e.g. maximum file size of crate, valid characters in filenames or use of symbolic links. - - -#### Validation phase - -A crate that has been validated according to RO-Crate specifications and this profile SHOULD _mention_ an _AssessAction _which _instrument_ refers to the profile entity, and an `additionalType` referring to `https://w3id.org/shp#ValidationCheck` - -Example: - -```json -{ - "@id": "#validate-1146f640-819e-4c86-b029-b763a0040896", - "type": "AssessAction", - "additionalType": {"@id": "https://w3id.org/shp#ValidationCheck"}, - "name": "Validation against Trusted Workflow Run Crate profile: approved", - "startTime": "2023-04-18T12:11:46+01:00", - "endTime": "2023-04-18T12:11:49+01:00", - "object": {"@id": "./"}, - "instrument": {"@id": "https://w3id.org/trusted-wfrun-crate/0.3"}, - "agent": {"@id": "#validator-a4a66c63-2fe0-4c57-830d-268a40718313"}, - "actionStatus": "http://schema.org/CompletedActionStatus" -} -``` - -The validation phase MAY perform any additional syntactic or semantic checks required by the particular TRE and workflow, e.g. correspondence between provided and expected input parameters, in which case this should be reflected by adding such entities to `object` (checked) and `instrument` (expected) as arrays. - - -#### Workflow retrieval phase - -The referenced workflow crate may be retrieved by the TRE before Sign-off or Workflow Execution, potentially using a local proxy (see [Finding the RO-Crate archive](#finding-the-ro-crate-archive) and [Security considerations](#security-considerations)). In this case, the retrieval SHOULD be indicated by a [DownloadAction](http://schema.org/DownloadAction) with the Workflow RO-Crate’s distribution as `object` (indicating the URL that was downloaded from, potentially following Signposting). - -Implementations MAY choose to unpack and add the Workflow Crate folder to the Bagit, in which case it SHOULD be indicated as an additional data entity referenced as _result_, which reference the `mainEntity` from `sameAs` and the download location in `distribution`. - -Example: - -```json -{ - "@id": "#download-8b51bf57-6b29-44da-b24b-638c8df91639", - "type": "DownloadAction", - "name": "Downloaded workflow RO-Crate via proxy", - "startTime": "2023-04-18T12:11:50+01:00", - "endTime": "2023-04-18T12:11:52+01:00", - "object": {"@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1"}, - "result": {"@id": "workflow/289/"}, - "agent": {"@id": "http://proxy.example.com/"}, - "actionStatus": "http://schema.org/CompletedActionStatus" -}, -{ - "@id": "workflow/289/", - "sameAs": { "@id": "https://workflowhub.eu/workflows/289?version=1" }, - "@type": "Dataset", - "name": "CWL Protein MD Setup tutorial with mutations", - "conformsTo": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}, - "distribution": { - "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1" - } -} -``` - - -#### Sign-off phase - -Before executing a Trusted Workflow Run Crate, the TRE SHOULD check if the requesting agent is permitted to execute the particular workflow on behalf of the responsible project. This SHOULD include checks against the Agreement policy data maintained by the TRE. This may be a manual and/or automated check, as indicated by `agent`. The `object` SHOULD additionally reference the workflow and responsible project (unless these were not part of the sign-off checks). - -Example: - -```json -{ - "@id": "#signoff-3b741265-cfef-49ea-8138-a2fa149bf2f0", - "type": "AssessAction", - "additionalType": {"@id": "https://w3id.org/shp#SignOff"}, - "name": "Sign-off of execution according to Agreement policy: approved", - "endTime": "2023-04-19T17:15:12+01:00", - "object": [ - {"@id": "./"}, - {"@id": "https://workflowhub.eu/workflows/289?version=1"}, - {"@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70"} - ], - "instrument": {"@id": "https://tre72.example.com/agreement-policy/81"}, - "agent": {"@id": "https://orcid.org/0000-0002-1825-0097"}, - "actionStatus": "http://schema.org/CompletedActionStatus" -}, -{ - "@id": "https://tre72.example.com/agreement-policy/81", - "@type": "CreativeWork", - "name": "Agreement policy for TRE72 for project 81" -} -``` - - -#### Workflow execution phase - -In this phase, the approved workflow execution is performed within the TRE. The `CreateAction` of the workflow execution will its `actionStatus` and acquire a `startTime` and `endTime`. - -When the execution is in `http://schema.org/CompletedActionStatus` or `http://schema.org/FailedActionStatus`, the crate SHOULD also follow the [Provenance Crate](https://w3id.org/ro/wfrun/provenance/0.1) profile, e.g. the workflow outputs data entities will be listed as `result`. - - -##### Execution states - -The states of the Trusted Workflow Run Crate is indicated by the `actionStatus` of this main action being one of the following string values: - -* `http://schema.org/PotentialActionStatus` -– The request is queued to be executed -* `http://schema.org/ActiveActionStatus` -– The request is currently executing -* `http://schema.org/CompletedActionStatus` -– The request has finished successfully -* `http://schema.org/FailedActionStatus` –- The request failed, but may have partial results or logs. - - -##### Example - -```json -{ - "@id": "#query-37252371-c937-43bd-a0a7-3680b48c0538", - "@type": "CreateAction", - "actionStatus": "http://schema.org/CompletetedActionStatus", - "startTime": "2023-04-18T13:52:19+01:00", - "endTime": "2023-04-18T14:00:19+01:00", - "agent": {"@id": "https://orcid.org/0000-0001-9842-9718"}, - "instrument": {"@id": "https://workflowhub.eu/workflows/289?version=1"}, - "name": "Execute query 12389 on workflow ", - "object": [ - {"@id": "input1.txt"} - ], - "result": [ - { "@id": "result/matches.txt"} - { "@id": "result/stats.txt"} - ] -} -``` - -Note that even if the workflow execution action is in `http://schema.org/CompletedActionStatus`, two additional phases are required to pass before the Trusted Workflow Run Crate can be considered “finished”, see the following subsections. - -#### Disclosure phase - -Before workflow results are returned from the TRE, a disclosure check SHOULD be performed, e.g. to verify the workflow execution has not revealed sensitive data. Depending on the workflow and TRE data this may be automated and/or manual as indicated by `agent`. - -In the example below, a person has been assigned, while the `actionStatus` indicates the disclosure check is pending (`startTime` in this case indicating predicted waiting time into the future). - -```json -{ - "@id": "#disclosure-b16c1f0a-ae7f-4582-9b28-7d9df3313e27", - "type": "AssessAction", - "additionalType": {"@id": "https://w3id.org/shp#DisclosureCheck"}, - "name": "Disclosure check of workflow results: pending (estimate: 1 week)", - "startTime": "2023-04-25T16:00:00+01:00", - "object": {"@id": "./"}, - "agent": {"@id": "https://orcid.org/0000-0002-1825-0097"}, - "actionStatus": "http://schema.org/PotentialActionStatus" -} -``` - -If a crate fails the disclosure phase, its content such as workflow results MUST NOT be included in the returned crate returned to the user. Likewise, its workflow execution `CreateAction` and corresponding output data entities SHOULD be removed from the metadata file. - - -#### Publishing phase - -Before a disclosure-approved Trusted Workflow Run Crate is published to the requesting user (or archived in a repository), some housekeeping tasks are to be completed. - -The root data entity’s `datePublished` SHOULD be updated to the time the manifest is last written. The `publisher` SHOULD be updated to reflect the executing TRE. The `mentions` MUST be expanded to include all the `AssessAction`s recorded by the TRE. `hasPart` MUST include (possibly through intermediate folders as `Dataset`) any `result` data entities now referred to from the workflow execution’s `CreateAction`. - -The _[licence](https://www.researchobject.org/ro-crate/1.1/contextual-entities.html#licensing-access-control-and-copyright)_ SHOULD be included to describe the licence of the workflow output data, either an open licence such as Creative Commons, or a restrictive (typically TRE-specific) conditions of access. - -```json -{ - "@id": "./", - "@type": "Dataset", - "conformsTo": {"@id": "https://w3id.org/trusted-wfrun-crate/0.3"}, - "datePublished": "2023-04-29T11:01:04+01:00", - "publisher": {"@id": "https://tre72.example.com/"}, - "licence": {"@id": "http://spdx.org/licenses/CC-BY-4.0"}, - "hasPart": [{"…":""}], - "mainEntity": {"@id": "https://workflowhub.eu/workflows/289?version=1"}, - "mentions": [{"…":""}], - "sourceOrganization": { - "@id": "#project-be6ffb55-4f5a-4c14-b60e-47e0951090c70" - } -}, -{ - "@id": "https://spdx.org/licenses/CC-BY-4.0", - "@type": "CreativeWork", - "name": "Creative Commons Attribution 4.0 International", - "identifier": "CC-BY-4.0" -} -``` - -TRE implementations MAY additionally [record changes](https://www.researchobject.org/ro-crate/1.1/provenance.html#recording-changes-to-ro-crates) to the RO-Crate as it has progressed through the execution, by associating a `CreateAction` and subsequent `UpdateAction` to the root data entity as `object`. - -Following the final update of the RO-Crate Metadata file and content, the BagIt payload manifests and tag manifests MUST be updated (as a minimum because the _ro-crate-metadata.json_ has been modified). The `result` entity is NOT recorded, as `../manifest-sha512.txt` would have escaped the RO-Crate root. The agent SHOULD delete manifest files it can’t re-generate. After the checksum calculation, the TRE SHOULD not do any further changes to the crate or BagIt files. - - -```json -{ - "@id": "#bagit-ce785c0b-c988-4043-8cbd-1489dcebc14f", - "type": "UpdateAction", - "startTime": "2023-04-29T12:12:25+01:00", - "additionalType": {"@id": "https://w3id.org/shp#GenerateCheckValue"}, - "name": "BagIt manifests of Crate updated", - "object": {"@id": "./"}, - "instrument": { - "@id": "https://www.iana.org/assignments/named-information#sha-512"}, - "agent": {"@id": "#validator-a4a66c63-2fe0-4c57-830d-268a40718313"}, - "actionStatus": "http://schema.org/CompletedActionStatus" -}, -{ - "@id": "https://www.iana.org/assignments/named-information#sha-512", - "@type": "DefinedTerm", - "name": "sha-512 algorithm" -} -``` - -**Note:** This action must be written to the _RO-Crate Metadata File_ **before** calculating the payload manifest, and therefore can’t include the correct `endTime`. The `actionStatus` should nevertheless reflect the status as if it has already completed. Likewise, the payload manifest must be calculated before updating the tag manifest, as it includes the checksum of the payload manifest. - - -#### Receiving phase - -Clients receiving a Trusted Workflow Run Crate SHOULD check the BagIt manifest checksums similar to the [Check phase](#check-phase), as well as the status of all the actions specified in this profile before further processing. - -It is NOT sufficient for clients to check the publishing AssessAction, as TRE implementations are permitted to expose partial crates which have failed approval phases or which are in pending/execution state. - -Clients MAY add additional post-processing data and/or metadata not specified in this profile to the crate (e.g. [ReceiveAction](http://schema.org/ReceiveAction)), in which case they SHOULD maintain the BagIt manifests accordingly. Manifest checksums can be used to detect accidental local changes in post-processing. - - -## Security considerations - -It is RECOMMENDED that implementers apply strong access control before accepting a Trusted Workflow Run Crate. - -Allowing execution of any Workflow Crate effectively allows execution of arbitrary code. It is RECOMMENDED to check against a list of pre-approved workflows (see -[Sign-off phase](#sign-off-phase)), e.g. using file checksums or cryptographic signatures. - -Clients parsing and unpacking ZIP files, JSON metadata, workflow definitions and BagIt manifests SHOULD apply reasonable security measures to limit the possibility of an attacker to consume excessive disk, CPU or memory resources, as well as escaping any file directory or execution container jails. For instance, clients should check for invalid file path characters, relative paths or symbolic links escaping the crate, as well guard against _zip bomb_ attacks. - -Pre-approved workflows could be exploited by a malicious attacker if they, the workflow engine or their tools themselves have security vulnerabilities, e.g. by using hand-crafted input parameters that by-passes command line escapes. Workflow executions are not guaranteed to complete in a given timescale; sufficient timeouts and resource usage restrictions SHOULD therefore be applied by the workflow engine. - -It is currently out of scope for this specification how to verify that a Trusted Workflow Run Crate was requested by the given person, or how to verify if the person has access to a particular TRE according to their Agreement policies. It is therefore RECOMMENDED that implementers check authentication and authorization of a submitted query and use strong encryption. Implementers SHOULD check that the `@id` and `affiliation` of the _Requesting Agent_ and _Responsible Project_ corresponds to the authentication, and MAY inject/overwrite client-submitted data. - -Malicious clients submitting a Trusted Workflow Run Crate may have included additional entities, properties and types, which may cause security concerns in an implementation. Implementers SHOULD sanity check inputs, including ensuring that all paths are relative within the bag or absolute URIs, and MUST remove references to any client-submitted _AssessAction_s, as these could be used to bypass the TRE compliance process. - -Malicious clients MAY attempt to reference URLs or IP addresses that are only accessible within a TRE. Implementers MUST perform any URL downloads (such as Workflow RO-Crates or container images) in a way that does not access the secured TRE network, e.g. from a _Demilitarized Zone_ (DMZ) with a network firewall restricting access to the TRE, or through a proxying repository controlled by TRE administrators. - -As an executed Trusted Workflow Run Crate may be intended for publishing (possibly following an embargo period), it SHOULD NOT include sensitive data or security tokens within the metadata file or the BagIt archive (e.g. in configuration or log files); TREs SHOULD verify this in the [Disclosure Phase](#disclosure-phase). It is RECOMMENDED to use keychain services or time-limited security access tokens that can be assured to be expired before the Crate is published. - -The crate MAY include references (e.g. S3 URIs) to sensitive data, in which case the implementation and executed workflow SHOULD protect against divulging sensitive information (directly or indirectly) in the _File_ identifiers, use UUID v5 hashing [[RFC4122](https://doi.org/10.17487/rfc4122)] to hide sensitive identifiers. -**Note:** predicable identifiers like `patient-456` would still be vulnerable in such hashing due to iteration attacks. - - - -## Media type and profiles - -When transferring a Trusted Workflow Run Crate using HTTP, implementations SHOULD use the following HTTP headers for content-type and profile: - -```http -GET http://example.com/crates/42.zip HTTP/1.1 - -HTTP/1.1 200 OK -Content-Type: application/zip -Link: ; rel="profile"` -``` - -HTML landing pages that reference a Trusted Workflow Run Crate SHOULD include [Signposting](https://signposting.org/) using HTTP `Link` headers that refer to the Crate’s ZIP download and the RO-Crate profile: - -```http -HEAD http://example.com/crates/42.html HTTP/1.1 - -HTTP/1.1 200 OK -Content-Type: text/html -Link: ; rel="item", type="application/zip" -Link: ; rel="profile"; type="application/zip"; - anchor="https://example.com/query-12389.zip" -``` - -Implementations MAY also provide direct public access to the RO-Crate metadata file, in which case they SHOULD follow the [RO-Crate media type recommendations](https://www.researchobject.org/ro-crate/1.2-DRAFT/appendix/jsonld.html#ro-crate-json-ld-media-type) for JSON-LD, in which case it is RECOMMENDED to convert the metadata file to [Detached RO-Crate](https://www.researchobject.org/ro-crate/1.2-DRAFT/appendix/relative-uris.html#converting-from-attached-to-detached-ro-crate) by establishing a [base URI](https://www.researchobject.org/ro-crate/1.1/appendix/relative-uris.html#establishing-a-base-uri-inside-a-zip-file) based on the BagIt `External-Identifier` UUID (e.g. `arcp://uuid,9796155a-fe44-4614-89b8-71945f718ffb/`). - - -## References - -[FIPS 180-4] Secure Hash Standard (SHS) [https://doi.org/10.6028/NIST.FIPS.180-4](https://doi.org/10.6028/NIST.FIPS.180-4) - -[Provenance Run Crate] Provenance Run Crate profile [https://w3id.org/ro/wfrun/provenance/0.1](https://w3id.org/ro/wfrun/provenance/0.1) - -[RFC2119] Key words for use in RFCs to Indicate Requirement Levels [https://doi.org/10.17487/RFC2119](https://doi.org/10.17487/RFC2119) - -[RFC3339] Date and Time on the Internet: Timestamps [https://doi.org/10.17487/RFC3339](https://doi.org/10.17487/RFC3339) - -[RFC4122] A Universally Unique IDentifier (UUID) URN Namespace \ -[https://doi.org/10.17487/rfc4122](https://doi.org/10.17487/rfc4122) - -[RFC8174] Ambiguity of Uppercase vs Lowercase in RFC 2119 Key Words [https://doi.org/10.17487/RFC8174](https://doi.org/10.17487/RFC8174) - -[RFC8493] The BagIt File Packaging Format (V1.0) \ -[https://doi.org/10.17487/rfc8493](https://doi.org/10.17487/rfc8493) - -[RO-Crate 1.1] RO-Crate Metadata Specification 1.1 \ -[https://w3id.org/ro/crate/1.1](https://w3id.org/ro/crate/1.1) - -[RO-Crate] Research Object Crate (RO-Crate) \ -[https://w3id.org/ro/crate](https://w3id.org/ro/crate) - -[schema] Schema.org vocabulary [http://schema.org/](http://schema.org/) - -[schema Action] Schema.org potential action [http://schema.org/docs/actions.html](http://schema.org/docs/actions.html) - -[Signposting] Signposting the Scholarly Web [https://signposting.org/](https://signposting.org/) - -[Workflow RO-Crate] Workflow RO-Crate profile [https://w3id.org/workflowhub/workflow-ro-crate/1.0](https://w3id.org/workflowhub/workflow-ro-crate/1.0) - -[Workflow Run Crate] Workflow Run Crate profile [https://w3id.org/ro/wfrun/workflow/0.1](https://w3id.org/ro/wfrun/workflow/0.1) - -[ZIP] APPNOTE.TXT - .ZIP File Format Specification 6.3.8 [http://www.pkware.com/documents/casestudies/APPNOTE.TXT](http://www.pkware.com/documents/casestudies/APPNOTE.TXT) diff --git a/0.3/ro-crate-metadata.json b/0.3/ro-crate-metadata.json deleted file mode 100644 index fe3e0e5..0000000 --- a/0.3/ro-crate-metadata.json +++ /dev/null @@ -1,461 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context", - "@graph": [ - { - "@type": "CreativeWork", - "@id": "ro-crate-metadata.json", - "about": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "licence": { - "@id": "http://spdx.org/licenses/CC0-1.0" - }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.2-DRAFT" - } - }, - { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3", - "@type": [ - "Dataset", - "Profile" - ], - "name": "Trusted Workflow Run Crate profile", - "cite-as": "https://w3id.org/trusted-wfrun-crate/0.3", - "version": "0.3", - "datePublished": "2023-05-15T10:32:00Z", - "licence": { - "@id": "http://spdx.org/licenses/MIT" - }, - "copyrightHolder": { - "@id": "https://ror.org/027m9bs27" - }, - "copyrightYear": 2023, - "hasPart": [ - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/index.html" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request.bagit.zip" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result.bagit.zip" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/" - }, - { - "@id": "http://schema.org/PotentialActionStatus" - }, - { - "@id": "http://schema.org/CompletedActionStatus" - }, - { - "@id": "http://schema.org/ActiveActionStatus" - }, - { - "@id": "http://schema.org/FailedActionStatus" - }, - { - "@id": "http://schema.org/CreateAction" - }, - { - "@id": "http://schema.org/AssessAction" - }, - { - "@id": "http://schema.org/DownloadAction" - }, - { - "@id": "http://schema.org/UpdateAction" - }, - { - "@id": "http://schema.org/grantee" - }, - { - "@id": "http://schema.org/DigitalDocument" - }, - { - "@id": "http://schema.org/DigitalDocumentPermission" - }, - { - "@id": "http://schema.org/hasDigitalDocumentPermission" - }, - { - "@id": "http://schema.org/ReadPermission" - }, - { - "@id": "https://bioschemas.org/FormalParameter" - }, - { - "@id": "https://w3id.org/shp#CheckValue" - }, - { - "@id": "https://w3id.org/shp#ValidationCheck" - }, - { - "@id": "https://w3id.org/shp#SignOff" - }, - { - "@id": "https://w3id.org/shp#DisclosureCheck" - }, - { - "@id": "https://w3id.org/shp#GenerateCheckValue" - } - ], - "hasResource": [ - { - "@id": "#hasSpecification" - }, - { - "@id": "#hasExampleRequest" - }, - { - "@id": "#hasExampleResult" - }, - { - "@id": "#usesSHP" - } - ], - "publisher": { - "@id": "https://trefx.uk/" - }, - "funding": { - "@id": "https://gtr.ukri.org/projects?ref=MC_PC_23007" - }, - "author": [ - { - "@id": "https://orcid.org/0000-0001-9842-9718" - }, - { - "@id": "https://orcid.org/0009-0003-2419-1964" - } - ] - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/index.html", - "@type": "CreativeWork", - "name": "Trusted Workflow Run Crate profile (specification)" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/", - "@type": "Dataset", - "name": "Example Crate in Request state", - "conformsTo": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "subjectOf": [ - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/ro-crate-metadata.json" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/ro-crate-preview.html" - } - ], - "distribution": { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request.bagit.zip" - } - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/", - "@type": "Dataset", - "name": "Example Crate in Request state", - "conformsTo": { - "@id": "https://w3id.org/trusted-wfrun-crate/0.3" - }, - "subjectOf": [ - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/ro-crate-metadata.json" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/ro-crate-preview.html" - } - ], - "distribution": { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result.bagit.zip" - } - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result.bagit.zip", - "@type": "DataDownload", - "name": "example-result.bagit.zip", - "description": "Example Result following the trusted-wfrun-crate profile, archived as BagIt ZIP", - "encodingFormat": "application/zip", - "conformsTo": { - "@id": "https://w3id.org/ro/crate" - } - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request.bagit.zip", - "@type": "DataDownload", - "name": "example-request.bagit.zip", - "description": "Example Request following the trusted-wfrun-crate profile, archived as BagIt ZIP", - "encodingFormat": "application/zip", - "conformsTo": { - "@id": "https://w3id.org/ro/crate" - } - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/ro-crate-metadata.json", - "@type": "CreativeWork", - "encodingFormat": "application/ld+json" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/ro-crate-preview.html", - "@type": "CreativeWork", - "encodingFormat": "text/html" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/ro-crate-metadata.json", - "@type": "CreativeWork", - "encodingFormat": "application/ld+json" - }, - { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/ro-crate-preview.html", - "@type": "CreativeWork", - "encodingFormat": "text/html" - }, - { - "@id": "https://bioschemas.org/FormalParameter", - "@type": "DefinedTerm" - }, - { - "@id": "https://w3id.org/shp", - "@type": "DefinedTermSet", - "name": "The Safe Haven Provenance (SHP) Ontology", - "version": "0.1" - }, - { - "@id": "https://w3id.org/shp#CheckValue", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#ValidationCheck", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#SignOff", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#DisclosureCheck", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#GenerateCheckValue", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#CheckValue", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#ValidationCheck", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#SignOff", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#DisclosureCheck", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://w3id.org/shp#GenerateCheckValue", - "@type": "DefinedTerm", - "inDefinedTermSet": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "https://www.iana.org/assignments/named-information#sha-512", - "@type": "DefinedTerm", - "name": "sha-512 algorithm" - }, - { - "@id": "#usesSHP", - "name": "uses vocabulary SHP", - "@type": "ResourceDescriptor", - "hasRole": { - "@id": "http://www.w3.org/ns/dx/prof/role/vocabulary" - }, - "hasArtifact": { - "@id": "https://w3id.org/shp" - } - }, - { - "@id": "#hasSpecification", - "@type": "ResourceDescriptor", - "name": "has specification", - "hasRole": { - "@id": "http://www.w3.org/ns/dx/prof/role/specification" - }, - "hasArtifact": { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/index.html" - } - }, - { - "@id": "#hasExampleRequest", - "@type": "ResourceDescriptor", - "name": "has example: Request", - "hasRole": { - "@id": "http://www.w3.org/ns/dx/prof/role/example" - }, - "hasArtifact": { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-request/data/" - } - }, - { - "@id": "#hasExampleResult", - "@type": "ResourceDescriptor", - "name": "has example: Result", - "hasRole": { - "@id": "http://www.w3.org/ns/dx/prof/role/example" - }, - "hasArtifact": { - "@id": "https://trefx.uk/trusted-wfrun-crate/0.3/example-result/data/" - } - }, - - { - "@id": "http://www.w3.org/ns/dx/prof/role/example", - "@type": [ - "DefinedTerm", - "ResourceRole" - ], - "name": "Example", - "description": "Sample instance data conforming to the profile" - }, - { - "@id": "http://www.w3.org/ns/dx/prof/role/specification", - "@type": [ - "DefinedTerm", - "ResourceRole" - ], - "name": "Specification", - "description": "Defining the profile in human-readable form" - }, - { - "@id": "http://www.w3.org/ns/dx/prof/role/vocabulary", - "@type": [ - "DefinedTerm", - "ResourceRole" - ], - "name": "Vocabulary", - "description": "Defines terms used in the profile specification" - }, - { - "@id": "http://spdx.org/licenses/CC0-1.0", - "@type": "CreativeWork", - "name": "Creative Commons Zero v1.0 Universal", - "identifier": "CC0-1.0", - "url": "https://creativecommons.org/publicdomain/zero/1.0/" - }, - { - "@id": "http://spdx.org/licenses/MIT", - "@type": "CreativeWork", - "name": "MIT Licence", - "identifier": "MIT" - }, - { - "@id": "https://gtr.ukri.org/projects?ref=MC_PC_23007", - "@type": "Grant", - "identifier": { - "@id": "_:ukri:MC_PC_23007" - }, - "name": "DARE-FX: Delivering a federated network of TREs to enable safe analytics", - "description": "", - "funder": { - "@id": "https://ror.org/001aqnf71" - }, - "sponsor": { - "@id": "https://dareuk.org.uk/" - } - }, - { - "@id": "https://dareuk.org.uk/", - "@type": "FundingScheme", - "name": "DARE UK", - "funder": { - "@id": "https://ror.org/001aqnf71" - } - }, - { - "@id": "_:ukri:MC_PC_23007", - "@type": "PropertyValue", - "name": "UKRI", - "value": "MC_PC_23007" - }, - { - "@id": "https://trefx.uk/", - "@type": "ResearchProject", - "name": "TRE-FX", - "description": "Delivering a federated network of TREs to enable safe analytics", - "funding": { - "@id": "https://gtr.ukri.org/projects?ref=MC_PC_23007" - } - }, - { - "@id": "https://ror.org/001aqnf71", - "@type": "FundingAgency", - "name": "UK Research and Innovation", - "alternateName": "UKRI", - "url": "https://www.ukri.org/" - }, - { - "@id": "https://orcid.org/0000-0001-9842-9718", - "@type": "Person", - "name": "Stian Soiland-Reyes", - "affiliation": { - "@id": "https://ror.org/027m9bs27" - }, - "memberOf": { - "@id": "https://trefx.uk/" - } - }, - { - "@id": "https://ror.org/027m9bs27", - "@type": "CollegeOrUniversity", - "name": "The University of Manchester", - "url": "https://www.manchester.ac.uk/" - }, - { - "@id": "https://orcid.org/0009-0003-2419-1964", - "@type": "Person", - "name": "Stuart Wheater", - "memberOf": { - "@id": "https://trefx.uk/" - } - } - ] -} \ No newline at end of file diff --git a/0.3/ro-crate-metadata.jsonld b/0.3/ro-crate-metadata.jsonld deleted file mode 120000 index 8024224..0000000 --- a/0.3/ro-crate-metadata.jsonld +++ /dev/null @@ -1 +0,0 @@ -ro-crate-metadata.json \ No newline at end of file diff --git a/0.3/ro-crate-preview.html b/0.3/ro-crate-preview.html deleted file mode 100644 index e3fbfe4..0000000 --- a/0.3/ro-crate-preview.html +++ /dev/null @@ -1,1312 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -
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Trusted Workflow Run Crate profile

- - -⬇️🏷️ Download all the metadata for Trusted Workflow Run Crate profile in JSON-LD format - - -
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Go to: Trusted Workflow Run Crate profile

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@idhttps://w3id.org/trusted-wfrun-crate/0.3
name [?]Trusted Workflow Run Crate profile
@type
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  • Dataset
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  • Profile
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datePublished [?]2023-05-15T10:32:00Z
author [?]
cite-as [?]https://w3id.org/trusted-wfrun-crate/0.3
version [?]0.3
licenceMIT Licence
copyrightHolder [?]The University of Manchester
copyrightYear [?]2023
hasPart [?]
hasResource [?]
publisher [?]TRE-FX
funding [?]DARE-FX: Delivering a federated network of TREs to enable safe analytics
Items that reference this one
about [?]ro-crate-metadata.json
conformsTo [?]
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Go to: Stian Soiland-Reyes

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@idhttps://orcid.org/0000-0001-9842-9718
name [?]Stian Soiland-Reyes
@typePerson
memberOf [?]TRE-FX
affiliation [?]The University of Manchester
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author [?]Trusted Workflow Run Crate profile
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Go to: Stuart Wheater

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@idhttps://orcid.org/0009-0003-2419-1964
name [?]Stuart Wheater
@typePerson
memberOf [?]TRE-FX
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author [?]Trusted Workflow Run Crate profile
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Go to: MIT Licence

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@idhttp://spdx.org/licenses/MIT
name [?]MIT Licence
@typeCreativeWork
identifier [?]MIT
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licenceTrusted Workflow Run Crate profile
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Go to: The University of Manchester

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@idhttps://ror.org/027m9bs27
name [?]The University of Manchester
@typeCollegeOrUniversity
url [?]https://www.manchester.ac.uk/
Items that reference this one
copyrightHolder [?]Trusted Workflow Run Crate profile
affiliation [?]Stian Soiland-Reyes
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Go to: Trusted Workflow Run Crate profile (specification)

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@idhttps://trefx.uk/trusted-wfrun-crate/0.3/index.html
name [?]Trusted Workflow Run Crate profile (specification)
@typeCreativeWork
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hasPart [?]Trusted Workflow Run Crate profile
hasArtifact [?]has specification
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Go to: example-request.bagit.zip

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@idhttps://trefx.uk/trusted-wfrun-crate/0.3/example-request.bagit.zip
name [?]example-request.bagit.zip
@typeDataDownload
description [?]Example Request following the trusted-wfrun-crate profile, archived as BagIt ZIP
encodingFormat [?]application/zip
conformsTo [?]https://w3id.org/ro/crate
Items that reference this one
hasPart [?]Trusted Workflow Run Crate profile
distribution [?]Example Crate in Request state
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Go to: Example Crate in Request state

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Go to: example-result.bagit.zip

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@idhttps://trefx.uk/trusted-wfrun-crate/0.3/example-result.bagit.zip
name [?]example-result.bagit.zip
@typeDataDownload
description [?]Example Result following the trusted-wfrun-crate profile, archived as BagIt ZIP
encodingFormat [?]application/zip
conformsTo [?]https://w3id.org/ro/crate
Items that reference this one
hasPart [?]Trusted Workflow Run Crate profile
distribution [?]Example Crate in Request state
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Go to: Example Crate in Request state

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Go to: https://bioschemas.org/FormalParameter

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@idhttps://bioschemas.org/FormalParameter
@typeDefinedTerm
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hasPart [?]Trusted Workflow Run Crate profile
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Go to: https://w3id.org/shp#CheckValue

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@idhttps://w3id.org/shp#CheckValue
@typeDefinedTerm
inDefinedTermSet [?]The Safe Haven Provenance (SHP) Ontology
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hasPart [?]Trusted Workflow Run Crate profile
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Go to: https://w3id.org/shp#ValidationCheck

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@idhttps://w3id.org/shp#ValidationCheck
@typeDefinedTerm
inDefinedTermSet [?]The Safe Haven Provenance (SHP) Ontology
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hasPart [?]Trusted Workflow Run Crate profile
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Go to: https://w3id.org/shp#SignOff

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@idhttps://w3id.org/shp#SignOff
@typeDefinedTerm
inDefinedTermSet [?]The Safe Haven Provenance (SHP) Ontology
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hasPart [?]Trusted Workflow Run Crate profile
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Go to: https://w3id.org/shp#DisclosureCheck

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@idhttps://w3id.org/shp#DisclosureCheck
@typeDefinedTerm
inDefinedTermSet [?]The Safe Haven Provenance (SHP) Ontology
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hasPart [?]Trusted Workflow Run Crate profile
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Go to: https://w3id.org/shp#GenerateCheckValue

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@idhttps://w3id.org/shp#GenerateCheckValue
@typeDefinedTerm
inDefinedTermSet [?]The Safe Haven Provenance (SHP) Ontology
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hasPart [?]Trusted Workflow Run Crate profile
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has specification

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@id#hasSpecification
name [?]has specification
@typeResourceDescriptor
hasRole [?]Specification
hasArtifact [?]Trusted Workflow Run Crate profile (specification)
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hasResource [?]Trusted Workflow Run Crate profile
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has example: Request

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@id#hasExampleRequest
name [?]has example: Request
@typeResourceDescriptor
hasRole [?]Example
hasArtifact [?]Example Crate in Request state
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hasResource [?]Trusted Workflow Run Crate profile
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has example: Result

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@id#hasExampleResult
name [?]has example: Result
@typeResourceDescriptor
hasRole [?]Example
hasArtifact [?]Example Crate in Request state
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hasResource [?]Trusted Workflow Run Crate profile
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uses vocabulary SHP

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@id#usesSHP
name [?]uses vocabulary SHP
@typeResourceDescriptor
hasRole [?]Vocabulary
hasArtifact [?]The Safe Haven Provenance (SHP) Ontology
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hasResource [?]Trusted Workflow Run Crate profile
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Go to: TRE-FX

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@idhttps://trefx.uk/
name [?]TRE-FX
@typeResearchProject
description [?]Delivering a federated network of TREs to enable safe analytics
funding [?]DARE-FX: Delivering a federated network of TREs to enable safe analytics
Items that reference this one
publisher [?]Trusted Workflow Run Crate profile
memberOf [?]
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Go to: DARE-FX: Delivering a federated network of TREs to enable safe analytics

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@idhttps://gtr.ukri.org/projects?ref=MC_PC_23007
name [?]DARE-FX: Delivering a federated network of TREs to enable safe analytics
@typeGrant
description [?]
funder [?]UK Research and Innovation
identifier [?]UKRI: MC_PC_23007
sponsor [?]DARE UK
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funding [?]
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