Open duncanpeacock opened 2 years ago
{
"application": {
"application_id": "datamanagerjobs.squonk.it",
"kind": "DataManagerJob"
},
"category": "comp chem",
"collection": "fragmenstein",
"command": "/code/merger.py --fragments{% for fragment in fragments %} '{{ fragment }}'{% endfor %} --protein '{{ protein }}' --outfile '{{ outfile }}' --count {{ count }} {% if removeHydrogens %}--remove-hydrogens{% endif %} --work-dir {{ DM_INSTANCE_DIRECTORY }}/output",
"command_encoding": "JINJA2_3_0",
"description": "Given 2 or more fragment molecules generate a merged molecule that combines aspects of those fragments. The merged molecules are minimised within the context of the protein.",
"doc_url": "https://discourse.squonk.it/t/job-fragmenstein/110",
"id": 92,
"image_name": "registry.gitlab.com/informaticsmatters/squonk-fragmenstein",
"image_project_directory": "/data",
"image_tag": "stable",
"image_type": "SIMPLE",
"image_working_directory": "/data",
"job": "fragmenstein-combine",
"keywords": [
"fragmenstein",
"fbdd"
],
"name": "Combine fragments into a single merged molecule",
"variables": {
"inputs": "{\"type\": \"object\", \"required\": [\"fragments\", \"protein\"], \"properties\": {\"fragments\": {\"title\": \"Fragment molecules\", \"multiple\": true, \"mime-types\": [\"chemical/x-mdl-molfile\"], \"type\": \"file\"}, \"protein\": {\"title\": \"PDB file for protein\", \"mime-types\": [\"chemical/x-pdb\"], \"type\": \"file\"}}}",
"options": "{\"type\": \"object\", \"required\": [\"outfile\", \"count\", \"removeHydrogens\"], \"properties\": {\"outfile\": {\"title\": \"Output file name\", \"type\": \"string\", \"default\": \"merged.sdf\", \"pattern\": \"^[A-Za-z0-9_/\\\\.\\\\-]+\\\\.sdf$\"}, \"count\": {\"title\": \"Number of molecules to generate\", \"type\": \"integer\", \"default\": 1, \"minimum\": 1}, \"removeHydrogens\": {\"title\": \"Remove hydrogens from the outputs\", \"type\": \"boolean\", \"default\": false}}}",
"order": {
"options": [
"outfile",
"count",
"removeHydrogens"
]
},
"outputs": "{\"type\": \"object\", \"properties\": {\"outputs\": {\"title\": \"Merged molecules\", \"mime-types\": [\"chemical/x-mdl-sdfile\"], \"creates\": \"{{ outfile }}\", \"type\": \"file\"}}}"
},
"version": "1.0.0",
"fragalysis-jobs": {
"inputs": {
"fragments": {"from": "lhs-fragments", "format": "chemical/x-mdl-molfile"},
"protein": {"from": "lhs-protein-apo-desolv", "format": "chemical/x-pdb"}
},
"options": {
"outfile": {"value": "fragalysis-jobs/{username}/{job_dir}/merged.sdf", "editable": false},
"count": {"value": 5}
}
}
}
squonk-endpoints:
# Host could be a deployment parameter so that this definition can be location independent
sdm-host: https://squonk.xchem.diamond.ac.uk/data-manager-api/api/
# These paths are effectively constants so could be hardcoded
# Path to the URL that GETs the full list of job definitions
sdm-jobs-path: job
# The job is launched with a POST request to the instance endpoint
# Executing the job returns a job instance ID
sdm-launch-path: instance
# Details of the job can be obtained from this path
sdm-instance-path: instance/{instance_id}
# These definitions define which files to copy to Squonk
# The keys are those used in the jobs.<job-name>.inputs.<input-name>.from elements
squonk-file-paths:
lhs-fragments:
molecule: {pdb_code}.mol
template: /fragalysis-files/{target_name}/{pdb_code}.mol
lhs-protein-apo-desolv:
molecule: {pdb_code}-apo_desolv.pdb
template: /fragalysis-files/{target_name}/{pdb_code}-apo_desolv.pdb
For high level design, see: