Spec

[mwinokan]

• [ ] User creates sub-directory named after target in bulkdock input root
• [ ] User adds SDF to the target subdirectory
• [ ] Bulkdock periodically checks for the SDF
• [ ] Validation of SDF (check for fragment inspiration column)
• [ ] Create Batch entry
• [ ] Copy SDF to working directory
• [ ] Check if Target exists
• [ ] If needed submit batch job to download and prepare the target specific animal
• [ ] Populate Ligand entries
• [ ] Submit batch placement job (potentially with target_prep job dependency)
• [ ] Aggregate outputs and copy to output directory

Schema

Table	Batch
Path	sdf_file
Path	output_dir
Foreign	Target
Enum	status
Datetime	request_date
String	request_user
Integer	job_id

Table	Target
String	name
Datetime	date
Path	database_path

Table	Ligand
Integer	compound
List[Integer]	inspirations

Table	Placement
Foreign	Ligand
Integer	reference_pose
Enum	Status
Float	RMSD
Float	ddG
Path	file
Integer	Pose ID

[mwinokan]

old:

0.1 Thin syndirella wrapper

• [ ] CLI for Syndirella scaffold placements with Typer
• [ ] Functions to manage file logistics

0.2 Job managing backend

• [ ] RichQueue 0.1
• [ ] Pony DB model
• [ ] Functions to manage job starting
• [ ] job monitoring
• [ ] job completion

0.3 Textualize UI

• [ ] RichQueue 0.2
• [ ] Augment RichQueue with buttons to manage jobs

0.4 Daemon

• [ ] Set up functions to monitor directories
• [ ] Try running as indefinite job
• [ ] Else run within screen or only when logged in
• [ ] Add auto-restart option to UI