Fixes for ATG-VS on Slurm, optional pose check and proximity checks for vina dockings #55
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Contributor
csecker
commented
Feb 7, 2024
csecker
commented
- Added the option to perform plausibility checks for molecule poses generated with vina-based docking programs
- Uses PoseBusters docking pose checks: https://github.com/maabuu/posebusters
mjkoop
requested changes
Mar 4, 2024
tools/templates/vfvs_run.py
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| 'output_dir': str(ligand_directory_directory) | ||
| 'output_dir': str(ligand_directory_directory), | ||
| 'run_pose_check': int(ctx['main_config']['run_pose_check']), | ||
| 'pose_check_timeout': int(ctx['main_config']['pose_check_timeout']) |
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If someone uses an old all.ctrl file, this will crash during the run. I'd suggest updating the vfvs_prepare_folders.py to check for empty and set a default (off) if not in the file. Look at line 255 for an example of when sensor_screen_mode was added.
tools/templates/vfvs_run.py
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| else: | ||
| return 0 | ||
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| print("Pose check with posebusters failed.") |
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Do this as logging.error("Pose check...")
| # Run pose check | ||
| if(posebusters_check(item, sdf_file, pdb_file, item['pose_check_timeout']) != 1): | ||
| item['score'] = None | ||
| item['status'] = "failed" |
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either set the item['log']['reason'] here with why it failed, or do it in the function. It looks like it only gets set in the function currently if it times out
…s, vfvs_get_top_results.py support for slurm, updating README-slurm.md and all.ctrl, setting slurm partition option in default template
Thank you Matt for the feedback! I have now changed the things you suggested. |
…ina-based docking programs, minor fixes
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Fixes #59 |
csecker
changed the title
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