Module for receptor-ligand docking#209
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asherpasha merged 28 commits intoBioAnalyticResource:devfrom Apr 25, 2024
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Add docking_pdb_path parameter to best_result function to avoid hard-coding file paths Modify snps.py to pass in receptor and ligand of interest through endpoint Change naming conventions to not include the date, and only run hex if the protein-ligand pair has not been run before Add a block in docking_utils.py to search for the receptor and ligand indicated by endpoints
The following classes were added: Receptor, MonomerReceptor, ComplexReceptor, Ligand, Docking, MonomerDocking, ComplexDocking, and Docker. __init__ methods were added for each class. Methods for creating receptor, ligand and docking objects were written in Docker class. Hex_docking function was written for Docking class, which is inherited by MonomerDocking and ComplexDocking.
Add a controller class called Docker, which creates instances of other classes for docking.
Receptors with more than 1000 residues will have pdb files where there is no space between columns 4 and 5. For example, it can look like this: A1000, whereas for earlier residues, it looks like this: A 345. A regex check is added to see which lines need to be further processed to separate and extract the residue number.
Files for testing include 1 small monomer receptor pdb, 1 small complex receptor pdb, 1 ligand sdf file and the hex results and outputs for these dockings. The complex receptor file was altered to create a small complex receptor, so it does not actually exist. The results for the dockings are stored in folders just as they would be in the /DATA/HEX_API/RESULTS folder.
Reformat output json to include path to results file and the date the docking was performed
Change json results when receptor or ligand not found
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #209 +/- ##
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- Coverage 85.35% 81.64% -3.71%
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Files 45 46 +1
Lines 1693 2103 +410
Branches 421 513 +92
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+ Hits 1445 1717 +272
- Misses 233 361 +128
- Partials 15 25 +10 ☔ View full report in Codecov by Sentry. |
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Module for receptor-ligand docking
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Changes were made to the original docking_utils.py module to follow OOP concepts and efficiently manage data during the docking process and post-docking analysis.