Ligand Docking and File Processing Scripts

This repository contains scripts used for ligand file preparation, docking job automation, file organization, and output parsing. These tools are useful for handling large-scale virtual screening workflows.

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📁 Script Overview

Script	Inputs	Outputs	Dependency	Function
andy_upgraded.py	config files.txt	CONFIG_FORMAT.txt	—	Sets paths in config files
eboxsize.pl	—	—	—	Prepares config files with specific ligand
combine_directories.py	Directory 1, Directory 2, Output Directory	Combined directory	—	Combines contents of two directories
count_affinities_decimal_upgraded_2.sh	Directory with Vina log files	affinity_counts.txt	—	Extracts and counts binding affinities
counting_logs_in_subdirs.sh	Path, Number of subdirectories	Zipped directory	—	Unzips logs, moves files, and counts them
file_combine_and_sort.py	Files to combine, Output name	Combined and sorted file	—	Combines and sorts files from low to high
file_splitting.py	Input file	Split files	—	Splits a file into 4 equal parts
find_common_to_all_files.py	Sets	Terminal output	—	Finds values common to all sets
identify_affinities_files_upgraded.sh	Directory name, Number of subdirectories	affinity_file_names.txt	—	Lists ligands and their affinities
isolate_candidates.sh	Directory name	candidates/	unzip_zips.py	Extracts files from defined ligand list
isolate_coconut_id.py	Directory name, List of indices	Terminal output	—	Retrieves Coconut ID (CNP) from .sdf files
isolate_coconut_name.py	Directory name, List of indices	Terminal output	—	Retrieves Coconut filenames from .sdf files
isolate_logs.sh	Ligand list, Number of subdirectories	candidates/	—	Moves selected log files to target directory
isolate_pdbqts.sh	Ligand list, Number of subdirectories	candidates/	—	Moves selected .pdbqt files to target directory
jobscript_subdir_prep.sh	Jobscript name, Directory name, Number of subdirectories	Multiple job scripts	—	Splits jobscript per ligand subdirectory
make_subdir.sh	Directory, Files per subdir	Subdirectories	—	Splits a directory into smaller subdirectories
mv_subdir_jobscript.sh	Base path, Index number	Flattened files	—	Moves files out of subdirectories
rename_script.py	Directory	Renamed files	—	Renames 3d_hydrated_coconut* to coconut*
sdf_to_pdbqt_converter_upgraded.sh	—	.pdbqt files	mk_prepare_ligand.py	Converts .sdf files to .pdbqt
shuttle_3digits.py	Source dir, Destination dir	Filtered ligands	—	Moves ligands sized 100–1000 kDa
shuttle_names.py	Source dir, Destination dir	Filtered ligands	—	Moves ligands whose names start with a letter
shuttle_trashing.py	Source dir, Destination dir, Search term	Filtered ligands	—	Moves undesired ligands
submit_script.sh	Directory name, Number of job scripts	—	—	Submits all prepared jobscripts
subdir_zipping.py	Directory name, Output directory	Zipped subdirectories	—	Zips all subdirectories of a directory
unzip_tars.py	—	Unzipped tar files	—	Unzips all .tar files in working directory
unzip_zips.py	Directory	Unzipped zip files	—	Unzips all .zip files in a directory
vf_compare_qvina_smina_results.py	qvina.txt, smina.txt, output.txt	output.txt	—	Compares qvina and smina results
vf_firstposes_sorter.py	Input file	output.txt	—	Sorts Vina results from low to high
vf_tranches_and_ligands.py	Input file, Output file	output.txt	—	Extracts tranches and ligand names
vina_upgraded.sh	Paths	Logs, Outputs	—	Runs AutoDock Vina using templates
zip_files_count.py	Directory	Terminal output	—	Counts files inside .zip archives

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🔧 Notes

• Ensure required dependencies such as AutoDock Vina, Python 3, and Perl are installed.
• Scripts marked with "other" or reused (e.g., eboxsize.pl, mk_prepare_ligand.py) may exist in multiple folders.
• Most file operations assume a specific directory structure; modify paths as needed for your workflow.

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🧪 Example Use Cases

• Prepare ligands: Convert .sdf files to .pdbqt using sdf_to_pdbqt_converter_upgraded.sh.
• Run docking jobs: Use vina_upgraded.sh with config files and ligands.
• Process outputs: Use vf_firstposes_sorter.py to rank ligand affinities.
• Manage data: Combine, filter, and isolate files with the various shuttle_*.py and isolate_*.sh scripts.