Utilities for analyzing and reporting results from Smina virtual screens.
The tools are written in Go and Bash.
smina_scan_logs scans smina log files for lowest scores or lowest ligand efficiencies with optional limits on heavy atom count (see smina_scan_logs -h). The tool copies the docking results that meet the criteria into a separate folder and creates a scores.txt summary file in the current dir.
smina_preprep prepares a folder generated by smina_scan_logs for reporting.
The generated scores.txt has to be put in the folder and a as.pdb containing the active site has to be present in the parent dir. smina_preprep has to be started from within the dir that smina_scan_logs created.
smina_preprep is a bash script that will not be directly executable when using the go tools (see below). After go-getting this repo, you can manually create a link to the file in one of your binary folders, e.g.
ln -s $GOPATH/src/github.com/apahl/vstools/scripts/smina_preprep.sh ~/bin/smina_preprep
smina_report creates HTML reports of the type shown below, where the binding site column is an interactive 3Dmol JS widget of the ligand in the active site (created by smina_preprep from the ligand .pdbqt file and the above mentioned as.pdb) that allows rotating and zooming. The ligands listed in scores.txt are shown in the report, optional remarks can be put in scores.txt at the end of each ligand line, separated by tab from the previous field.
go get -u github.com/apahl/vstools/...
For a tutorial on how to prepare the receptor and the ligands, see the excellent blog post Ligand docking with Smina by E.J. Bjerrum.
Example uses of the tools and additional scripts (including for running smina on a cluster (platform LSF)) can be found in the smina file.
More detailed documentation will follow.