Repository Contents

• Bash
  • assemblefpt.sh creates an aggregate .fpt structure file from the molecules specified in a res-like file
  • assemblesdf.sh creates an aggregate .sdf structure file from the molecules specified in a res-like file
  • fetchlib.sh fetches tar files from the sciurus server and decompresses them
  • procres.sh processes results of a segment of the ZINC library
  • sort.sh finds each result file of a segment of the ZINC library and sorts them based on predicted binding affinity
  • unzipper.sh processes the .sdf.gz files taken from the ZINC library and turns them into zipped directories (.tar.gz)
  • usual.sdf.gz is the script provided by ZINC to download every segment of the "Drugs Now" subset of the ZINC12 library
• Data
  • bottomfeat.txt is a list of the bottom 10 features as predicted by the regression from finalres.txt
  • conf.txt is a parameter file used to run AutoDock Vina
  • dP2.pdb is a structure file containing the delta-P2 structure of SurA from the PDB
  • dP2.pdbqt is dP2.pdb converted into the filetype accepted by AutoDock Vina
  • final.txt is a sorted results file produced by sort.sh
  • finalres.txt is the scores of each feature output by the regression
  • guide.txt is the list of features corresponding to each bit position in the "FP4" fingerprint
  • job.index is a list of jobs to be run in an array, produced by Raccoon2
  • mega.sdf structure files for all molecules with predicted binding affinities equal to or better than -9.2 kcal/mol
  • reflist.txt is the list of ZINC library segments to be run through genres.py
  • res.txt is a results file from a virtual screen. The formatting of this file is referred to as "res-like"
  • results.html is a file openable in a web browser that presents information about the top hits of the virtual screen
  • SMARTS_InteLigand.txt is the definition file of the "FP4" fingerprint protocol in OpenBabel
  • style.css is a stylesheet to help format results.html
  • thresh.txt is a res-like file containing all molecules above the threshold specified in thresh.py
  • topfeat.txt is a list of the top 10 features as predicted by the regression from finalres.txt
• Python
  • energystats.py calculates the mean and standard deviation of the binding affinity of any res-like file
  • genres.py creates results.html based off of the res.txt files in the directories specified by reflist.txt
  • ligsort.py sorts a res-like file and returns a user specified number of top hits (set to 1000 in sort.sh)
  • procfpt.py processes .fpt files and adds binding affinity information for use in regression
  • randomset.py generates random sets of molecules from an aggregate res-like file
  • regres.py compiles results from different regressions into one results file
  • regress.py runs a regression on a set of molecules specified in a .csv file
  • thresh.py returns all molecules from a sorted res-like file that meet a binding affinity threshold