Dockenv Scripts

Jump to: navigation, search


DOCK Blaster Pipeline

DOCK Expert

  • scoreopt2 - score molecule in xpdb against grids (DOCK3.5! mods?)

WINC Pipeline

ZINC Pipeline

ZINC Curation

Conversion tools

  • getsdf - extract by code a subset of sdf file
  • getxpdb - subselect molecules based on molecule code


  • abut - put two files next to each other (source?)
  • molcharge_pdb - net molecule charges from xpdb format (e.g. .eel1)
  • mkpdbfmt - make pdb from xpdb (.eel1) file for viewing by midas
  • mkxpdb - make xpdb from (.eel1?) format file (purpose?)
  • get - get a molecule from an sdf file, make mol2 using omega
  • molcharge - original DL version - net charge on mols in mol2 format file
  • molcharge2 - rounding to two decimals
  • molcharge3 - rounding, uses PREFIX env variable
  • pc2unix - remove trailing \r from windows (uses tab2space, ctrl_m)
  • rename.csh - rename file en masse - modifyable script
  • amb2xpdb - convert amber to xpdb format - used during dock prep / Makefile
  • sph2pdb - convert spheres to PDB format
  • - takes input .db or .db.gz files and splits them into smaller files respecting hierarchy boundaries
  • - takes input .mol2 file and run amsol & mol2db on it, but not omega. it must be protonated correctly as well.

Historical interest only

  • get-green-sph.csh - wbq script to extract atoms from midas

legacy - inherited scripts that ought to be adapted, reformulated or abandonded

  awk-scripts - bits of code for testing the database / atomtyp.txt
  awk.ctof - reformat mol2 to pdb; superceded by convsyb
  awk.tosph - reformat PDB to sph; superceded by pdb2sph
  bestscores - extract best scores from OUTDOCK file
  charge.spl - Sybyl based method to add H and compute charges
               superceded by omega (and amsol)
  chargrank - analysis - analyse eel1 output and compute charges (correct?)
  countcharge - analysis - count charges (correct?) superceded by docksum
  clu2pdb - convert cluster(?) format to pdb (usage?)
  conf_gen.spl - old sybyl script to generate conformations. not used.
  conversmi.csh - convert smiles to SLN - old script
  count_res - count residues in a PDB file (not used) - A McLachlan program to manipulate protein PDB files
  fitatom.loop - variant on the above
  getsdf.csh - extract sdf file and use filter during atomtyp.txt testing
  h-bond - make hb.coord and hb.1 from test.eel1 for midas
  hierstat - dockable database statistics
  midas2pdb - convert midas output to normal PDB
  mkc1 - coordinate file reformatting script bks 1996
  mklvlfmt - reformat file. (purpose?) - convert mol2 to sln strings in sybyl
  extractcode.csh - get code, energy from eel1 file
  various old versions of
  various old versions of getnext

devtools - developer tools, not used for docking. not distributed

  hier_check - basic paranoia check on integrity of dockable database
               run on STDOUT from mol2db
  num - postpend line number to each line
  make_surf - command line to make a surface. usage of dms - pick molecules randomly from list - get sequence from PDB file
  lclint - source checker - Linux - 3rd party - hash-encypted password creator
  snap.csh - take picture using indycam and put on web page
  splitdb.csh - script to split a database into chunks - analyze output logs from database creation to give
               summary statistics for database production
  superdbmake.csh - script to subselect database from dockable database
  s_superdbmake.csh  - database subselection script - convert 3 letter codes to 1 letter aa codes for seq


scripts - non-executable files

  midock - used by midas to set up colors
  tab2space and ctrl_m should go here
  Makefile - site preparation (original by DL)
  add_h.spl - used by Makefile to add H to amber-format PDB
  dock.con - condor script 
  filt.params - STDIN to filt.exe to find residues for input to ms/dms
  grids - templates for grid directory. instantiated by Makefile
  header.db - database color header
  inhier - small_mol_db_prep - input parameter template for mol2db
  inhier_prot - protein db prep - inhier template for protein-protein docking
  lig - templates for lig directory. instantiated by Makefile
  search - templates for search directory. instantiated by Makefile
  sph - templates for sph directory. instantiated by Makefile
  testing - templates for testing directory. instantiated by Makefile

etc - scripts


setup - set up the environment

login - set up paths to scripts

dbprep - general database preparation - unique sort based on first token (e.g. smiles files) - convert ISIS sdf into openeye-ready sdf - convert AMSOL output into a database one tranche at a time - split up solv files rename.csh - rename files - customize as required