Dockenv Scripts

DOCK Expert

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

Conversion tools

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

Utilities

• 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
• splitdb.py - takes input .db or .db.gz files and splits them into smaller files respecting hierarchy boundaries
• multimol2db.py - 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

  cod2smi.pl
  extractcode.csh
  fprint
  fprint2
  fprint3
  dl_fp
  fprint_all.csh
  reprocess.csh

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  awk.ctof - reformat mol2 to pdb; superceded by convsyb
  awk.tosph - reformat PDB to sph; superceded by pdb2sph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               superceded by omega (and amsol)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 superceded by docksum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)
  fitatom.com - 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?)
  mol2sln.com - convert mol2 to sln strings in sybyl
  extractcode.csh - get code, energy from eel1 file
  various old versions of fmtSDF.pl
  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
  extract_random.pl - pick molecules randomly from list
  getseq.pl - get sequence from PDB file
  lclint - source checker - Linux - 3rd party
  passwd.pl - hash-encypted password creator
  snap.csh - take picture using indycam and put on web page
  splitdb.csh - script to split a database into chunks
  sumtime.pl - 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
  three21.pl - convert 3 letter codes to 1 letter aa codes for seq

alignment

scripts - non-executable files

  colortest.txt
  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

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login - set up paths to scripts

dbprep - general database preparation

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usort1tok.pl - unique sort based on first token (e.g. smiles files) fmtSDF.pl - convert ISIS sdf into openeye-ready sdf makedb.com - convert AMSOL output into a database one tranche at a time splitmol.pl - split up solv files rename.csh - rename files - customize as required