Dockenv Scripts - Revision history

Frodo: asdf

2024-05-02T17:25:07Z

asdf

← Older revision		Revision as of 17:25, 2 May 2024
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	[[Category:ZINC]]		[[Category:ZINC]]
	[[Category:Internal]]		[[Category:Internal]]
	[[Category:~~NEED ATTENTION~~]]		[[Category:Obsolete]]

Khtang at 23:10, 9 January 2019

2019-01-09T23:10:40Z

← Older revision		Revision as of 23:10, 9 January 2019
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	[[Category:ZINC]]		[[Category:ZINC]]
	[[Category:Internal]]		[[Category:Internal]]
			[[Category:NEED ATTENTION]]

Frodo at 03:13, 13 March 2014

2014-03-13T03:13:25Z

← Older revision		Revision as of 03:13, 13 March 2014
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	[[Category:DOCK]]		[[Category:DOCK 3.6]]
	[[Category:ZINC]]		[[Category:ZINC]]
	[[Category:Internal]]		[[Category:Internal]]

Therese: 5 revisions

2012-10-08T20:11:54Z

5 revisions

← Older revision

Revision as of 20:11, 8 October 2012

Rgc: /* Utilities */

2012-02-03T22:26:14Z

Utilities

← Older revision		Revision as of 22:26, 3 February 2012
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	* sph2pdb - convert spheres to PDB format		* sph2pdb - convert spheres to PDB format
	* [[splitdb.py]] - takes input .db or .db.gz files and splits them into smaller files respecting hierarchy boundaries		* [[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 =		= Historical interest only =

Rgc: new code

2011-11-12T00:04:49Z

new code

← Older revision		Revision as of 00:04, 12 November 2011
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	* amb2xpdb - convert amber to xpdb format - used during dock prep / Makefile		* amb2xpdb - convert amber to xpdb format - used during dock prep / Makefile
	* sph2pdb - convert spheres to PDB format		* sph2pdb - convert spheres to PDB format
			* [[splitdb.py]] - takes input .db or .db.gz files and splits them into smaller files respecting hierarchy boundaries

	= Historical interest only =		= Historical interest only =

JohnIrwin at 08:32, 30 November 2007

2007-11-30T08:32:17Z

@@ Line 1: / Line 1: @@
-getsdf - extract by code a subset of sdf file
+= AMSOL =
 getxpdb - subselect molecules based on molecule code
-(rmsd added here)
+= DOCK Blaster Pipeline =
 abut - put two files next to each other (source?)
-scoreopt2 - score molecule in xpdb against grids (DOCK3.5! mods?)
+= DOCK Expert =
     cod2smi.pl
     extractcode.csh
@@ Line 87: / Line 118: @@
 ------
 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
@@ Line 118: / Line 127: @@
 [[Category:ZINC]]
 [[Category:Internal]]

JohnIrwin at 18:34, 21 September 2007

2007-09-21T18:34:12Z

← Older revision		Revision as of 18:34, 21 September 2007
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	amb2xpdb - convert amber to xpdb format - used during dock prep / Makefile		amb2xpdb - convert amber to xpdb format - used during dock prep / Makefile
	sph2pdb - convert spheres to PDB format		sph2pdb - convert spheres to PDB format


			[[Category:DOCK]]
			[[Category:ZINC]]
			[[Category:Internal]]


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

Frodo at 18:09, 21 September 2006

2006-09-21T18:09:30Z

New page

getsdf - extract by code a subset of sdf file
getxpdb - subselect molecules based on molecule code
(rmsd added here)
abut - put two files next to each other (source?)
scoreopt2 - score molecule in xpdb against grids (DOCK3.5! mods?)
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
-----
login - set up paths to scripts

dbprep - general database preparation
------
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

utility - general purpose tools (mol2 and pdb manipulation)
-------
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

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