Automated Database Preparation - Revision history

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2024-05-09T06:06:37Z

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	[[Category:Tutorials]]		[[Category:Tutorials]]
			[[Category:Databases]]
			[[Category:Obsolete]]

TBalius: /* Automatic Decoy Generation */

2014-06-06T20:45:37Z

Automatic Decoy Generation

← Older revision		Revision as of 20:45, 6 June 2014
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	awk 'BEGIN{count=1}{printf "%s TEMP%d\n",$1,count; count=count+1}' ligands.smi > ligands.mod.smi		awk 'BEGIN{count=1}{printf "%s TEMP%d\n",$1,count; count=count+1}' ligands.smi > ligands.mod.smi

	To generate decoys and ligands for DOCK3.7, you could run the these scripts which generated smiles file for the decoys. you can then run this smiles file with [Ligand preparation].		To generate decoys and ligands for DOCK3.7, you could run the these scripts which generated smiles file for the decoys. you can then run this smiles file with [[Ligand preparation]].

	→ Back to [[Tutorials]]		→ Back to [[Tutorials]]

	[[Category:Tutorials]]		[[Category:Tutorials]]

TBalius: /* Automatic Decoy Generation */

2014-06-06T20:45:22Z

Automatic Decoy Generation

← Older revision		Revision as of 20:45, 6 June 2014
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	awk 'BEGIN{count=1}{printf "%s TEMP%d\n",$1,count; count=count+1}' ligands.smi > ligands.mod.smi		awk 'BEGIN{count=1}{printf "%s TEMP%d\n",$1,count; count=count+1}' ligands.smi > ligands.mod.smi

			To generate decoys and ligands for DOCK3.7, you could run the these scripts which generated smiles file for the decoys. you can then run this smiles file with [Ligand preparation].

	→ Back to [[Tutorials]]		→ Back to [[Tutorials]]

	[[Category:Tutorials]]		[[Category:Tutorials]]

TBalius: /* Automatic Decoy Generation */

2013-11-08T16:39:04Z

Automatic Decoy Generation

@@ Line 64: / Line 64: @@
   $dud/dudgen.py -i INFILE                     # Fully rebuild ligands and DUD style decoys
 This last script could probably have many more command line options, so let me know 1) if you use it and 2) if you think of something you would like to change.
 &rarr; Back to [[Tutorials]]
 [[Category:Tutorials]]

Therese: 22 revisions

2012-10-08T18:10:26Z

22 revisions

New page

==Automated Docking Database Tools==

#[[#Automatic Database Generation]]: You want to generate DOCK 3.5 hierarchy databases for your molecules
#[[#Automatic Decoy Generation]]: You want to generate DUD style decoys property matched to your active ligands

==Automatic Database Generation==

If you just want to make a docking database for some molecules, then this is the section for you.

===Simple Database Generation===
*For automated database generation on small input files (say < 5000 molecules). Making a new directory is a good idea because these scripts generate a LOT of output files.
mkdir new_dir_name
cd new_dir_name
dbgen.csh INPUT
< or >
dbgen.csh INPUT [PROTONATION]

*Setup:
Scripts in this section are automatically put in your path by the DOCK login scripts. If they are not, then inside a csh first do the following:
setenv DOCK_BASE /raid1/soft/dockenv
source $DOCK_BASE/etc/login

*Options:
You can use dbgen.csh alone to get help. INPUT is a file containing the input molecules. Either use a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PROTONATION argument can be used to generate databases containing extended protonation states. The available protonation types are as follows:
#ref - only the reference protonation
#mid - reference plus middle protonation [default]
#lo - reference, middle, and lo protonation
#hi - reference, middle, and hi protonation
#all - all protonation ranges

*Caveats:
dbgen.csh is most useful when you want to test out a dockable database without worrying about ZINC. If you like the molecules and decide to add them to ZINC, it should be easy using the output of dbgen.csh. Please contact me (Michael Mysinger) if you want to do this at any time, as it should be easy but is untested at the moment. If you want to add the molecules to ZINC from the beginning then you can use the XML-RPC interface of DOCKBlaster like so:
xmlclient.py upload my.smi # uploads ligands to server
xmlclient.py qup ID # later on, get docking database back
where ID is the job id returned by the upload command.

===Complex Database Generation===

*If you want to do automated database generation on a large scale (> 5000 molecules), then look here. First, <i>NOTA BENE</i> that this process is demanding and has been known to fill all space on the file servers, slam them into submission, or overload the entire SGE cluster. For estimation purposes, assume the processes take ~40GB of disk per 100k molecules.
ssh sgehead.compbio.ucsf.edu # go to cluster head node
set dud=~mysinger/code/dud/trunk # setup variable for path
$dud/dbmake.py -i my.smi |& tee dbmake.log # run the large scale database generation

Options:
Use -n to change the name of the output database. Use -p to change the protonation type to one of the protonation options listed for dbgen.csh above.

If instead you want to load the molecules directly into ZINC, then John's corresponding script is 'mas.csh SETNAME INFILE'.

==Automatic Decoy Generation==

If you just want DUD style computational decoys property matched specifically to your ligands, then look here. For the fastest turnaround given the molecules already have ZINC ids, use decoys.py. To regenerate everything from scratch like [[#Automatic Database Generation]] above, use dudgen.py.

*Generate DUD style decoys starting from known ZINC ids, pulling the pre-generated hierarchy databases directly from ZINC

set dud=~mysinger/code/dud/trunk # setup variable for path
$dud/decoys.py -i INFILE # make DUD style decoys
It pulls ZINC IDs from the first column of stdin (or INFILE if -i is used), but the id column can be changed with -c COL. Use -n X to change the number of decoys generated per ligand from 35 to X. Use -s to output selected decoys but skip final database assembly.

*Generate DUD style decoys starting from smiles. This script first builds the ligands, then parses them to get the ligand properties, the selecting and building

The ids in the smiles file must be either ZINC ids or numbers. When not using ZINC ids the ligands and decoys will have the same ids (P000001, P000002, ...), so you will need to edit the ligands database file and change the ids.

ssh sgehead.compbio.ucsf.edu # go to cluster head node
$dud/dudgen.py -i INFILE # Fully rebuild ligands and DUD style decoys
This last script could probably have many more command line options, so let me know 1) if you use it and 2) if you think of something you would like to change.

→ Back to [[Tutorials]]

[[Category:Tutorials]]

Mysinger at 23:01, 29 October 2008

2008-10-29T23:01:29Z

← Older revision		Revision as of 23:01, 29 October 2008
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	$dud/dudgen.py -i INFILE # Fully rebuild ligands and DUD style decoys		$dud/dudgen.py -i INFILE # Fully rebuild ligands and DUD style decoys
	This last script could probably have many more command line options, so let me know 1) if you use it and 2) if you think of something you would like to change.		This last script could probably have many more command line options, so let me know 1) if you use it and 2) if you think of something you would like to change.

			→ Back to [[Tutorials]]

Mysinger at 23:00, 29 October 2008

2008-10-29T23:00:56Z

← Older revision		Revision as of 23:00, 29 October 2008
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	*Generate DUD style decoys starting from known ZINC ids, pulling the pre-generated hierarchy databases directly from ZINC		*Generate DUD style decoys starting from known ZINC ids, pulling the pre-generated hierarchy databases directly from ZINC
	$dud/decoys.py -i INFILE		set dud=~mysinger/code/dud/trunk # setup variable for path
			$dud/decoys.py -i INFILE # make DUD style decoys
	It pulls ZINC IDs from the first column of stdin (or INFILE if -i is used), but the id column can be changed with -c COL. Use -n X to change the number of decoys generated per ligand from 35 to X. Use -s to output selected decoys but skip final database assembly.		It pulls ZINC IDs from the first column of stdin (or INFILE if -i is used), but the id column can be changed with -c COL. Use -n X to change the number of decoys generated per ligand from 35 to X. Use -s to output selected decoys but skip final database assembly.

	*Generate DUD style decoys starting from smiles. This script first builds the ligands, then parses them to get the ligand properties, the selecting and building		*Generate DUD style decoys starting from smiles. This script first builds the ligands, then parses them to get the ligand properties, the selecting and building
	$dud/dudgen.py -h		ssh sgehead.compbio.ucsf.edu # go to cluster head node
			$dud/dudgen.py -i INFILE # Fully rebuild ligands and DUD style decoys
	If you ~~need~~ to ~~do this~~		This last script could probably have many more command line options, so let me know 1) if you use it and 2) if you think of something you would like to change.

Mysinger at 22:35, 29 October 2008

2008-10-29T22:35:56Z

← Older revision		Revision as of 22:35, 29 October 2008
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	==Automatic Decoy Generation==		==Automatic Decoy Generation==

	If you just want DUD style computational decoys property matched specifically to your ligands, then look here. For the fastest turnaround given the molecules already have ZINC ids, use decoys.py. To regenerate everything from scratch like [[Automatic Database Generation]] above, use dudgen.py.		If you just want DUD style computational decoys property matched specifically to your ligands, then look here. For the fastest turnaround given the molecules already have ZINC ids, use decoys.py. To regenerate everything from scratch like [[#Automatic Database Generation]] above, use dudgen.py.

	*Generate DUD style decoys starting from known ZINC ids, pulling the pre-generated hierarchy databases directly from ZINC		*Generate DUD style decoys starting from known ZINC ids, pulling the pre-generated hierarchy databases directly from ZINC
Line 55:		Line 55:
	It pulls ZINC IDs from the first column of stdin (or INFILE if -i is used), but the id column can be changed with -c COL. Use -n X to change the number of decoys generated per ligand from 35 to X. Use -s to output selected decoys but skip final database assembly.		It pulls ZINC IDs from the first column of stdin (or INFILE if -i is used), but the id column can be changed with -c COL. Use -n X to change the number of decoys generated per ligand from 35 to X. Use -s to output selected decoys but skip final database assembly.

	Generate DUD ~~type~~ decoys, ~~including rebuilding~~ the ~~hierarchy databases from scratch~~		*Generate DUD style decoys starting from smiles. This script first builds the ligands, then parses them to get the ligand properties, the selecting and building
	$dud/dudgen.py -h		$dud/dudgen.py -h

	If you need to do this		If you need to do this

Mysinger at 22:32, 29 October 2008

2008-10-29T22:32:05Z

← Older revision		Revision as of 22:32, 29 October 2008
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	==Automated Docking Database Tools==		==Automated Docking Database Tools==

	#[[#Automatic Database Generation]]: You want to generate ~~your own hierarchy databases as ligand inputs to~~ DOCK 3.5		#[[#Automatic Database Generation]]: You want to generate DOCK 3.5 hierarchy databases for your molecules
	#[[#Automatic Decoy Generation]]: You want to generate DUD style decoys ~~from~~ your ~~set of input~~ ligands		#[[#Automatic Decoy Generation]]: You want to generate DUD style decoys property matched to your active ligands

	==Automatic Database Generation==		==Automatic Database Generation==

			If you just want to make a docking database for some molecules, then this is the section for you.

	===Simple Database Generation===		===Simple Database Generation===
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	*Options:		*Options:
	You can use dbgen.csh alone to get help. INPUT is a file containing the ~~ligand~~ molecules~~, either~~ a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PROTONATION argument can be used to generate databases containing extended protonation states. The available protonation types are as follows:		You can use dbgen.csh alone to get help. INPUT is a file containing the input molecules. Either use a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PROTONATION argument can be used to generate databases containing extended protonation states. The available protonation types are as follows:
	#ref - only the reference protonation		#ref - only the reference protonation
	#mid - reference plus middle protonation [default]		#mid - reference plus middle protonation [default]
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	ssh sgehead.compbio.ucsf.edu # go to cluster head node		ssh sgehead.compbio.ucsf.edu # go to cluster head node
	set dud=~mysinger/code/dud/trunk # setup variable for path		set dud=~mysinger/code/dud/trunk # setup variable for path
	$dud/dbmake.py -i my.smi \|& tee dbmake.log # run the ~~parallel make~~		$dud/dbmake.py -i my.smi \|& tee dbmake.log # run the large scale database generation

	Options:		Options:
	Use -n to change the name of the output database. Use -p to change the protonation type to one of the protonation options listed for dbgen.csh above.		Use -n to change the name of the output database. Use -p to change the protonation type to one of the protonation options listed for dbgen.csh above.

	If you want to load the ~~molcules~~ into ZINC, ~~the~~ John's corresponding script is 'mas.csh SETNAME INFILE'.		If instead you want to load the molecules directly into ZINC, then John's corresponding script is 'mas.csh SETNAME INFILE'.

	==Automatic Decoy Generation==		==Automatic Decoy Generation==

	~~==Section 2==~~		If you just want DUD style computational decoys property matched specifically to your ligands, then look here. For the fastest turnaround given the molecules already have ZINC ids, use decoys.py. To regenerate everything from scratch like [[Automatic Database Generation]] above, use dudgen.py.

	*~~bullet3~~		*Generate DUD style decoys starting from known ZINC ids, pulling the pre-generated hierarchy databases directly from ZINC
	*bullet4		$dud/decoys.py -i INFILE
			It pulls ZINC IDs from the first column of stdin (or INFILE if -i is used), but the id column can be changed with -c COL. Use -n X to change the number of decoys generated per ligand from 35 to X. Use -s to output selected decoys but skip final database assembly.

			Generate DUD type decoys, including rebuilding the hierarchy databases from scratch
			$dud/dudgen.py -h

			If you need to do this

Mysinger at 22:13, 29 October 2008

2008-10-29T22:13:00Z

← Older revision		Revision as of 22:13, 29 October 2008
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	*Options:		*Options:
	You can use dbgen.csh alone to get help. INPUT is a file containing the ligand molecules, either a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PROTONATION argument can be used to generate databases containing extended protonation states. The available protonation types are as follows:		You can use dbgen.csh alone to get help. INPUT is a file containing the ligand molecules, either a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PROTONATION argument can be used to generate databases containing extended protonation states. The available protonation types are as follows:
	#ref - only the reference protonation"		#ref - only the reference protonation
	#mid - reference plus middle protonation [default]"		#mid - reference plus middle protonation [default]
	#lo - reference, middle, and lo protonation"		#lo - reference, middle, and lo protonation
	#hi - reference, middle, and hi protonation"		#hi - reference, middle, and hi protonation
	#all - all protonation ranges"		#all - all protonation ranges

	*Caveats:		*Caveats: