DOCK 3.7 2016/09/16 abl1 Tutorial(building) - Revision history

Jklyu at 00:16, 18 September 2016

2016-09-18T00:16:33Z

← Older revision		Revision as of 00:16, 18 September 2016
Line 174:		Line 174:
	## TO DO - rename this outside in the dir structure and call in blbalbalbabla script		## TO DO - rename this outside in the dir structure and call in blbalbalbabla script
	if (-s $dude_dir) then		if (-s $dude_dir) then
	echo " $dude_dir exist"		echo " $dude_dir exist"
	else		else
	# this is something to modified in future.		# this is something to modified in future.
	# probably better to exit if it is not there.		# probably better to exit if it is not there.
	echo "databases do not exist. "		echo "databases do not exist. "
	echo "consider making a symbolic link to the database files"		echo "consider making a symbolic link to the database files"
	~~#echo "making a symbolic link:"~~
	~~#echo "ln -s /mnt/nfs/work/users/fischer/VDR/27Jan2014_learningDOCKrgc/databases_all_xtal-ligand_decoy $dude_dir"~~
	~~#ln -s /mnt/nfs/work/users/fischer/VDR/27Jan2014_learningDOCKrgc/databases_all_xtal-ligand_decoy $dude_dir~~
	endif		endif

	set list = "2HYY"		set list = "2HYY"
	~~#set list = `cat $1`~~		# CHANGE THIS (pdbname)
	~~#set list = `cat file`~~
	# CHANGE THIS (pdbname)
	foreach pdbname ( $list )		foreach pdbname ( $list )

	# creates "ligands" and "decoys" and has the aim to dock all of the subsets for those two		# creates "ligands" and "decoys" and has the aim to dock all of the subsets for those two
	foreach db_type ( "ligands" "decoys" )		foreach db_type ( "ligands" "decoys" )
	set workdir1 = "${mountdir}/${pdbname}/~~ligands-decoys~~/${~~db_type~~}"		set workdir1 = "${mountdir}/${pdbname}/${db_type}"
			set workdir2 = "${mountdir}/${pdbname}"
			#
	echo $mountdir		echo $mountdir
	echo $workdir1		echo $workdir1
			echo $workdir2
			#
	mkdir -p ${workdir1}		mkdir -p ${workdir1}
	cd ${workdir1}		cd ${workdir1}

	#creat dirlist for *.db2.gz files prepared for docking		#creat dirlist for *.db2.gz files prepared for docking
	ls ${dude_dir}/${db_type}/*.db2.gz > ${db_type}_files.txt		ls ${dude_dir}/${db_type}/*.db2.gz > ${db_type}_files.txt
	cp ../INDOCK .		#copy the files needed for dock
	ln -s ../dockfiles/ .		cp ${workdir2}/INDOCK ${workdir1}
			ln -s ${workdir2}/dockfiles/ ${workdir1}
			#use dirlist to creat chunks for job submission
	python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ chunk ./${db_type}_files.txt 500 count		python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ chunk ./${db_type}_files.txt 500 count
			#
			csh $DOCKBASE/docking/submit/submit.csh

	~~csh /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7-beta3/docking/submit/submit.csh~~		end # db_type
			end # pdbname

	* Run the above script		* Run the above script

	csh 0003.lig-decoy_enrichment_submit.csh		csh 0003.lig-decoy_enrichment_submit.csh

Jklyu at 23:41, 17 September 2016

2016-09-17T23:41:27Z

@@ Line 159: / Line 159: @@
 The 0003_new.lig-decoy_enrichment.csh script above will ONLY submit one job but with 1-many subjobs.
-== Submit an enrichment calculation via submit.csh ==
+== Submit an enrichment calculation via  0003.lig-decoy_enrichment_submit.csh ==
-* For the part of ligands, write a file called ligands
+* Write a file called 0003.lig-decoy_enrichment_submit.csh
-mkdir decoys
+ #!/bin/csh
-cd decoys
-#creat dirlist for *.db2.gz files prepared for docking
+ #This script provides a alternative way to dock a DUD-e like ligand-decoy-database for the enrichment evaluation of actives over decoys
-ls /mnt/nfs/home/jklyu/work/DOCK_tutorial/databases/decoys/*.db2.gz > decoys_files.txt
+ #It assumes that ligands and decoys have been pre-prepation (see script blablabla_ToDo) which needs to be run in SF.
 cp ../INDOCK .
-ln -s ../dockfiles/ .
+ set filedir = "/mnt/nfs/home/jklyu/work/DOCK_tutorial"  #CHANGE THIS
-python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ chunk ./decoys_files.txt 500  count
+* Run the above script
-qstat
-/mnt/nfs/soft/dock/versions/dock37/DOCK-3.7-beta3/docking/submit/submit.csh
+ csh 0003.lig-decoy_enrichment_submit.csh

Jklyu at 23:26, 17 September 2016

2016-09-17T23:26:26Z

@@ Line 24: / Line 24: @@
+                                |
                                 ------ ligands.ism and decoys.ism files
   #!/bin/csh
@@ Line 151: / Line 153: @@
   end # pdbname
-== Submit a virtual screening job via submit.csh ==
+mkdir decoys
-* There are two ways to get databases:
+python /nfs/home/tbalius/zzz.github/DOCK/docking/setup/setup_db2_zinc15_file_number.py ./ chunk ./decoys_files.txt 500  count

Jklyu at 23:10, 17 September 2016

2016-09-17T23:10:55Z

@@ Line 25: / Line 25: @@
                                 ------ ligands.ism and decoys.ism files
-== Submit  ==
+== Submit a virtual screening job via submit.csh ==
 * There are two ways to get databases:

Jklyu at 23:01, 17 September 2016

2016-09-17T23:01:59Z

← Older revision		Revision as of 23:01, 17 September 2016
Line 7:		Line 7:
	* Go to the working directory of your account		* Go to the working directory of your account

	cd /nfs/home/$USERNAME/work		cd /nfs/home/$USERNAME/work/DOCK_tutorial

	PS: $USERNAME is your username log on the cluster.		PS: $USERNAME is your username log on the cluster.

			The hierarchy of the working directory:

			DOCK_tutorial ----- 2HYY ------ dockfiles
			\| \|
			\| \|----- working
			\| \|
			\| ------ other files generated by 0001.be_balsti_py.csh
			\|
			----- databases ------ decoys
			\|
			\|----- ligands
			\|
			------ ligands.ism and decoys.ism files

	* Create directory called "DOCK_tutorial"

	~~mkdir DOCK_tutorial~~

	== ~~Get databases~~ ==		== Submit ==

	* There are two ways to get databases:		* There are two ways to get databases:

	1. get databases via the script autodude_db_download.py in the DOCK 3.7		1. get databases via the script autodude_db_download.py in the DOCK 3.7

Jklyu at 22:38, 17 September 2016

2016-09-17T22:38:10Z

← Older revision		Revision as of 22:38, 17 September 2016
Line 1:		Line 1:
	This tutorial uses the DOCK-3.7-beta3. This is a supplemental tutorial for DOCK 3.7 2015/04/15 abl1 Tutorial. Former one works well and is very simple and clear~~, but~~ some updates ~~should be mentioned~~ in ~~this tutorial~~.		This tutorial uses the DOCK-3.7-beta3. This is a supplemental tutorial for DOCK 3.7 2015/04/15 abl1 Tutorial. Former one works well and is very simple and clear. This tutorial mentions some updates in job submissions.

	This is for a Linux environment and the scripts assume that you are running on SGE queueing system.		This is for a Linux environment and the scripts assume that you are running on SGE queueing system.

	== ~~Set up directories~~ ==		== Submit an enrichment calculation via new 0003.lig-decoy_enrichment.csh ==

	* Go to the working directory of your account		* Go to the working directory of your account

Jklyu at 19:20, 17 September 2016

2016-09-17T19:20:07Z

← Older revision		Revision as of 19:20, 17 September 2016
Line 1:		Line 1:
	This tutorial uses the DOCK-3.7-beta3.		This tutorial uses the DOCK-3.7-beta3. This is a supplemental tutorial for DOCK 3.7 2015/04/15 abl1 Tutorial. Former one works well and is very simple and clear, but some updates should be mentioned in this tutorial.

	This is for a Linux environment and the scripts assume that you are running on SGE queueing system.		This is for a Linux environment and the scripts assume that you are running on SGE queueing system.
Line 16:		Line 16:

	== Get databases ==		== Get databases ==

			* There are two ways to get databases:

			1. get databases via the script autodude_db_download.py in the DOCK 3.7

Jklyu at 19:05, 17 September 2016

2016-09-17T19:05:10Z

← Older revision		Revision as of 19:05, 17 September 2016
Line 3:		Line 3:
	This is for a Linux environment and the scripts assume that you are running on SGE queueing system.		This is for a Linux environment and the scripts assume that you are running on SGE queueing system.

	== ~~set~~ up directories ==		== Set up directories ==

	Go to the working directory of your account		* Go to the working directory of your account

	cd /nfs/home/$USERNAME/work		cd /nfs/home/$USERNAME/work
Line 11:		Line 11:
	PS: $USERNAME is your username log on the cluster.		PS: $USERNAME is your username log on the cluster.

	Create directory called "DOCK_tutorial"		* Create directory called "DOCK_tutorial"

	mkdir DOCK_tutorial		mkdir DOCK_tutorial

	== ~~get~~ databases ==		== Get databases ==

Jklyu at 00:08, 17 September 2016

2016-09-17T00:08:33Z

← Older revision		Revision as of 00:08, 17 September 2016
Line 7:		Line 7:
	Go to the working directory of your account		Go to the working directory of your account

	cd /nfs/home/$USERNAME/work		cd /nfs/home/$USERNAME/work

	PS: $USERNAME is your username log on the cluster.		PS: $USERNAME is your username log on the cluster.
Line 13:		Line 13:
	Create directory called "DOCK_tutorial"		Create directory called "DOCK_tutorial"

	mkdir DOCK_tutorial		mkdir DOCK_tutorial

	== get databases ==		== get databases ==

Jklyu: Created page with "This tutorial uses the DOCK-3.7-beta3. This is for a Linux environment and the scripts assume that you are running on SGE queueing system. == set up directories == Go to th..."

2016-09-17T00:06:28Z

Created page with "This tutorial uses the DOCK-3.7-beta3. This is for a Linux environment and the scripts assume that you are running on SGE queueing system. == set up directories == Go to th..."

New page

This tutorial uses the DOCK-3.7-beta3.

This is for a Linux environment and the scripts assume that you are running on SGE queueing system.

== set up directories ==

Go to the working directory of your account

cd /nfs/home/$USERNAME/work

PS: $USERNAME is your username log on the cluster.

Create directory called "DOCK_tutorial"

mkdir DOCK_tutorial

== get databases ==