Building The 3D Pipeline ZINC22 - Revision history

Sevigneron: /* Script Arguments */

2024-06-04T22:46:59Z

Script Arguments

← Older revision		Revision as of 22:46, 4 June 2024
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	Sets what pH to generate the compound(s) at. Default is a pH of 7.4		Sets what pH to generate the compound(s) at. Default is a pH of 7.4


			Note: For addition of new variables, that variable needs also needs to be added to the 'optional_vars' line of submit-all.bash

	== Omega Arguments ==		== Omega Arguments ==

2024-06-04T22:36:50Z

Script Arguments

← Older revision		Revision as of 22:36, 4 June 2024
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	==== pH_LEVEL ====		==== pH_LEVEL ====

	Sets what pH to generate the compound at. Default is 7.4		Sets what pH to generate the compound(s) at. Default is a pH of 7.4

	== Omega Arguments ==		== Omega Arguments ==

2024-06-04T22:36:10Z

Script Arguments

← Older revision		Revision as of 22:36, 4 June 2024
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	How many nitrogen flapping configurations of each protomer corina should generate. By default only one is generated.		How many nitrogen flapping configurations of each protomer corina should generate. By default only one is generated.


	==== pH_LEVEL ====		==== pH_LEVEL ====

2024-06-04T22:35:56Z

Script Arguments

← Older revision		Revision as of 22:35, 4 June 2024
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	How many nitrogen flapping configurations of each protomer corina should generate. By default only one is generated.		How many nitrogen flapping configurations of each protomer corina should generate. By default only one is generated.


			==== pH_LEVEL ====

			Sets what pH to generate the compound at. Default is 7.4

	== Omega Arguments ==		== Omega Arguments ==

2023-03-09T18:11:51Z

Software Options

← Older revision		Revision as of 18:11, 9 March 2023
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	* EXTRALIBS_VERSION		* EXTRALIBS_VERSION
			Note on EXTRALIBS- Run the pipeline with an empty EXTRALIBS package (but all other software accounted for) and see which shared libraries come up as missing in the error log. Locate all missing libraries and toss them in EXTRALIBS, they will be added to LD_LIBRARY_PATH

	* JAVA_VERSION		* JAVA_VERSION

2023-03-02T21:45:45Z

2023-03-02T20:34:17Z

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 setenv OUTPUT_DEST $HOME/myoutput
 submit-all-jobs-sge.bash</nowiki>
 = Script Arguments =
@@ Line 56: / Line 64: @@
 Prior to running the script.
 == Required Arguments ==

2023-03-02T20:33:09Z

← Older revision		Revision as of 20:33, 2 March 2023
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	Prior to running the script.		Prior to running the script.

			== Repackaging Output For Docking ==

			The output of the 3D pipeline scripts will be a number of tar.gz files with roughly LINES_PER_JOB molecules contained per package.

			It is standard practice to repackage these smaller packages into larger packages for docking, as 50 molecules do not take long to process with DOCK.

			See this wiki page for how to do this: [[Repackaging_DB2_DOCK38]]

	== Required Arguments ==		== Required Arguments ==

2023-02-10T00:04:24Z

Job Submission Arguments

← Older revision		Revision as of 00:04, 10 February 2023
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	== Job Submission Arguments ==		== Job Submission Arguments ==

			==== SUBMIT_MODE ====

			Choose the job submission method, choose between SGE, SLURM, or TEST_LOCAL. This will be automatically set if you use the job controller's corresponding superscript, e.g submit-all-jobs-slurm.bash. TEST_LOCAL will bypass the job controller and run the first input chunk in your shell.

	==== LINES_PER_BATCH ====		==== LINES_PER_BATCH ====

2023-02-09T23:53:40Z

Examples

← Older revision		Revision as of 23:53, 9 February 2023
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	<nowiki>		<nowiki>
	export INPUT_FILE=$PWD/example.smi		export INPUT_FILE=$PWD/example.smi
	export OUTPUT_DEST=/~~nfs/exb/zinc22/tarballs~~		export OUTPUT_DEST=$PWD/ligand_building
	export SBATCH_ARGS="--time=02:00:00"		export SBATCH_ARGS="--time=02:00:00"
	export LINES_PER_BATCH=20000		export LINES_PER_BATCH=20000
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	<nowiki>		<nowiki>
	export INPUT_FILE=$PWD/example.smi		export INPUT_FILE=$PWD/example.smi
	export OUTPUT_DEST=/~~wynton/group/bks/zinc22~~		export OUTPUT_DEST=$PWD/ligand_building
	export QSUB_ARGS="-l s_rt=00:28:30 -l h_rt=00:30:00 -r y"		export QSUB_ARGS="-l s_rt=00:28:30 -l h_rt=00:30:00 -r y"
	bash submit-all-jobs-sge.bash</nowiki>		bash submit-all-jobs-sge.bash</nowiki>