Restartable DOCK37 - Revision history

Frodo: asdf

2024-05-02T20:49:31Z

asdf

← Older revision		Revision as of 20:49, 2 May 2024
Line 85:		Line 85:

	As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option in INDOCK.		As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option in INDOCK.

			[[DOCK 3.7]]
			[[Category:Developer]]

2020-11-20T18:59:00Z

Running & Restartability

← Older revision		Revision as of 18:59, 20 November 2020
Line 79:		Line 79:
	btingle@desktop:~> zcat test.mol2.gz.* > test.mol2.gz		btingle@desktop:~> zcat test.mol2.gz.* > test.mol2.gz
	</nowiki>		</nowiki>

			You don't need to worry about interrupting dock at the wrong time- dock will recognize the signal, finish up it's current work unit and exit.

	==== Additional Notes ====		==== Additional Notes ====

	As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option in INDOCK.		As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option in INDOCK.

2020-11-20T07:34:02Z

Required Input

← Older revision		Revision as of 07:34, 20 November 2020
Line 9:		Line 9:
	The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_index and expect it to be in the working directory.		The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_index and expect it to be in the working directory.
	split_database_index should contain a list of paths to db2.gz files. I've been generating this file using a command like this:		split_database_index should contain a list of paths to db2.gz files. I've been generating this file using a command like this:

	~~All example code is written in bash.~~

	<nowiki>		<nowiki>
Line 17:		Line 15:

	Where DB2_SOURCE_DIR is just some directory containing a bunch of db2 files.		Where DB2_SOURCE_DIR is just some directory containing a bunch of db2 files.

			All example code is written in bash.

	==== Running & Restartability ====		==== Running & Restartability ====

2020-11-20T07:30:00Z

Required Input

← Older revision		Revision as of 07:30, 20 November 2020
Line 1:		Line 1:
	==== Required Input ====		==== Required Input ====

	1. INDOCK		1. INDOCK (dock parameters)

	2. split database index file		2. dockfiles (receptor stuff)

			2. split database index file (db2 list)

	The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_index and expect it to be in the working directory.		The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_index and expect it to be in the working directory.

2020-11-20T07:28:00Z

Additional Notes

← Older revision		Revision as of 07:28, 20 November 2020
Line 80:		Line 80:
	==== Additional Notes ====		==== Additional Notes ====

	As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option ~~enabled~~.		As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option in INDOCK.

2020-11-20T07:26:40Z

Required Input

← Older revision		Revision as of 07:26, 20 November 2020
Line 7:		Line 7:
	The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_index and expect it to be in the working directory.		The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_index and expect it to be in the working directory.
	split_database_index should contain a list of paths to db2.gz files. I've been generating this file using a command like this:		split_database_index should contain a list of paths to db2.gz files. I've been generating this file using a command like this:

			All example code is written in bash.

	<nowiki>		<nowiki>

2020-11-20T07:25:07Z

Running & Restartability

← Older revision		Revision as of 07:25, 20 November 2020
Line 21:		Line 21:
	dock=/path/to/dock/dock64		dock=/path/to/dock/dock64
	INDOCK=/path/to/indock/INDOCK		INDOCK=/path/to/indock/INDOCK
			dockfiles=/path/to/dockfiles

	mkdir -p /tmp/~~workdir~~		mkdir -p /tmp/docking/working
	pushd /tmp/~~workdir~~		ln -s $dockfiles /tmp/docking/dockfiles
			pushd /tmp/docking/working

	find /path/to/db2/files -name '*.db2.gz' > split_database_index		find /path/to/db2/files -name '*.db2.gz' > split_database_index

2020-11-20T05:24:32Z

Running & Restartability

← Older revision		Revision as of 05:24, 20 November 2020
Line 16:		Line 16:
	==== Running & Restartability ====		==== Running & Restartability ====

	Here's what you might do if you were to run ~~the script~~:		Here's what you might do if you were to run dock:

	<nowiki>		<nowiki>

2020-11-20T02:10:36Z

← Older revision		Revision as of 02:10, 20 November 2020
Line 73:		Line 73:
	btingle@desktop:~> zcat test.mol2.gz.* > test.mol2.gz		btingle@desktop:~> zcat test.mol2.gz.* > test.mol2.gz
	</nowiki>		</nowiki>

			==== Additional Notes ====

			As of right now this restartability function is only implemented for the default docking mode, i.e without any ensemble_docking_mode option enabled.

2020-11-20T02:04:15Z

Required Input