Docking Analysis in DOCK3.8 - Revision history

Btingle: /* Usage */

2023-03-03T04:34:52Z

Usage

← Older revision		Revision as of 04:34, 3 March 2023
Line 67:		Line 67:

	<nowiki>		<nowiki>
			usage: top_poses.py [-h] [-n NPOSES] [-o OUTPREFIX] [-j NPROCESSES] [--id-file INPUT_ID_FILE]
	[--verbose] [--quiet] [--log-interval LOG_INTERVAL]		[--verbose] [--quiet] [--log-interval LOG_INTERVAL]
	[--find-min-size FIND_MIN_SIZE]		[--find-min-size FIND_MIN_SIZE]

Btingle: /* Usage */

2023-03-03T04:34:32Z

Usage

← Older revision		Revision as of 04:34, 3 March 2023
Line 67:		Line 67:

	<nowiki>		<nowiki>
	~~usage: top_poses.py~~ [-~~h] [~~-~~n NPOSES~~] [-~~o OUTPREFIX] [~~-~~j NPROCESSES~~] [--id-~~file INPUT_ID_FILE~~] [--~~verbose] [--quiet] [~~--~~log-interval LOG_INTERVAL~~] dockresults_path		[--verbose] [--quiet] [--log-interval LOG_INTERVAL]
			[--find-min-size FIND_MIN_SIZE]
			dockresults_path

	Retrieve the top N poses from docking results		Retrieve the top N poses from docking results

	positional arguments:		positional arguments:
	dockresults_path Can be either a directory containing docking results, or a file where each line points to a docking results file.		dockresults_path Can be either a directory containing docking results, or a file where each
			line points to a docking results file.

	optional arguments:		optional arguments:
	-h, --help show this help message and exit		-h, --help show this help message and exit
	-n NPOSES How many top poses to retrieve, default of 150000		-n NPOSES How many top poses to retrieve, default of 150000
	-o OUTPREFIX Output file prefix. Each run will produce two files, a mol2.gz containing pose data, and a .scores file containing relevant score information. Default is "top_poses"		-o OUTPREFIX Output file prefix. Each run will produce two files, a mol2.gz containing
	-j NPROCESSES How many processes should be dedicated to this run, default is 2. If your files are spread across multiple disks, increasing this number will improve performance.		pose data, and a .scores file containing relevant score information.
			Default is "top_poses"
			-j NPROCESSES How many processes should be dedicated to this run, default is 2. If your
			files are spread across multiple disks, increasing this number will
			improve performance.
	--id-file INPUT_ID_FILE		--id-file INPUT_ID_FILE
	Only retrieve poses matching ids specified in an external file.		Only retrieve poses matching ids specified in an external file.
Line 85:		Line 92:
	--log-interval LOG_INTERVAL		--log-interval LOG_INTERVAL
	number of poses between log statements. Ignored if --quiet enabled		number of poses between log statements. Ignored if --quiet enabled
			--find-min-size FIND_MIN_SIZE
			filter out test.mol2.gz* files below a minimum bytes size
	</nowiki>		</nowiki>

Btingle: /* Conda Environment */

2023-03-02T21:30:25Z

Conda Environment

← Older revision		Revision as of 21:30, 2 March 2023
Line 12:		Line 12:

	<nowiki>		<nowiki>
	conda create -n py311 python==3.11</nowiki>		conda create -n py311 python==3.11
			conda activate py311</nowiki>

	No other packages are required!		No other packages are required!

Btingle: /* Location of new scripts/Install Instructions */

2023-03-02T21:30:01Z

Location of new scripts/Install Instructions

← Older revision		Revision as of 21:30, 2 March 2023
Line 1:		Line 1:
	== Location of new scripts/Install Instructions ==		== Location of new scripts/Install Instructions ==

	You can retrieve these scripts from the ~~DOCK 3.8~~ repository ~~@ https://~~github.~~com/docking-org/DOCK/tree/dev~~		You can retrieve these scripts from the "docktop" repository on github, which is public.

	<nowiki>		<nowiki>git clone https://github.com/docking-org/docktop.git</nowiki>
	git clone https://github.com/docking-org/docktop.git
	~~cd DOCK~~
	~~git checkout dev~~</nowiki>

	~~The scripts are located @ analysis/top_poses in the DOCK repository.~~

	= Python 3.8+ =		= Python 3.8+ =

Btingle: /* Location of new scripts/Install Instructions */

2023-03-02T21:18:56Z

Location of new scripts/Install Instructions

← Older revision		Revision as of 21:18, 2 March 2023
Line 4:		Line 4:

	<nowiki>		<nowiki>
	git clone https://github.com/docking-org/~~DOCK~~.git		git clone https://github.com/docking-org/docktop.git
	cd DOCK		cd DOCK
	git checkout dev</nowiki>		git checkout dev</nowiki>

Btingle: /* Conda Environment */

2023-03-02T21:07:51Z

Conda Environment

← Older revision		Revision as of 21:07, 2 March 2023
Line 17:		Line 17:

	<nowiki>		<nowiki>
	conda create -n ~~py38~~ python>=3.8</nowiki>		conda create -n py311 python==3.11</nowiki>

	No other packages are required!		No other packages are required!

Btingle: /* Manual Install */

2023-03-02T21:02:43Z

Manual Install

← Older revision		Revision as of 21:02, 2 March 2023
Line 22:		Line 22:

	== Manual Install ==		== Manual Install ==

	You need to include a link to a python3.8 executable in the top_poses directory for run_top_poses.bash and run_top_poses_mr.bash to work. This needs to be a link, you cannot copy the executable- it expects to be installed in particular directory. There are no pip requirements, just a blank python 3.8 install.

	<b>On Wynton you can use the version installed @ /wynton/group/bks/soft/python-versions/python-3.8-install</b>		<b>On Wynton you can use the version installed @ /wynton/group/bks/soft/python-versions/python-3.8-install</b>

Btingle: /* Python 3.8+ */

2023-03-02T21:02:14Z

Python 3.8+

@@ Line 46: / Line 46: @@
 # rm Python-3.8.8.tgz</nowiki>
-== Scripts Description ==
+= top_poses.py =
-=== top_poses.py ===
+== Description ==
 Main pose retrieval algorithm, runs on multiple processes.
@@ Line 72: / Line 70: @@
 Output prefix is where the top N poses will be written out when the script has finished. e.g /scratch/top_poses.mol2.gz, as well as a human-readable .scores file.
-==== Usage ====
+== Usage ==
   <nowiki>
@@ Line 95: / Line 93: @@
 </nowiki>
-==== Note on Parallel Processing ====
+== Note on Parallel Processing ==
 By default, this script allocates two extra threads (-j 2) to read in files. This ensures that the main thread can sort poses uninterrupted, while the others take care of the grunt work of reading and annotating files. Increasing the number of reader threads beyond two does not guarantee an improvement in performance, but depending on the filesystem(s) your docking poses live on, they could. For example, on Wynton it can be helpful to allocate up to 8 extra threads for reading files, due to the way the filesystem works on Wynton. On the BKS cluster, increasing the number of reader threads beyond two will have a negligible (or even negative) impact, unless your files happen to be striped across multiple servers.
 == Checking Logs ==
-After your jobs have finished, check the logs to see if anything went wrong.
+If everything went smoothly, your log should end with a string of text that looks like this:
   <nowiki>
@@ Line 154: / Line 106: @@
 done processing! writing out...
 / 300000</nowiki>
 You may also see a message that looks like this:
@@ Line 165: / Line 113: @@
 This just indicates slowness in the file reading, and is common to see at the beginning of a log or when the filesystem is under high load.
 [[Category:DOCK 3.8]]

Btingle at 20:59, 2 March 2023

2023-03-02T20:59:35Z

← Older revision		Revision as of 20:59, 2 March 2023
Line 10:		Line 10:
	The scripts are located @ analysis/top_poses in the DOCK repository.		The scripts are located @ analysis/top_poses in the DOCK repository.

	=== Python 3.8+ ===		= Python 3.8+ =

	== Conda Environment ==		== Conda Environment ==

Btingle: /* Python 3.8 */

2023-03-02T20:59:16Z

Python 3.8

← Older revision		Revision as of 20:59, 2 March 2023
Line 10:		Line 10:
	The scripts are located @ analysis/top_poses in the DOCK repository.		The scripts are located @ analysis/top_poses in the DOCK repository.

	=== Python 3.8 ===		=== Python 3.8+ ===

			== Conda Environment ==

			The simplest way to source python 3.8+ is to just install via conda.

			<nowiki>
			conda create -n py38 python>=3.8</nowiki>

			No other packages are required!

			== Manual Install ==

	You need to include a link to a python3.8 executable in the top_poses directory for run_top_poses.bash and run_top_poses_mr.bash to work. This needs to be a link, you cannot copy the executable- it expects to be installed in particular directory. There are no pip requirements, just a blank python 3.8 install.		You need to include a link to a python3.8 executable in the top_poses directory for run_top_poses.bash and run_top_poses_mr.bash to work. This needs to be a link, you cannot copy the executable- it expects to be installed in particular directory. There are no pip requirements, just a blank python 3.8 install.