MotiveValidator:MotifExtractor Help - Revision history

Dave: Dave moved page MotiveValidator: MotifExtractor Help to MotiveValidator:MotifExtractor Help

2014-06-11T15:26:04Z

Dave moved page MotiveValidator: MotifExtractor Help to MotiveValidator:MotifExtractor Help

← Older revision	Revision as of 15:26, 11 June 2014
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Dave: Dave moved page MotiveValidator MotifExtractor Help to MotiveValidator: MotifExtractor Help

2014-06-11T15:23:10Z

Dave moved page MotiveValidator MotifExtractor Help to MotiveValidator: MotifExtractor Help

← Older revision	Revision as of 15:23, 11 June 2014
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Dave: /* Execution */

2013-12-14T16:41:58Z

Execution

← Older revision		Revision as of 16:41, 14 December 2013
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	== Execution ==		== Execution ==
	* Windows		* Windows
	: Open the utility cmd, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as "MotiveQuery.exe path_to_output motifs.json~~" (without the ")~~. For example:		: Open the utility cmd, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as <code>MotiveQuery.exe path_to_output motifs.json</code>. For example:
	<pre>MotiveQuery c:\data\nag_motifs motifs.json</pre>		<pre>MotiveQuery c:\data\nag_motifs motifs.json</pre>

	* Linux and MacOS		* Linux and MacOS
	: Open a terminal, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as "mono MotiveQuery.exe path_to_output motifs.json~~" (without the ")~~.		: Open a terminal, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as <code>mono MotiveQuery.exe path_to_output motifs.json</code>.

Dave at 16:28, 14 December 2013

2013-12-14T16:28:26Z

← Older revision		Revision as of 16:28, 14 December 2013
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	== Output ==		== Output ==
	A .zip ~~archive~~ containing		A folder containing:
	* ~~Folders~~ with motifs in PDB format.		* Information about the progress of the computation (<code>log.txt</code>, <code>status.json</code>).
	* CSV files with ~~list~~ of motifs ~~and their unique identifier (motif index)~~.		* ZIP file <code>result\motives.zip</code> containing:
			:* A folder with motifs in PDB format (one for each motif specified in the input).
			:* CSV files with detailed information about the found motifs.
			* JSON file <code>result\summary.json</code> with the number of found motifs.

	== Execution ==		== Execution ==

Dave: Created page with "MotifExtractor is a simple automated script for extracting the motifs of interest from biomolecule structure files. You may define one or more motifs to be extracted from a se..."

2013-12-14T16:06:33Z

Created page with "MotifExtractor is a simple automated script for extracting the motifs of interest from biomolecule structure files. You may define one or more motifs to be extracted from a se..."

New page

MotifExtractor is a simple automated script for extracting the motifs of interest from biomolecule structure files. You may define one or more motifs to be extracted from a set of biomolecules stored in PDB format.

== Requirements ==
* Windows: .NET 4.5 or newer
* Linux and MacOS: MONO 3.2.3 or newer

== Input ==
* A folder with a set of biomolecules in PDB format.
* A .json file with settings, defining the motif(s) to be extracted. The key parameters of the .json file are encoded in attributes, that you will need to edit depending on what you want to extract and from where:

:# Location of the folder with biomolecules - attribute "InputFolders". When writing the path to your folder, note that backslashes must be escaped (so <code>C:\Data\pdb</code> should be written as <code>C:\\Data\\pdb</code>), or forward slash can be used (<code>C:/Data/pdb</code>).
:# Name of query residue - attributes "Id", "Name", and "Residues". Write the 3-letter code for the residue of interest.

== Output ==
A .zip archive containing
* Folders with motifs in PDB format.
* CSV files with list of motifs and their unique identifier (motif index).

== Execution ==
* Windows
: Open the utility cmd, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as "MotiveQuery.exe path_to_output motifs.json" (without the "). For example:
<pre>MotiveQuery c:\data\nag_motifs motifs.json</pre>

* Linux and MacOS
: Open a terminal, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as "mono MotiveQuery.exe path_to_output motifs.json" (without the ").