MotiveValidator:Technical details - Revision history

Lukas at 15:18, 10 August 2015

2015-08-10T15:18:49Z

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	</references>		</references>


			'''Return to the [[MotiveValidator:UserManual \| Table of contents]].'''

Lukas at 16:08, 5 August 2015

2015-08-05T16:08:44Z

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 This is help for version 1.1.14.11.7c or newer. The help text for other versions be viewed using the --help command when running the application.
 == Running the Service ==
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 In .NET languages, the file can be parsed into the type <code>WebChemistry.MotiveValidator.DataModel.ValidationResult</code> from the library <code>WebChemistry.MotiveValidator.DataModel</code> using the <code>Newtonsoft.Json</code> or similar library. Other straightforward analysis tool for this file is JavaScript (for example in browser or using Node.js).

Lukas: Lukas moved page MotiveValidator:Command Line Help to MotiveValidator:Technical details

2015-08-05T16:05:56Z

Lukas moved page MotiveValidator:Command Line Help to MotiveValidator:Technical details

← Older revision	Revision as of 16:05, 5 August 2015
(No difference)

Lukas: /* index.json */

2015-08-05T15:58:24Z

index.json

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	File that contains complete information about the result of validation of each motif, as well as list of warnings and errors, list of general errors, number of validated motifs, validation type and MotiveValidator version. This file is used to display the data in the web UI.		File that contains complete information about the result of validation of each motif, as well as list of warnings and errors, list of general errors, number of validated motifs, validation type and MotiveValidator version. This file is used to display the data in the web UI.

	In .NET languages, the file can be parsed into the type WebChemistry.MotiveValidator.DataModel.ValidationResult from the library 'WebChemistry.MotiveValidator.DataModel' using the Newtonsoft.Json or similar library. Other straightforward analysis tool for this file is JavaScript (for example in browser or using Node.js).		In .NET languages, the file can be parsed into the type <code>WebChemistry.MotiveValidator.DataModel.ValidationResult</code> from the library <code>WebChemistry.MotiveValidator.DataModel</code> using the <code>Newtonsoft.Json</code> or similar library. Other straightforward analysis tool for this file is JavaScript (for example in browser or using Node.js).

Lukas at 22:59, 10 November 2014

2014-11-10T22:59:37Z

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	* '''ModelsSource''' [ String ]		* '''ModelsSource''' [ String ]
	: ''Folder or zip file with models in PDB (and SD/SDF/MOL for bonds) format. Alternatively, use the new PDB standard '''mmCIF'''.''		: ''Folder or zip file with models in PDB (and SD/SDF/MOL for bonds) format. Alternatively, use the new PDB standard '''mmCIF (*.cif)'''.''

	* '''IsModelsSourceComponentDictionary''' [ Boolean ]		* '''IsModelsSourceComponentDictionary''' [ Boolean ]

Lukas at 22:59, 10 November 2014

2014-11-10T22:59:02Z

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	* '''InputFolder''' [ String ]		* '''InputFolder''' [ String ]
	: ''Folder with the input data. Each molecule to be validated has to be in a separate file. Supported file formats: .pdb; .pdbX, .cif, .pqr, .mol. Gzip compression (.~~gzip~~) is also supported.''		: ''Folder with the input data. Each molecule to be validated has to be in a separate file. Supported file formats: .pdb; .pdbX, .cif, .pqr, .mol. Gzip compression (.gz) is also supported.''

	* '''ModelsSource''' [ String ]		* '''ModelsSource''' [ String ]

Lukas: /* Attributes */

2014-11-10T22:55:26Z

Attributes

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	* '''InputFolder''' [ String ]		* '''InputFolder''' [ String ]
	: ''Folder with the input data.''		: ''Folder with the input data. Each molecule to be validated has to be in a separate file. Supported file formats: .pdb; .pdbX, .cif, .pqr, .mol. Gzip compression (.gzip) is also supported.''

	* '''ModelsSource''' [ String ]		* '''ModelsSource''' [ String ]
	: ''Folder or zip file with models in PDB (and SD/SDF/MOL for bonds) format.''		: ''Folder or zip file with models in PDB (and SD/SDF/MOL for bonds) format. Alternatively, use the new PDB standard '''mmCIF'''.''

	* '''IsModelsSourceComponentDictionary''' [ Boolean ]		* '''IsModelsSourceComponentDictionary''' [ Boolean ]

Lukas: /* ValidationTypes */

2014-11-10T22:13:10Z

ValidationTypes

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	* '''CustomModels'''		* '''CustomModels'''
	: ''Automatically identifies and validates input models.''		: ''Automatically identifies and validates input models within the PDB structures.''

	* '''Database'''		* '''Database'''

Lukas at 22:11, 10 November 2014

2014-11-10T22:11:05Z

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	This is help for version 1.1.14.11.7b or newer. The help text for other versions be viewed using the --help command when running the application.		This is help for version 1.1.14.11.7c or newer. The help text for other versions be viewed using the --help command when running the application.
	== Running the Service ==		== Running the Service ==
	The service can be executed using the command (latest .NET Framework required):		The service can be executed using the command (latest .NET Framework required):

Lukas: Update to version 1.1.14.11.7b

2014-11-10T21:24:51Z

Update to version 1.1.14.11.7b

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	This is help for version 1.0.13.12.3 or newer. The help text for other versions be viewed using the --help command when running the application.		This is help for version 1.1.14.11.7b or newer. The help text for other versions be viewed using the --help command when running the application.
	== Running the Service ==		== Running the Service ==
	The service can be executed using the command (latest .NET Framework required):		The service can be executed using the command (latest .NET Framework required):
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	In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:		In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:
	<pre>mono WebChemistry.MotiveValidator.Service.exe workingFolder configuration.json</pre>		<pre>mono WebChemistry.MotiveValidator.Service.exe workingFolder configuration.json</pre>
	~~To run the application, OpenBabel 2.3.2 must be installed. The application was only tested on Windows (.NET) environment and might not work correctly on Linux/MacOS due to the OpenBabel requirement.~~

	== Configuration ==		== Configuration ==
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	=== Configuration Example ===		=== Configuration Example ===
	This is the general shape of the JSON input configuration.		This is the general shape of the JSON input configuration.
	<pre> {		<pre>{
	"ValidationType": "Model",		"ValidationType": "Model",
	"InputFolder": "./MAN",		"InputFolder": "./MAN",
	"ModelsSource": "./MAN_Models",		"ModelsSource": "./MAN_Models",
			"IsModelsSourceComponentDictionary": false,
			"IgnoreObsoleteComponentDictionaryEntries": false,
	"SummaryOnly": false,		"SummaryOnly": false,
	}		"DatabaseModeMinModelAtomCount": 0,
	</pre>		"DatabaseModeIgnoreNames": [],
			"MaxDegreeOfParallelism": 8
			}</pre>

	There has to be exactly one configuration file for each validation run. Every value, as well as settings' names, is surrounded in quotation marks (" " or ' '). Backslashes (\) have to be escaped (\\). File system paths can be absolute as well as relative (/ works as well in paths).		There has to be exactly one configuration file for each validation run. Every value, as well as settings' names, is surrounded in quotation marks (" " or ' '). Backslashes (\) have to be escaped (\\). File system paths can be absolute as well as relative (/ works as well in paths).
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	: ''Folder with the input data.''		: ''Folder with the input data.''

	* '''~~ModelsFolder~~''' [ String ]		* '''ModelsSource''' [ String ]
	: ''Folder with models in PDB (and SD/SDF/MOL for bonds) format.''		: ''Folder or zip file with models in PDB (and SD/SDF/MOL for bonds) format.''

			* '''IsModelsSourceComponentDictionary''' [ Boolean ]
			: ''Determines if the ModelsSource is a CIF file containing models to be validated.''

			* '''IgnoreObsoleteComponentDictionaryEntries''' [ Boolean ]
			: ''Determines if to ignore Component Dictionary entries with _chem_comp.pdbx_release_status = OBS flag.''

	* '''SummaryOnly''' [ Boolean ], Default value = false		* '''SummaryOnly''' [ Boolean ], Default value = false
	: ''Determines whether to compute only the summary file and not files with motifs.''		: ''Determines whether to compute only the summary file and not files with motifs.''

			* '''DatabaseModeMinModelAtomCount''' [ Int32 ]
			: ''Determines the minimum number of atoms a model needs to have.''

			* '''DatabaseModeIgnoreNames''' [ String[] ]
			: ''Residues to ignore in the database mode.''

			* '''MaxDegreeOfParallelism''' [ Int32 ], Default value = 8
			: ''Max degree of parallelism.''

	=== Descriptions ===		=== Descriptions ===
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	* '''CustomModels'''		* '''CustomModels'''
	: ''Automatically identifies and validates input models.''		: ''Automatically identifies and validates input models.''

			* '''Database'''
			: ''Special mode for creating ValidatorDB.''

			* '''DatabaseCustom'''
			: ''Special mode for creating custom ValidatorDB analysis.''

	== Output Description ==		== Output Description ==
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	* '''result''' - ''Folder with computation result.''		* '''result''' - ''Folder with computation result.''
	:: result.zip - ''A zip archive with compressed result.''		:: result.zip - ''A zip archive with compressed result.''
	::: ~~[[#index.csv_description \| index~~.csv]] - ''File that contains complete information about the result of validation of each motif in a compressed manner.''		::: result.csv - ''File that contains complete information about the result of validation of each motif in a compressed manner.''
	::: ~~[[#index.json_description \| index~~.json]] - ''File that contains complete information about the result of validation of each motif, as well as list of warnings and errors, list of general errors, number of validated motifs, validation type and MotiveValidator version.''		::: result.json - ''File that contains complete information about the result of validation of each motif, as well as list of warnings and errors, list of general errors, number of validated motifs, validation type and MotiveValidator version.''
	::: general_errors.csv - ''File that contains list of general errors.''		::: general_errors.csv - ''File that contains list of general errors.''
	::* '''[3-letter residue code]''' - ''A folder for each input model.''		::* '''[3-letter residue code]''' - ''A folder for each input model.''
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	:::* '''mols''' - ''Folder that contains validated motifs in mol format.''		:::* '''mols''' - ''Folder that contains validated motifs in mol format.''
	:::* '''motifs''' - ''Folder that contains validated motifs in PDB format.''		:::* '''motifs''' - ''Folder that contains validated motifs in PDB format.''
			:::* '''notanalyzed''' - ''Folder that contains motifs that were not validated.''
	:::: errors.csv - ''File that contains list of errors.''		:::: errors.csv - ''File that contains list of errors.''
	~~:::: chirality.csv - ''File that contains summary information about chirality problems among validated motifs.''~~
	:::: pairing.csv - ''File that contains pairing matrix of motifs' atoms versus model's atoms.''		:::: pairing.csv - ''File that contains pairing matrix of motifs' atoms versus model's atoms.''
	:::: summary.json - ''File that contains rich summary of each single validation run.''		:::: summary.json - ''File that contains rich summary of each single validation run.''
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	* '''Id''' [ String ]		* '''Id''' [ String ]
	: ''Name of the validated motif without extension.''		: ''Name of the validated motif without extension.''
			* '''State''' [ String ]
			: ''Validation state of the entry.''
	* '''MainResidue''' [ String ]		* '''MainResidue''' [ String ]
	: ''Name and number of main residue of validated motif''		: ''Name and number of main residue of validated motif''
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	: ''Number of atoms in validated motif that have been substituted with other element.''		: ''Number of atoms in validated motif that have been substituted with other element.''
	* '''WrongBondCount''' [ Number ]		* '''WrongBondCount''' [ Number ]
	: ''Number of wrong bonds~~. Currently unused~~.''		: ''Number of wrong bonds.''
	* '''~~InternalBabelBondDiscrepancy~~''' [ Number ]		* '''BondDiscrepancy''' [ Number ]
	: ''Signals whether the ~~OpenBabel~~ bond(s) differ from the ~~internally computed~~ ones.''		: ''Signals whether the matched motif bond(s) differ from the model ones.''
	* '''MissingAtoms''' [ String ]		* '''MissingAtoms''' [ String ]
	: ''List of atoms from validated motif that are considered missing. Each entry of this list consists of atom name, atom element and index of atom from the model that does not have its counterpart in this motif.''		: ''List of atoms from validated motif that are considered missing. Each entry of this list consists of atom name, atom element and index of atom from the model that does not have its counterpart in this motif.''