Workflow Entry: Structure_or_ID

Created at: 06/06/08 @ 05:57:31

Version 1 (of 1)

Version created on: 06/06/08 @ 05:57:31 by: Hamish McWilliam | Revision comments Expand

Title: Structure_or_ID

Type: Taverna 1

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Description

Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format.

If a structure identifier, in database:identifier format, is input the EBI’s WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output.

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Workflow Components

Inputs (1)

Name	Description
Structure_or_ID	Either a atructure in PDB format or a PDB entry identifer in database:identifier format (e.g. PDB:1crn).

Processors (5)

Name	Type	Description
Fail_if_identifer	local	Fails if the workflow input is an identifier (i.e. is an actual structure).
Fail_if_structure	local	Fails if the workflow input was a structure (i.e. is an identifer).
Is_structure	beanshell	Return true if the input is a structure or false if the input is a structure identifer (e.g. PDB:1crn).
fetchData	arbitrarywsdl	Fetch the structure in PDB format from the identifer using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
Use_structure	beanshell	Pass the input structure to the output.

Outputs (1)

Name	Description
Structure	Structure in PDB format.

Links (7)

Sink	Source
Is_structure:structure	Structure_or_ID
fetchData:query	Structure_or_ID
Fail_if_identifer:test	Is_structure:is_structure
Fail_if_structure:test	Is_structure:is_structure
Use_structure:in_structure	Structure_or_ID
Structure	Use_structure:out_structure
Structure	fetchData:fetchDataReturn