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DaliLite (REST)

Description

Pairwise alignment of structures using DaliLite 1) 2).

For more information see:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 30 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

Retirement notice: DaliLite will be retired from service in August 2015. If you have any questions/concerns please contact the helpdesk.

Clients

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
Perl dalilite_lwp.pl LWP and XML::Simple

For further details of these tool-kits and workflow platforms see our Guide to Web Services.

WADL

The WADL for the DaliLite (REST) service: http://www.ebi.ac.uk/Tools/services/rest/dalilite?wadl

Resources

The service consists of a number of resources which indicate errors through the use of HTTP status codes.

parameters

List parameter names.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/dalilite/parameters/

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/parameterdetails/$parameterId
Parameters $parameterId: the name of the parameter

Response

An XML document providing details about the parameter.

For example: http://www.ebi.ac.uk/Tools/services/rest/dalilite/parameterdetails/structure1.

If the named parameter does not exist for the tool, a 400 HTTP status code will be returned with the message “com.sun.jersey.api.container.ContainerCheckedException: java.lang.Exception: parameter not found”.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
structure1 First structure. Either a PDB identifier (in DB:id format) or coordinates in PDB format.
chainid1 Identifier of a chain in the first structure to align, if not specified all chains will be aligned.
structure2 Second structure. Either a PDB identifier (in DB:id format) or coordinates in PDB format.
chainid2 Identifier of a chain in the second structure to align, if not specified all chains will be aligned.

Note: this request must be made using POST, if GET is used a 405 HTTP status is returned with the description “The specified HTTP method is not allowed for the requested resource”.

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

Response

A plain text document containing the job identifier.

status

Get the status of a submitted job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/status/$jobId
Parameters $jobId: job identifier

Response

A plain text document containing the job status.

The values for the status are:

  • RUNNING: the job is currently being processed.
  • FINISHED: job has finished, and the results can then be retrieved.
  • ERROR: an error occurred attempting to get the job status.
  • FAILURE: the job failed.
  • NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: JDispatcher.

resulttypes

Get available result types for a finished job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/resulttypes/$jobId
Parameters $jobId: job identifier

Response

An XML document detailing the available result types.

result

Get the job result of the specified type.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/result/$jobId/$resultType
Parameters $jobId: job identifier
$resultType: type of result to retrieve. See resulttypes.

or

URL http://www.ebi.ac.uk/Tools/services/rest/dalilite/result/$jobId/$resultType?alignmentno=$alignmentno
Parameters $jobId: job identifier
$resultType: type of result to retrieve. See resulttypes.
$alignmentno: number of the alignment to retrieve.

Response

A document containing the result in the requested format. The MIME type of the returned document is set according to the format.

When retrieving a result where more than one specific result is available, for example the calphatraces and rt result types where there is a result for each alignment pair, the specific result to retrieve is specified using the optional alignmentno parameter. The number of alignments is available in the nalignments result type, see resulttypes for details of the available result types for the job.

1) Holm L. and Sander C. (1996)
Mapping the protein universe.
Science 273(5275):595-603
PMID: 8662544
DOI: 10.1126/science.273.5275.595
2) Holm L. and Park J. (2000)
DaliLite workbench for protein structure comparison.
Bioinformatics 16(6):566-7
PMID: 10980157
DOI: 10.1093/bioinformatics/16.6.566
 
services/structure/dalilite_rest.txt · Last modified: 2015/02/27 10:18 by apc
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