DASiR (version 1.12.0)

getDasStructure: Query a protein 3D structure to session's DAS server

Description

This function retrieves the 3D structure,including metadata and coordinates for the given query(ID of the reference structure) using the data source id (or title) in the session's DAS server.

Usage

getDasStructure(source, query)

Arguments

source

Data source id (or title). See getDasSource

query

Query id

Value

data.frame with the following columns: x,y,z,atomName,atomID, occupancy,tempFactor,type,groupID,name, which match with the contents of the reference structure of the given query.If there are not matching results, output is NULL.

Details

This function allows to query the DAS server and returns the the 3D structure,including metadata and coordinates for the given query (id of the reference structure).

Please, be sure to pass the identifiers EXACTLY as the values returned by the functions available here (DAS is case-sensitive). It is also recommended that you check the capabilities for each of the data sources.

Please, notice that this function codes the parameters in a URL to query the server. This function could fail if you ask for a reference structure that does not exist. Also, notice that the speed of the query depends on the number of elements and the load in the server.

Please, use this function smartly and do not overload servers.

See Also

getDasFeature getDas-functions getDasSequence

Examples

    # Set DAS server
    setDasServer(server="http://das.cathdb.info/das")

    source <- "cath_pdb"
    query <- "1hck"  # PDB code

    structure <- getDasStructure(source, query)
    head(structure)