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.
Fails if the workflow input is an identifier (i.e. is an actual structure).
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Fails if the workflow input was a structure (i.e. is an identifer).
org.embl.ebi.escience.scuflworkers.java.FailIfTrue
Return true if the input is a structure or false if the input is a structure identifer (e.g. PDB:1crn).
lineLen = structure.indexOf("\n");
if(lineLen < 1) {
lineLen = structure.length();
}
if(!structure.startsWith("ID ") &&
structure.indexOf(":") > 0 &&
structure.indexOf(":") < lineLen) {
is_structure = "false";
} else {
is_structure = "true";
}
structure
is_structure
Fetch the structure in PDB format from the identifer using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
pdb
raw
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl
fetchData
Pass the input structure to the output.
out_structure = in_structure;
in_structure
out_structure
Either a atructure in PDB format or a PDB entry identifer in database:identifier format (e.g. PDB:1crn).
chemical/x-pdb
Structure in PDB format.
Completed
Fail_if_structure
fetchData
Scheduled
Running
Completed
Fail_if_identifer
Use_structure
Scheduled
Running