Fetch PDB flatfile from RCSB server
Created: 2010-07-04 18:34:57
Last updated: 2010-07-04 18:34:59
Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB
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Workflow Components
Authors (1)
Titles (1)
Fetch PDB flatfile from RCSB server |
Descriptions (1)
Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB |
Dependencies (0)
Inputs (1)
Name |
Description |
pdbID |
PDB identifier such as '1crn'
|
Processors (5)
Name |
Type |
Description |
AddPrefixToID |
localworker |
Scriptoutput = string1 + string2; |
AddSuffix |
localworker |
Scriptoutput = string1 + string2; |
FetchPage |
localworker |
ScriptURL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
} else {
inputURL = new URL(url);
}
byte[] contents;
if (inputURL.openConnection().getContentLength() == -1) {
// Content size unknown, must read first...
byte[] buffer = new byte[1024];
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
totalBytesRead += bytesRead;
bytesRead = is.read(buffer, 0, 1024);
}
contents = new byte[totalBytesRead];
} else {
contents = new byte[inputURL.openConnection().getContentLength()];
}
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
totalBytesRead += bytesRead;
if (contents.length==totalBytesRead) break;
}
image = contents;
|
RCSBPrefix |
stringconstant |
Valuehttp://www.rcsb.org/pdb/cgi/export.cgi/1CRN.pdb?format=PDB&pdbId= |
RCSBSuffix |
stringconstant |
Value&compression=None |
Outputs (1)
Name |
Description |
pdbFlatFile |
|
Datalinks (6)
Source |
Sink |
RCSBPrefix:value |
AddPrefixToID:string1 |
pdbID |
AddPrefixToID:string2 |
RCSBSuffix:value |
AddSuffix:string2 |
AddPrefixToID:output |
AddSuffix:string1 |
AddSuffix:output |
FetchPage:url |
FetchPage:image |
pdbFlatFile |
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Version 1
(of 1)
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