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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include "version.h"
using namespace std;
using namespace BALL;
int main(int argc, char* argv[])
{
// instantiate CommandlineParser object
CommandlineParser parpars("ExtractProteinChains", "separate all chains of a pdb file into separate pdb files", VERSION, String(__DATE__), "Preparation");
parpars.registerMandatoryInputFile("pdb", "input pdb file ");
parpars.registerOptionalStringParameter("chain_id", "chain to extract ");
//TODO
//parpars.registerFlag("skip_nonaa", "skip all non aminoacids", false);
parpars.registerMandatoryOutputFile("o", "output file name ");
parpars.setParameterAsHidden("o");
// parameters for galaxy for handling multiple output files
parpars.registerOptionalGalaxyOutputId("o_id", "output id", "$o.id");
// need to be hidden in command line mode
parpars.setParameterAsAdvanced("o_id");
parpars.setParameterAsHidden("o_id");
// parameters for galaxy for handling multiple output files
parpars.registerOptionalGalaxyOutputFolder("o_dir", "output directory for 2nd to last solution", "$__new_file_path__");
// need to be hidden in command line mode
parpars.setParameterAsAdvanced("o_dir");
parpars.setParameterAsHidden("o_dir");
// the manual
String man = String("This tool splits a pdb file into its chains.");
parpars.setToolManual(man);
parpars.setSupportedFormats("pdb", "pdb");
parpars.setSupportedFormats("o", "pdb");
// parse the command line
parpars.parse(argc, argv);
PDBFile pdb;
pdb.open(parpars.get("pdb"), std::ios::in);
if (!pdb)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("pdb") << " for input." << std::endl;
exit(2);
}
System sys;
pdb >> sys;
pdb.close();
// called as command line or e.g. via galaxy?
bool is_cmd = !parpars.has("env")
|| ((parpars.has("env") && parpars.get("env")=="cmdline"));
// get the optional chain_id
String chain_id = "";
if (parpars.has("chain_id"))
{
chain_id = parpars.get("chain_id");
}
/* else if ( is_cmd && (parpars.get("o_dir") == "$__new_file_path__"))
{
Log.error() << endl << "unspecified parameter o_dir. Abort." << endl;
return 2;
}
*/
int export_counter = 0;
ChainConstIterator c_it = sys.beginChain();
for (; +c_it ; ++c_it)
{
if ((chain_id == "") || (chain_id == c_it->getName()))
{
// create the output name
String outfile_name = String(parpars.get("o")) + "chain_" + String(export_counter) + ".pdb";
//TODO this is a temporary hack :-(
// are we given a parameter o_dir
if (parpars.has("o_dir") && is_cmd && (parpars.get("o_dir") != "$__new_file_path__"))
{
outfile_name = String(parpars.get("o_dir")) + "/" + c_it->getName() + "_" + outfile_name;
}
// NOTE: Galaxy requires this strange naming convention
// including the fact, that zero-th element has a different name
if (!is_cmd)
{
outfile_name = (export_counter == 0) ? String(parpars.get("o"))
: String(parpars.get("o_dir")) + "/primary_"
+ String(parpars.get("o_id")) + "_chain" + String(export_counter)
+ "_visible_pdb";
}
// now write the chain
PDBFile outfile(outfile_name, ios::out);
if (outfile.bad())
{
Log.error() << endl << "cannot write file " << outfile_name << endl;
return 2;
}
outfile << *c_it;
outfile.close();
Log << "wrote file " << outfile_name << endl;
export_counter++;
}
}
return 0;
}
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