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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// A very simple utility for splitting a trajectory file into
// several pdb snapshots of a system
//
#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/trajectoryFile.h>
#include <BALL/FORMAT/trajectoryFileFactory.h>
#include <BALL/MOLMEC/COMMON/snapShot.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <iostream>
#include "version.h"
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
CommandlineParser parpars("TrajectoryFile2PDBSplitter", "splits SnapShots into PDB files ", VERSION, String(__DATE__), "Convert, combine and store");
parpars.registerMandatoryInputFile("i_traj", "input trajectory file");
parpars.registerMandatoryInputFile("i_pdb", "input pdb-file");
parpars.registerMandatoryOutputFile("o", "output pdb-file for first solution");
parpars.setParameterAsHidden("o");
// parameters for galaxy for handling multiple output files
parpars.registerOptionalGalaxyOutputId("o_id", "output id", "$o.id");
// need to be hidden in command line mode
parpars.setParameterAsAdvanced("o_id");
parpars.setParameterAsHidden("o_id");
// parameters for galaxy for handling multiple output files
parpars.registerOptionalGalaxyOutputFolder("o_dir", "output directory for 2nd to last pdb file", "$__new_file_path__");
// need to be hidden in command line mode
parpars.setParameterAsAdvanced("o_dir");
parpars.setParameterAsHidden("o_dir");
// the manual
String man = "This tool splits SnapShots of a given TrajectoryFile and the reference PDBFile into separate PDBFiles.\n\nParameters are the input SnapShots as TrajectoryFile (-i_traj), the corresponding reference pdb file that was originally used to create the TrajectoryFile (-i_pdb) and a naming schema for the results (-o).\n\nOutput of this tool is a number of PDBFiles each containing one SnapShot.";
parpars.setToolManual(man);
// here we set the types of I/O files
parpars.setSupportedFormats("i_traj", "dcd");
parpars.setSupportedFormats("i_pdb", "pdb");
parpars.setSupportedFormats("o", "pdb");
parpars.parse(argc, argv);
//////////////////////////////////////////////////
// read the input
PDBFile pdb;
pdb.open(parpars.get("i_pdb"));
System sys;
pdb.read(sys);
SnapShot ss;
TrajectoryFile *traj_file = TrajectoryFileFactory::open(parpars.get("i_traj"));
Size num_ss = traj_file->getNumberOfSnapShots();
// called as command line or e.g. via galaxy?
bool is_cmd = !parpars.has("env")
|| ((parpars.has("env") && parpars.get("env")=="cmdline"));
for (Size i=0; i< num_ss; i++)
{
// create the output name
String outfile_name = String(parpars.get("o")) + "_snapshot_" + String(i) + ".pdb";
if (parpars.has("o_dir"))
{
outfile_name = String(parpars.get("o_dir")) + "/" + 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 = (i == 0) ? String(parpars.get("o"))
: String(parpars.get("o_dir")) + "/primary_"
+ String(parpars.get("o_id")) + "_snapshot" + String(i)
+ "_visible_pdb";
}
Log << " write SnapShot " << i << " as " << outfile_name << endl;
if (traj_file->read(ss))
{
System sys_temp(sys);
ss.applySnapShot(sys_temp);
PDBFile file(outfile_name, ios::out);
if (file.bad())
{
Log.error() << "cannot write file " << outfile_name << endl;
return 2;
}
file << sys_temp;
file.close();
}
else
break;
}
Log << "done." << endl;
return 0;
}
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