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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// A very simple utility for converting trajectory files like DCD
// into rigid transformations
//
#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/DOCKING/COMMON/poseClustering.h>
#include <BALL/FORMAT/DCDFile.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/lineBasedFile.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("Trajectory2RigidTransformation", "converts a trajectory file into a rigid transformation file ", VERSION, String(__DATE__), "Convert, combine and store");
parpars.registerMandatoryInputFile("i_dcd", "input trajectory file");
parpars.registerMandatoryInputFile("i_pdb", "input pdb-file");
parpars.registerMandatoryOutputFile("o", "output file for the rigid transformations");
parpars.setParameterAsHidden("o");
// the manual
String man = "This tool converts SnapShots of a given TrajectoryFile and the reference PDBFile into a rigid transformation file.\n\nParameters are the input SnapShots as TrajectoryFile (-i_dcd), the corresponding reference pdb file that was originally used to create the TrajectoryFile (-i_pdb) and a naming schema for the resulting transformation file (-o).\n\nOutput of this tool is a file storing each given SnapShot as rigid transformation per line.";
parpars.setToolManual(man);
// here we set the types of I/O files, for example sdf is also allowed
parpars.setSupportedFormats("i_dcd", "dcd");
parpars.setSupportedFormats("i_pdb", "pdb");
parpars.setSupportedFormats("o", "txt");
parpars.parse(argc, argv);
//////////////////////////////////////////////////
// read the input
PDBFile pdb;
pdb.open(parpars.get("i_pdb"));
System sys;
pdb.read(sys);
ConformationSet cs;
cs.setup(sys);
cs.readDCDFile(parpars.get("i_dcd"));
cs.resetScoring();
PoseClustering pc;
pc.options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::RIGID_RMSD);
pc.setConformationSet(&cs);
// now convert
pc.convertSnaphots2Transformations();
std::vector< PoseClustering::PosePointer > poses = pc.getPoses();
String outfile_name = String(parpars.get("o"));
LineBasedFile file(outfile_name, ios::out);
if (file.bad())
{
Log.error() << "cannot write file " << outfile_name << endl;
return 2;
}
Log << "write rigid poses into file " << outfile_name << endl;
for (Size i=0; i<poses.size(); i++)
{
Eigen::Matrix3f const & rot = poses[i].trafo->rotation;
Eigen::Vector3f const & transl = poses[i].trafo->translation;
file << "A A " << " 0.0 "
<< rot(0) << " " << rot(1) << " " << rot(2) << " " << transl[0] << " "
<< rot(3) << " " << rot(4) << " " << rot(5) << " " << transl[1] << " "
<< rot(6) << " " << rot(7) << " " << rot(8) << " " << transl[2] << " "
<< " 0.0 0.0 0.0 0.0"
<< endl;
}
file.close();
Log << "done." << endl;
return 0;
}
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