Example #1
0
int main(int argc, char** argv)
{

    if (argc != 3)
    {
        Log << "Usage:" << argv[0] << " <PDB infile> <PDB outfile> [<amber parameter file>]" << endl;

        return 1;
    }

    System system;

    PDBFile f;
    f.open(argv[1]);
    if (f.bad())
    {
        Log.error() << "cannot read PDB file " << argv[1] << endl;
        return 2;
    }
    f >> system;
    f.close();

    FragmentDB db("");

    // ResidueChecker check(db);
    // system.apply(check);


    db.normalize_names.setNamingStandard("Amber");
    system.apply(db.normalize_names);

    system.apply(db.build_bonds);

    Size cyx_counter = 0;
    Size hip_counter = 0;

    ResidueIterator it = system.beginResidue();
    for (; +it; ++it)
    {
        if (it->getFullName() == "CYS-S")
        {
            it->setName("CYX");
            cyx_counter++;
        }
        if (it->getFullName() == "HIS")
        {
            it->setName("HIP");
            hip_counter++;
        }
    }

    if (cyx_counter > 0)
    {
        Log.info() << "Renamed " << cyx_counter << " residues from CYS-S to CYX"
                   << endl;
    }

    if (hip_counter > 0)
    {
        Log.info() << "Renamed " << hip_counter << " residues from HIS to HIP"
                   << endl;
    }

    PDBFile g;
    g.open(argv[2], ios::out);
    if (g.bad())
    {
        Log.error() << "cannot write PDB file " << argv[2] << endl;
        return 2;
    }


    g << system;
    g.close();

    Log.info()
            << endl
            << "Conversion to AMBER naming scheme done. Please note that you might"
            << endl
            << "have to edit the resulting file by hand (if there are HIS or CYS"
            << endl
            << "residues in the original file, e. g.)"
            << endl
            << endl
            << "Good luck."
            << endl;

}
Example #2
0
int main(int argc, char* argv[])
{
	FDPB fdpb;

	// instantiate CommandlineParser object
	CommandlineParser parpars("CalculateSolvationFreeEnergy", "calculate solvation free energy of a protein using AMBER ", VERSION, String(__DATE__), "ForceFields");
	parpars.registerParameter("pdb",  "input pdb file ", INFILE,  true);
	parpars.registerParameter("epsilon_medium", "dielectric constant in medium", DOUBLE, false,  fdpb.options.getReal(FDPB::Option::SOLVENT_DC));
	parpars.registerParameter("epsilon_vacuum", "dielectric constant in vacuum", DOUBLE, false, 1);

	// the manual
	String man = String("This tool computes the solvation free energy of a pdb file using the Jackson-Sternberg approach (bonded energy using a force field and a non bonded energy (electrostatics only) by solving the Poisson-Boltzmann equation. Parameters are the dielectric constants for the medium (-epsilon_medium) and the vacuum (-epsilon_vacuum).");

	parpars.setToolManual(man);

	parpars.setSupportedFormats("pdb", "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();

	// normalize the names and build all bonds
	FragmentDB db("");
	sys.apply(db.normalize_names);
	sys.apply(db.build_bonds);

	// TODO: Ask ResidueChecker if everything is ok! see tool CalculateEnergy

	// create an AMBER force field without non-bonded interactions
	AmberFF FF(sys);

	// calculate the total energy
	float total_energy = FF.updateEnergy();
	//Log << FF.getResults() << std::endl;
	//Log << "   total energy using force field evaluation: " << total_energy << " kJ/mol" << std::endl;

	//Log << "removing non bonded energy terms ..." << std::endl;
	FF.removeComponent("Amber NonBonded");

	// calculate the internal energy (neglecting internal VdW interactions)
	float internal_energy = FF.updateEnergy();
	//Log << FF.getResults() << std::endl;
	Log << "  internal energy: " << internal_energy << " kJ/mol" << std::endl;

	// assign atom radii
	AssignRadiusProcessor radius_processor("radii/PARSE.siz");
	sys.apply(radius_processor);

	// calculate the electrostatic part of the solvation energy	
	//FDPB fdpb;

	float dielectric_const = fdpb.options.getReal(FDPB::Option::SOLVENT_DC);
	if (parpars.has("epsilon_medium"))
		dielectric_const = parpars.get("epsilon_medium").toFloat();
	fdpb.options[FDPB::Option::SOLVENT_DC] = dielectric_const;
	Log << "... using dielectric constant in medium: " << fdpb.options[FDPB::Option::SOLVENT_DC].toFloat() << std::endl;

	fdpb.setup(sys);
	fdpb.solve();

	float solvent_energy = fdpb.getEnergy();

	dielectric_const = 1.0;
	if (parpars.has("epsilon_vacuum"))
		dielectric_const = parpars.get("epsilon_vacuum").toFloat();
	fdpb.options[FDPB::Option::SOLVENT_DC] = dielectric_const;
	Log << "... using dielectric constant in vacuum: " << fdpb.options[FDPB::Option::SOLVENT_DC].toFloat() << std::endl;

	fdpb.setup(sys);
	fdpb.solve();

	float vacuum_energy = fdpb.getEnergy();
	Log << "\n  electrostatic solvation free energy: "	<< solvent_energy - vacuum_energy << std::endl;

	Log << "\n  total energy using a combination of force field and FDPB evaluation: "
		  << internal_energy - vacuum_energy + solvent_energy << " kJ/mol" << std::endl;

	return 0;
}
Example #3
0
int main(int argc, char** argv)
{
    CommandlineParser parpars("PoseIndices2PDB", "converts pose indices into PDB files ", VERSION, String(__DATE__), "Convert, combine and store");

    parpars.registerMandatoryInputFile("i_clust", "input cluster index file");
    parpars.registerMandatoryInputFile("i_trans", "input tranformation file");
    parpars.registerMandatoryInputFile("i_pdb",   "input reference pdb file");

    parpars.registerMandatoryOutputFile("o", "output file name prefix for resulting pdb files");
    parpars.setParameterAsHidden("o");

    // parameters for galaxy for handling multiple output files
    parpars.registerOptionalGalaxyOutputId("o_id", "output file name prefix for 2nd to last pdb file", "$o.id");
    // need to be hidden in command line mode
    parpars.setParameterAsHidden("o_id");
    parpars.setParameterAsAdvanced("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.setParameterAsHidden("o_dir");
    parpars.setParameterAsAdvanced("o_dir");

    // the manual
    String man = "This tool converts all pose indices from a given transformation file and the corresponding reference PDBFile into separate PDBFiles.\n\nParameters are the input pose index file (-i_clust), the original transformation file (-i_trans), the corresponding reference pdb file (-i_pdb) and a naming schema for the resulting pdb files (-o). \n\nOutput of this tool is a set of PDBFiles representing the docking poses belonging to the given input cluster.";

    parpars.setToolManual(man);

    // here we set the types of I/O files
    parpars.setSupportedFormats("i_clust","txt");
    parpars.setSupportedFormats("i_trans","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);

    PoseClustering pc;

    if (parpars.has("i_trans"))
    {
        pc.options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::RIGID_RMSD);
        pc.setBaseSystemAndTransformations(sys, parpars.get("i_trans"));
    }

    //std::vector< std::set<Index> > clusters;

    LineBasedFile file(parpars.get("i_clust"), std::ios::in);
    vector<String> fields;

    String cluster_id = -1;
    String pose_id    = -1;

    // called as command line or e.g. via galaxy?
    bool is_cmd =    !parpars.has("env")
                     || ((parpars.has("env") && parpars.get("env")=="cmdline"));
    bool first_sol = true;

    while (file.LineBasedFile::readLine())
    {
        // get the line
        String current_cluster = file.getLine();
        if (current_cluster.getField(1) == "cluster")
        {
            cluster_id = current_cluster.getField(2);
            pose_id = -1;

            if (file.LineBasedFile::readLine())
            {
                current_cluster = file.getLine();
                fields.clear();
                current_cluster.split(fields);
                for (Size i=0; i < fields.size(); i++)
                {
                    System new_pose_sys(sys);

                    pose_id = fields[i];
                    pc.applyTransformation2System(pose_id.toInt(), new_pose_sys);

                    // create the output name
                    String outfile_name = String(parpars.get("o"))
                                          + "_clust_" + cluster_id
                                          + "_pose_" + String(pose_id) + ".pdb";

                    if (parpars.has("o_dir") && is_cmd && (parpars.get("o_dir") != "$__new_file_path__"))
                    {
                        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 = (first_sol) ? String(parpars.get("o"))
                                       :   String(parpars.get("o_dir")) + "/primary_"
                                       + String(parpars.get("o_id"))  + "_clust_" + cluster_id
                                       + "_pose_" + String(pose_id)
                                       + "_visible_pdb";
                    }
                    PDBFile file(outfile_name, ios::out);

                    if (file.bad())
                    {
                        Log.error() << "cannot write file " << outfile_name << endl;
                        return 2;
                    }
                    file << new_pose_sys;
                    file.close();

                    // needed for galaxy output
                    if (first_sol)
                        first_sol = false;

                    Log << "wrote file " << outfile_name << endl;
                }
            }
        }
    }

    Log << "done." << endl;

    return 0;
}
Example #4
0
int main(int argc, char* argv[])
{
	// instantiate CommandlineParser object
	CommandlineParser parpars("CalculateEnergy", "calculate free energy of a protein ", VERSION, String(__DATE__), "ForceFields");
	parpars.registerMandatoryInputFile("pdb", "input pdb file ");

	// TODO: offer upload of a distinguished fragDB file?

	// choice of force field
	parpars.registerOptionalStringParameter("force_field", "force field (AMBER, MMFF94)", "AMBER");
	list<String> force_fields;
	force_fields.push_back("AMBER");
	force_fields.push_back("MMFF94");
	// TODO: shall we offer CHARM as well?
	parpars.setParameterRestrictions("force_field", force_fields);

	// TODO: shall we offer a force field parameter file upload?

	// TODO: check the naming!
	parpars.registerOptionalDoubleParameter("non_bond_cutoff",  "cutoff radius in calculations of nonbonded interactions", 20.0);
	parpars.registerOptionalDoubleParameter("elec_stat_cuton", "electrostatic cuton", 13.0);
	parpars.registerOptionalDoubleParameter("elec_stat_cutoff", "electrostatic cutoff", 15.0);
	parpars.registerFlag("dist_dep_dielec", "apply distance dependent dielectric constant", false);
	// NOTE: assign is the default
	//parpars.registerFlag("assign_typenames","automatically assign type names to the system", false);
	//parpars.registerFlag("assign_types","automatically assign types to the system if missing", false);
	//parpars.registerFlag("assign_charges", "automatically assign charges to the system if missing", false);
	// TODO: if we only allow PDBFile to upload then from where do we get stuff to overwrite?? 
	parpars.registerFlag("overwrite_types", "overwrite even non-empty type names", false);
	parpars.registerFlag("overwrite_charges","overwrite even non-zero charges", false);

	// the manual
	String man = String("This tool computes the free energy of a pdb file using a specified force field (-force_field) and force field parameters (-non_bond_cutoff, -elec_stat_cuton ... ).");

	parpars.setToolManual(man);

	parpars.setSupportedFormats("pdb", "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();

	// normalize the names and build all bonds
	FragmentDB db("");
	sys.apply(db.normalize_names);
	sys.apply(db.build_bonds);

	// check the structure
	Log.info() << " checking residues..." << std::endl;
	ResidueChecker rc(db);
	sys.apply(rc);

	if (!rc.getStatus())
	{
		Log.error() << "There are errors in the given structure. Use the ResidueChecker tool for further investigation." << std::endl;
		exit(2);
	}

	// create a force field	
	AmberFF* amber_force_field = NULL;
	MMFF94*  mmff_force_field = NULL;
	ForceField* force_field = NULL;

	if (parpars.has("force_field"))
	{
		String penalty_table = parpars.get("force_field");
		if (penalty_table == "AMBER")
		{
			amber_force_field = new AmberFF();
			force_field = amber_force_field;
			Log << " using the amber force field" << std::endl;
		}
		else if (penalty_table == "MMFF94")
		{
			mmff_force_field = new MMFF94();
			force_field = mmff_force_field;
			Log << " using the MMFF94 force field" << std::endl;
		}
		else
		{
			Log.error() << "Unknown force field " << parpars.get("force_field") << " Abort." << std::endl;
			exit(2);
		}
	}

	if (!amber_force_field && !mmff_force_field)
	{
		Log.error() << "Invalid force field. Abort." << std::endl;
		exit(2);
	}

	// set the ff options according the parameters
	float non_bonded_cutoff = 0;
	if (parpars.has("non_bond_cutoff"))
	{
		non_bonded_cutoff = parpars.get("non_bond_cutoff").toFloat();

		if (amber_force_field)
		{
			//TODO: something wents awfully wrong with the FF default options!
//	cout  << "non_bond_cutoff " << amber_force_field->options.getReal(AmberFF::Option::NONBONDED_CUTOFF) << " "<< amber_force_field->options.getReal(AmberFF::Default::NONBONDED_CUTOFF)  << endl;
			amber_force_field->options[AmberFF::Option::NONBONDED_CUTOFF] = non_bonded_cutoff;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::NONBONDED_CUTOFF] = non_bonded_cutoff;
		}
		Log << " used non bonded cutoff: " << non_bonded_cutoff << std::endl;
	}

	float elec_stat_cuton = 0;
	if (parpars.has("elec_stat_cuton"))
	{
		elec_stat_cuton = parpars.get("elec_stat_cuton").toFloat();

		if (amber_force_field)
		{
//	cout  << "elec_stat_cuton" << force_field->options[AmberFF::Option::ELECTROSTATIC_CUTON]  << endl;
			amber_force_field->options[AmberFF::Option::ELECTROSTATIC_CUTON] = elec_stat_cuton;
		}
		else if (mmff_force_field)
		{
//	cout  << "elec_stat_cuton" << force_field->options[MMFF94::Option::ELECTROSTATIC_CUTON]  << endl;
			mmff_force_field->options[MMFF94::Option::ELECTROSTATIC_CUTON] = elec_stat_cuton;
		}
		Log << " used electrostatic cuton: " << elec_stat_cuton << std::endl;
	}

	float elec_stat_cutoff = 0;
	if (parpars.has("elec_stat_cutoff"))
	{
		elec_stat_cutoff = parpars.get("elec_stat_cutoff").toFloat();

		if (amber_force_field)
		{
			amber_force_field->options[AmberFF::Option::ELECTROSTATIC_CUTOFF] = elec_stat_cutoff;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::ELECTROSTATIC_CUTOFF] = elec_stat_cutoff;
		}
		Log << " used electrostatic cutoff: " << elec_stat_cutoff << std::endl;
	}

	bool dist_dep_dielectric = true;
	if (parpars.has("dist_dep_dielec"))
	{
		dist_dep_dielectric = parpars.get("dist_dep_dielec").toBool();

		if (amber_force_field)
		{
			amber_force_field->options[AmberFF::Option::DISTANCE_DEPENDENT_DIELECTRIC] = dist_dep_dielectric;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::DISTANCE_DEPENDENT_DIELECTRIC] = dist_dep_dielectric;
		}
	}
	Log << " distance dependent dielectric constant " << (dist_dep_dielectric ? "on" : "off") << std::endl;

	// we handle ASSIGN_TYPES and ASSIGN_TYPENAMES together
	bool assign_types = true;
	if (parpars.has("assign_types"))
	{
		assign_types = parpars.get("assign_types").toBool();

		if (amber_force_field)
		{
			amber_force_field->options[AmberFF::Option::ASSIGN_TYPENAMES] = assign_types;
			amber_force_field->options[AmberFF::Option::ASSIGN_TYPES] = assign_types;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::ASSIGN_TYPENAMES] = assign_types;
			mmff_force_field->options[MMFF94::Option::ASSIGN_TYPES] = assign_types;
		}
	}
	Log << " assignment of missing types " << (assign_types ? "on" : "off") << std::endl;


	bool overwrite_types = true;
	if (parpars.has("overwrite_types"))
	{
		overwrite_types = parpars.get("overwrite_types").toBool();

		if (amber_force_field)
		{
			amber_force_field->options[AmberFF::Option::OVERWRITE_TYPENAMES] = overwrite_types;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::OVERWRITE_TYPENAMES] = overwrite_types;
		}
	}
	Log << " overwrite types " << (overwrite_types ? "on" : "off") << std::endl;


	bool assign_charges = true;
	if (parpars.has("assign_charges"))
	{
		assign_charges = parpars.get("assign_charges").toBool();

		if (amber_force_field)
		{
			amber_force_field->options[AmberFF::Option::ASSIGN_CHARGES] = assign_charges;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::ASSIGN_CHARGES] = assign_charges;
		}
	}
	Log << " assignment of missing charges " << (assign_charges ? "on" : "off") << std::endl;

	bool overwrite_charges = true;
	if (parpars.has("overwrite_charges"))
	{
		overwrite_charges = parpars.get("overwrite_charges").toBool();

		if (amber_force_field)
		{
			amber_force_field->options[AmberFF::Option::OVERWRITE_CHARGES] = overwrite_charges;
		}
		else if (mmff_force_field)
		{
			mmff_force_field->options[MMFF94::Option::OVERWRITE_CHARGES] = overwrite_charges;
		}
	}
	Log << " overwrite charges " << (overwrite_charges ? "on" : "off") << std::endl;

	// setup the force field
	Log.info() << " setting up the force field..." << endl;
	force_field->setup(sys);

	// setup successful?
	if (   (force_field->getUnassignedAtoms().size() > 0)
		  || !force_field->isValid())
	{
		Log.error() << "There are parameterless atoms in the structure. Use the ResidueChecker tool for further investigation." << std::endl;
		exit(2);
	}

	// trigger the energy computations
	force_field->updateEnergy();

	// print the result
	Log.info() << force_field->getResults() << endl;

	return 0;
}
Example #5
0
int main (int argc, char **argv)
{
	// instantiate CommandlineParser object supplying
	// - tool name
	// - short description
	// - version string
	// - build date
	// - category
	CommandlineParser parpars("DockPoseClustering", "clusters docking poses ", VERSION, String(__DATE__), "Docking");

	// we register an input file parameter 
	// - CLI switch
	// - description
	// - Inputfile
	parpars.registerMandatoryInputFile("i_pdb", "input pdb-file");
	parpars.registerOptionalInputFile("i_dcd", "input dcd-file");
	///TODO: offer the alternatives in a more elegant way!
	parpars.registerOptionalInputFile("i_trans", "or input transformation file for rigid rmsd clustering ");

	// we register an output file parameter 
	// - CLI switch
	// - description	
	// - parameter type	
	// - required
	// - default value
	// - hidden in galaxy
	parpars.registerMandatoryOutputFile("o_index_list", "output file name for the index list ");
	parpars.setParameterAsHidden("o_index_list");
	parpars.registerOptionalOutputFile("o_score_matrix", "output file name for scoring matrix ");
	parpars.setParameterAsHidden("o_score_matrix");
	parpars.registerOptionalOutputFile("o_dcd", "output file name for the first cluster dcd file ");
	parpars.setParameterAsHidden("o_dcd");

	parpars.registerOptionalGalaxyOutputId("o_dcd_id", "output id ", "$o_dcd.id");
	// need to be hidden in command line mode
	parpars.setParameterAsAdvanced("o_dcd_id");
	parpars.setParameterAsHidden("o_dcd_id");

	parpars.registerOptionalGalaxyOutputFolder("o_dcd_dir", "output directory for 2nd to last cluster dcd file (if needed) ", "$__new_file_path__");
	// need to be hidden in command line mode
	parpars.setParameterAsAdvanced("o_dcd_dir");
	parpars.setParameterAsHidden("o_dcd_dir");

	// register String parameter for supplying minimal rmsd between clusters
	parpars.registerOptionalDoubleParameter("rmsd_cutoff", "minimal rmsd between the final clusters (default 5.0) ", 5.0);
	parpars.setParameterRestrictions("rmsd_cutoff", 0, 100);

	// choice of cluster algorithm  
	parpars.registerOptionalStringParameter("alg", "algorithm used for clustering (CLINK_DEFAYS, CLINK_ALTHAUS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE) ", "CLINK_DEFAYS");
	list<String> cluster_algs;
	cluster_algs.push_back("CLINK_DEFAYS");
	cluster_algs.push_back("CLINK_ALTHAUS");
	cluster_algs.push_back("TRIVIAL_COMPLETE_LINKAGE");
	cluster_algs.push_back("NEAREST_NEIGHBOR_CHAIN_WARD");
	cluster_algs.push_back("SLINK_SIBSON");
	parpars.setParameterRestrictions("alg", cluster_algs);

	// choice of atom rmsd scope 
	parpars.registerOptionalStringParameter("scope", "atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS) ", "C_ALPHA");
	list<String> rmsd_levels;
	rmsd_levels.push_back("C_ALPHA");
	//rmsd_levels.push_back("HEAVY_ATOMS"); //TODO
	rmsd_levels.push_back("BACKBONE");
	rmsd_levels.push_back("ALL_ATOMS");
	parpars.setParameterRestrictions("scope", rmsd_levels);

	// choice of rmsd type
	parpars.registerOptionalStringParameter("rmsd_type", "rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE) ", "SNAPSHOT_RMSD");
	list<String> rmsd_types;
	rmsd_types.push_back("SNAPSHOT_RMSD");
	rmsd_types.push_back("RIGID_RMSD");
	rmsd_types.push_back("CENTER_OF_MASS_DISTANCE");
	parpars.setParameterRestrictions("rmsd_type", rmsd_types);

	// further optional output parameters
	parpars.registerOptionalOutputFile("o_red_dcd", "output file for the reduced cluster set (dcd with one structure per final cluster) ");

	// write the final cluster tree in boost::serialize format, if it was computed
	parpars.registerOptionalOutputFile("o_cluster_tree", "output file containing the cluster tree in boost::serialize format (if the tree was computed) ");

	// register bool parameter for using pre-clustering
	parpars.registerFlag("use_refinement", "Apply a second clustering run with different options (-refine_alg <string>, -refine_rmsd_type <string>, and -refine_rmsd_scope <string>)", false, true);

	// refinement algorithm
	parpars.registerOptionalStringParameter("refine_alg", "algorithm used for second clustering run (CLINK_DEFAYS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE) ", "CLINK_DEFAYS");
	parpars.setParameterAsHidden("refine_alg");
	parpars.setParameterRestrictions("refine_alg", cluster_algs);

	// refinement rmsd type
	parpars.registerOptionalStringParameter("refine_rmsd_type", "rmsd type used for second clustering run (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE) ", "SNAPSHOT_RMSD");
	parpars.setParameterAsHidden("refine_rmsd_type");
	parpars.setParameterRestrictions("refine_rmsd_type", rmsd_types);

	// refinement rmsd scope
	parpars.registerOptionalStringParameter("refine_rmsd_scope", "atoms to be considered for rmsd score in second clustering run (C_ALPHA, BACKBONE, ALL_ATOMS) ", "C_ALPHA");
	parpars.setParameterAsHidden("refine_rmsd_scope");
	parpars.setParameterRestrictions("refine_rmsd_scope", rmsd_levels);

	// force serial execution, even if the algorithm supports parallel runs
	parpars.registerFlag("run_serial", "force serial excecution, even if parallel execution would be supported by the algorithm", false, true);

	// the manual
	String man = "This tool computes clusters of docking poses given as conformation set or a list of rigid transformations.\n\nParameters are either the input ConformationSet (-i_dcd) and one corresponding pdb file (-i_pdb), or a transformation file (-i_trans). Output can be a cluster index list (-o_index_list), a cluster scoring matrix (-o_score_matrix), or dcd files per cluster (-o_dcd). Optional parameters are the algorithm (-alg), the minimal rmsd between the final clusters (-rmsd_cutoff), the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope). The optional parameter -o_red_dcd sets the output file for the reduced cluster set (one representative per cluster). The optional parameter -o_cluster_tree specifies the output file for storing the cluster tree.\n\nOutput of this tool depends in the choice of the output parameters.";

	parpars.setToolManual(man);

	// here we set the types of I/O files
	parpars.setSupportedFormats("i_dcd","dcd");
	parpars.setSupportedFormats("i_pdb","pdb");
	parpars.setSupportedFormats("i_trans","txt");
	parpars.setSupportedFormats("o_index_list","txt");
	parpars.setSupportedFormats("o_score_matrix","txt");
	parpars.setSupportedFormats("o_dcd","dcd");
	parpars.setSupportedFormats("o_red_dcd","dcd");
	parpars.setSupportedFormats("o_cluster_tree","dat");

	parpars.parse(argc, argv);

	//////////////////////////////////////////////////

	if (parpars.has("o_dcd"))
	{
		if (!parpars.has("o_dcd_dir") || !parpars.has("o_dcd_id"))
		{
			Log << "Output type \"dcd\" requires setting the options \"o_dir\" \"o_id\"! Abort!" << endl;
			return 1;
		}
	}

	if (     parpars.has("o_cluster_tree")
			&& (!parpars.has("alg") || parpars.get("alg") != "NEAREST_NEIGHBOR_CHAIN_WARD"))
	{
		Log << "Output of cluster tree requires Ward algorithm! Abort!" << endl;
		return 1;
	}

	// read the input	
	PDBFile pdb;
	pdb.open(parpars.get("i_pdb"));
	System sys;
	pdb.read(sys);

	ConformationSet cs;
	cs.setup(sys);

	if (parpars.has("i_dcd"))
	{
		cs.readDCDFile(parpars.get("i_dcd"));
	}

	cs.resetScoring();

	PoseClustering pc;

	if (parpars.has("i_trans"))
	{
		pc.setBaseSystemAndTransformations(sys, parpars.get("i_trans"));
	}

	if (parpars.has("rmsd_cutoff"))
	{
		float rmsd = parpars.get("rmsd_cutoff").toInt();
		pc.options.setReal(PoseClustering::Option::DISTANCE_THRESHOLD, rmsd);
	}

	if (parpars.has("scope"))
	{
		String scope = parpars.get("scope");
		if (scope == "C_ALPHA")
			pc.options.set(PoseClustering::Option::RMSD_LEVEL_OF_DETAIL, PoseClustering::C_ALPHA);
		else if (scope == "BACKBONE")
			pc.options.set(PoseClustering::Option::RMSD_LEVEL_OF_DETAIL, PoseClustering::BACKBONE);
		else if (scope == "ALL_ATOMS")
			pc.options.set(PoseClustering::Option::RMSD_LEVEL_OF_DETAIL, PoseClustering::ALL_ATOMS);
		else
			Log.info() << "Unknown value " << scope  << " for option scope." << endl;
	}

	if (parpars.has("alg"))
	{
		String alg = parpars.get("alg");
		if (alg == "CLINK_DEFAYS")
			pc.options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::CLINK_DEFAYS);
		else if (alg == "CLINK_ALTHAUS")
			pc.options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::CLINK_ALTHAUS);
		else if (alg == "SLINK_SIBSON")
			pc.options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::SLINK_SIBSON);
		else if (alg == "TRIVIAL_COMPLETE_LINKAGE")
			pc.options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::TRIVIAL_COMPLETE_LINKAGE);
		else if (alg == "NEAREST_NEIGHBOR_CHAIN_WARD")
			pc.options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::NEAREST_NEIGHBOR_CHAIN_WARD);
		else
			Log.info() << "Unknown value " << alg  << " for option alg." << endl;
	}

	if (parpars.has("rmsd_type"))
	{
		String type = parpars.get("rmsd_type");
		if (type == "SNAPSHOT_RMSD")
			pc.options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::SNAPSHOT_RMSD);
		else if (type == "RIGID_RMSD")
			pc.options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::RIGID_RMSD);
		else if (type == "CENTER_OF_MASS_DISTANCE")
		{
			pc.options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::CENTER_OF_MASS_DISTANCE);
			Log << "Parameter scope will be ignored!" << endl;
		}
		else
			Log.info() << "Unknown value " << type  << " for option rmsd_type." << endl;

	}

	if (parpars.has("run_serial"))
	{
		pc.options.set(PoseClustering::Option::RUN_PARALLEL, false);
	}
	else
	{
		pc.options.set(PoseClustering::Option::RUN_PARALLEL, true);
	}

	if (parpars.has("i_dcd"))
	{
		pc.setConformationSet(&cs);
	}

	pc.compute();

	// do we need a second clustering run?
	if (parpars.has("use_refinement"))
	{
		// get the options
		Options refine_options = pc.options;
		if (parpars.has("refine_rmsd_scope"))
		{
			String scope = parpars.get("refine_rmsd_scope");
			if (scope == "C_ALPHA")
				refine_options.set(PoseClustering::Option::RMSD_LEVEL_OF_DETAIL, PoseClustering::C_ALPHA);
			else if (scope == "BACKBONE")
				refine_options.set(PoseClustering::Option::RMSD_LEVEL_OF_DETAIL, PoseClustering::BACKBONE);
			else if (scope == "ALL_ATOMS")
				refine_options.set(PoseClustering::Option::RMSD_LEVEL_OF_DETAIL, PoseClustering::ALL_ATOMS);
			else
				Log.info() << "Unknown value " << scope  << " for option refine_rmsd_scope." << endl;
		}

		if (parpars.has("refine_alg"))
		{
			String alg = parpars.get("refine_alg");
			if (alg == "CLINK_DEFAYS")
				refine_options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::CLINK_DEFAYS);
			else if (alg == "CLINK_ALTHAUS")
				refine_options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::CLINK_ALTHAUS);
			else if (alg == "SLINK_SIBSON")
				refine_options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::SLINK_SIBSON);
			else if (alg == "TRIVIAL_COMPLETE_LINKAGE")
				refine_options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::TRIVIAL_COMPLETE_LINKAGE);
			else if (alg == "NEAREST_NEIGHBOR_CHAIN_WARD")
				refine_options.set(PoseClustering::Option::CLUSTER_METHOD, PoseClustering::NEAREST_NEIGHBOR_CHAIN_WARD);
			else
				Log.info() << "Unknown value " << alg  << " for option refine_alg." << endl;
		}

		if (parpars.has("refine_rmsd_type"))
		{
			String type = parpars.get("refine_rmsd_type");
			if (type == "SNAPSHOT_RMSD")
				refine_options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::SNAPSHOT_RMSD);
			else if (type == "RIGID_RMSD")
				refine_options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::RIGID_RMSD);
			else if (type == "CENTER_OF_MASS_DISTANCE")
			{
				refine_options.set(PoseClustering::Option::RMSD_TYPE, PoseClustering::CENTER_OF_MASS_DISTANCE);
				Log << "Parameter scope will be ignored!" << endl;
			}
			else
				Log.info() << "Unknown value " << type  << " for option refine_rmsd_type." << endl;
		}

		pc.refineClustering(refine_options);
	}

	Size num_clusters = pc.getNumberOfClusters();

	Log << "Computed " <<  num_clusters << " clusters, start writing..." << endl;

	if (parpars.has("o_dcd"))
	{
		for (Size i = 0; i < num_clusters; i++)
		{
			Log << "   Cluster " << i << " has " << pc.getClusterSize(i) << " members." << endl;

			boost::shared_ptr<ConformationSet> new_cs = pc.getClusterConformationSet(i);

			String outfile_name = (i == 0) ? String(parpars.get("o_dcd"))
				: String(parpars.get("o_dcd_dir")) + "/primary_"
				+ String(parpars.get("o_dcd_id"))  + "_cluster" + String(i)
				+ "_visible_dcd";
			//Log << "   Writing solution " << String(i) << " as " << outfile_name << endl;

			new_cs->writeDCDFile(outfile_name);
		}
	}
	if (parpars.has("o_index_list"))
	{
		String outfile_name = String(parpars.get("o_index_list"));

		File cluster_outfile(outfile_name, std::ios::out);

		pc.printClusters(cluster_outfile);
	}
	if (parpars.has("o_score_matrix"))
	{
		String outfile_name = String(parpars.get("o_score_matrix"));

		File cluster_outfile(outfile_name, std::ios::out);

		pc.printClusterScores(cluster_outfile);
	}

	// print
	pc.printClusters();
	pc.printClusterScores();

	if (parpars.has("o_cluster_tree"))
	{
		File cluster_out(parpars.get("o_cluster_tree"), std::ios::out);
		pc.serializeWardClusterTree(cluster_out, true);
		cluster_out.close();
	}

	if (parpars.has("o_red_dcd"))
	{
		String outfile_name = String(parpars.get("o_red_dcd"));
		boost::shared_ptr<ConformationSet> cs = pc.getReducedConformationSet();
		cs->writeDCDFile(outfile_name);
	}

	Log << "done." << endl;

	return 0;
}