C++ PDBFile::read方法代码示例

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)
                    {
//.........这里部分代码省略.........

//.........这里部分代码省略.........
	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")