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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// A utility for converting Pose indices of a clustering run
// into pdb files
//
#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/lineBasedFile.h>
#include <BALL/DOCKING/COMMON/poseClustering.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("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;
}
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