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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/STRUCTURE/assignBondOrderProcessor.h>
#include <BALL/FORMAT/MOL2File.h>
#include <BALL/KERNEL/system.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <iostream>
#include "version.h"
using namespace std;
using namespace BALL;
int main (int argc, char **argv)
{
// instantiate CommandlineParser object supplying
// - tool name
// - short description
// - version string
// - build date
// - category
CommandlineParser parpars("BondOrderAssigner", "computes bond order assignments for a ligand ", VERSION, String(__DATE__), "Preparation");
// we register an input file parameter
// - CLI switch
// - description
// - Inputfile
// - required
parpars.registerMandatoryInputFile("i", "input mol2-file");
// we register an output file parameter
// - description
// - Outputfile
// - required
parpars.registerMandatoryOutputFile("o", "output mol2-file name for first solution");
parpars.setParameterAsHidden("o");
// parameters for galaxy for handling multiple output files
parpars.registerOptionalGalaxyOutputId("o_id", "output id", "$o.id");
// need to be hidden in command line mode
parpars.setParameterAsAdvanced("o_id");
parpars.setParameterAsHidden("o_id");
// parameters for galaxy for handling multiple output files
parpars.registerOptionalGalaxyOutputFolder("o_dir", "output directory for 2nd to last solution", "$__new_file_path__");
// need to be hidden in command line mode
parpars.setParameterAsAdvanced("o_dir");
parpars.setParameterAsHidden("o_dir");
// register String parameter for supplying max number of solutions
parpars.registerOptionalIntegerParameter("max_sol", "maximal number of assignments solutions to compute", 25);
parpars.setParameterRestrictions("max_sol", 0, 100);
// parameter for computing sub-optimal solutions
parpars.registerFlag("non_opt", "compute sub-optimal assignments as well", false);
// option for hydrogen addition
// TODO: test and then release :-)
//parpars.registerFlag("add_hyd", "add hydrogens as well", false);
// choice of penalty table
parpars.registerOptionalStringParameter("scr_pen", "penalty table (Antechamber, BALL)", "Antechamber");
list<String> ini_files;
ini_files.push_back("Antechamber");
ini_files.push_back("BALL");
parpars.setParameterRestrictions("scr_pen", ini_files);
// the manual
String man = String("This tool computes optimal and sub-optimal bond order assignments based on an atomic penalty function for a given ligand in mol2 file format.\n\nOptional parameters are the maximal number of solutions to be computed ('-max_sol'), the penalty table specifiying the atomic penalty rules ('-scr_pen'),and a flag indicating if sub-optimal solutions should be computed as well ('-non_opt')") + // and a flag indicating if hydrogens should be computed as well ('-add_hyd')
".\n\nOutput of this tool is a number of mol2 files each containing one bond order assignment.\n\nTo upload an input file please use the upload tool (Get Data -> Upload File).\n\n**Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help.\n\nPlease cite the following: Dehof, A.K., Rurainski, A., Bui, Q.B.A., Boecker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011";
parpars.setToolManual(man);
// here we set the types of I/O files, for example sdf is also allowed
parpars.setSupportedFormats("i","mol2");
parpars.setSupportedFormats("o","mol2");
parpars.parse(argc, argv);
// read the input
MOL2File f0;
f0.open(parpars.get("i"));
System system;
f0 >> system;
AssignBondOrderProcessor abop;
// the combination of the following two options causes the computation of all optimal solutions
abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, 0);
abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, false);
if (parpars.has("max_sol"))
{
int max_sol = parpars.get("max_sol").toInt();
Log << " Limit number of solutions to " << max_sol << endl;
abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, String(max_sol).toInt());
}
bool non_opt = false;
if (parpars.has("non_opt"))
{
non_opt = parpars.get("non_opt").toBool();
if (non_opt)
Log << " Compute also non-optimal solutions." << endl;
abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, non_opt);
}
if (parpars.has("add_hyd"))
{
bool add_hyd = parpars.get("add_hyd").toBool();
//if (add_hyd)
// cout << " Add hydrogens as well." << endl;
abop.options.setBool(AssignBondOrderProcessor::Option::ADD_HYDROGENS, add_hyd);
}
if (parpars.has("scr_pen"))
{
String penalty_table = parpars.get("scr_pen");
if (penalty_table == "Antechamber")
{
Log << " Use Antechamber scoring function" << endl;
abop.options[AssignBondOrderProcessor::Option::INIFile] = "/bond_lengths/BondOrderGAFF.xml";
}
else
{
Log << " Use BALL scoring function" << endl;
abop.options[AssignBondOrderProcessor::Option::INIFile] = "/bond_lengths/BondOrder.xml";
}
}
// set the solver
abop.options.set(AssignBondOrderProcessor::Option::ALGORITHM, AssignBondOrderProcessor::Algorithm::FPT);
//Log << "parameters are: " << endl;
//abop.options.dump();
Log << "run ..." << endl;
system.apply(abop);
Size num_of_sols = abop.getNumberOfComputedSolutions();
if (num_of_sols == 0)
{
Log << "No valid bond order assignment found!" << endl;
return 1;
}
else
{
// called as command line or e.g. via galaxy?
bool is_cmd = !parpars.has("env")
|| ((parpars.has("env") && parpars.get("env")=="cmdline"));
//Log << "Found " << num_of_sols << " solutions:" << endl;
for (Size i=0; (i<num_of_sols) && (non_opt || (abop.getTotalPenalty(0)==abop.getTotalPenalty(i))); i++)
{
Log << " Solution " << i << " has penalty " << abop.getTotalPenalty(i) << " ... ";
// apply the solution
if (abop.apply(i))
{
// create the output name
String outfile_name = String(parpars.get("o")) + "solution_" + String(i) + ".mol2";
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 = (i == 0) ? String(parpars.get("o"))
: String(parpars.get("o_dir")) + "/primary_"
+ String(parpars.get("o_id")) + "_solution" + String(i)
+ "_visible_mol2";
}
//Log << " Writing solution " << String(i) << " as " << outfile_name << endl;
// GenericMolFile* outfile = MolFileFactory::open(outfile_name, ios::out);
MOL2File outfile(outfile_name, ios::out);
if (outfile.bad())
{
Log.error() << endl << "cannot write file " << outfile_name << endl;
return 2;
}
system.beginMolecule()->setProperty("BOA_Constructor_penalty", abop.getTotalPenalty(i));
outfile << system;
outfile.close();
Log << "wrote file " << outfile_name << endl;
}
}
}
Log << "done." << endl;
return 0;
}
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