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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/DOCKING/COMMON/structurePreparer.h>
#include <BALL/DOCKING/COMMON/dockingAlgorithm.h>
#include <BALL/COMMON/exception.h>
#include <BALL/DATATYPE/options.h>
#include <BALL/SCORING/COMMON/gridBasedScoring.h>
#include <BALL/SCORING/FUNCTIONS/gridedPLP.h>
#include <BALL/SCORING/FUNCTIONS/gridedMM.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/rotamerLibrary.h>
#include <BALL/STRUCTURE/peptideBuilder.h>
#include "version.h"
using namespace BALL;
using namespace std;
GridBasedScoring* createScoringFunction(AtomContainer* receptor, AtomContainer* ref_ligand, String scoring_type, list<Constraint*>* constraints, Options* option)
{
GridBasedScoring* gbs = 0;
if (scoring_type == "GridedMM")
{
gbs = new GridedMM(*receptor, *ref_ligand, *option);
}
else if (scoring_type == "GridedPLP")
{
gbs = new GridedPLP(*receptor, *ref_ligand, *option);
}
for (list < Constraint* > ::iterator it = constraints->begin(); it != constraints->end(); it++)
{
gbs->constraints.push_back(*it);
(*it)->setScoringFunction(gbs);
}
return gbs;
}
int main(int argc, char* argv[])
{
CommandlineParser parpars("SideChainGridBuilder", "build side chain grid", VERSION, String(__DATE__), "Docking");
parpars.registerMandatoryInputFile("param", "parameter file");
parpars.registerMandatoryStringParameter("d", "output directory");
parpars.setSupportedFormats("param", "ini");
parpars.setToolManual("This tool precalculates a side chain grid.");
parpars.parse(argc, argv);
//Log.setMinLevel(cout, 10);
Options option;
list<Constraint*> constraints;
if (parpars.get("param") == CommandlineParser::NOT_FOUND)
{
cout<<"[Error:] ini file must be given" << std::endl;
exit (1);
}
String inifile = parpars.get("param");
DockingAlgorithm::readOptionFile(inifile, option, constraints);
String scoring_type = option.get("scoring_type");
String grid_file = option.get("grid_file");
// Support for using one and the same config-file for grid precalculation and docking
String precalc_nonbonded_cuttoff = option.get("nonbonded_cutoff_precalculation");
if (precalc_nonbonded_cuttoff != "")
{
option.set("nonbonded_cutoff", precalc_nonbonded_cuttoff);
}
if (scoring_type == "")
{
cout<<"[Error:] scoring_type must be specified in the config-file!"<<endl;
exit(1);
}
if (scoring_type != "GridedMM" && scoring_type != "GridedPLP")
{
cout<<"[Error:] specified scoring_type is not grid-based, so no grid can be build for it!"<<endl;
exit(1);
}
String par_file = option.get("filename");
if (par_file == "" && !scoring_type.hasSubstring("GH"))
{
cout<<"[Error:] 'filename' for force-field parameter file must be specified in the config-file !"<<endl;
return(1);
}
if (grid_file == "")
{
cout<<"'grid_file' must be specified in the config-file !"<<endl;
return(1);
}
StructurePreparer* sp;
bool use_PLP = 0;
if (scoring_type.hasSubstring("PLP"))
{
use_PLP = 1;
sp = new StructurePreparer("PLP");
}
else
{
use_PLP = 0;
sp = new StructurePreparer;
}
String at = option.get("atom_types");
set<String> types;
if (!use_PLP && at != "")
{
Size no = at.countFields(", ");
for (Size i = 0; i < no; i++)
{
String type_i = at.getField(i, ", ");
type_i.trim();
types.insert(type_i);
}
}
// Angles are irrelevant, since we construct only single amino acids
Angle angle(0);
if (parpars.get("d") == CommandlineParser::NOT_FOUND)
{
cout<<"[Error:] out directory must be given" << std::endl;
exit (1);
}
String prefix = parpars.get("d");
prefix += "/";
FragmentDB frag_db("fragments/Fragments.db");
RotamerLibrary rotamer_lib("rotamers/bbind02.May.lib", frag_db);
String one_letter_codes = "ARNDCQEGHILKMFPSTWYV";
for (Size i = 0; i < 20; i++)
{
Peptides::PeptideBuilder pb(one_letter_codes[i], angle, angle, angle);
pb.setFragmentDB(&frag_db);
Protein* protein_template = pb.construct();
sp->prepare(protein_template, par_file);
Residue* residue = protein_template->getResidue(0);
ResidueRotamerSet* rotamer_set = rotamer_lib.getRotamerSet(*residue);
if (!rotamer_set) // GLY and ALA have no rotamers
{
cout<<"No rotamers for "<<residue->getName()<<" found."<<endl;
continue;
}
// Remove atoms that are not part of the residue templates
for (AtomIterator atom_it = protein_template->beginAtom(); +atom_it; atom_it++)
{
const String& name = atom_it->getName();
if (name == "1H" || name == "2H" || name == "3H" || name == "OXT")
{
atom_it->select();
}
}
protein_template->removeSelected();
// Do for each rotamer of the current amino acid
for (ResidueRotamerSet::ConstIterator it = rotamer_set->begin(); it != rotamer_set->end(); it++)
{
rotamer_set->setRotamer(*residue, *it);
Protein protein = *protein_template; // make a copy
/// Remove backbone atoms!!
/// Grids should only contain contributions for side-chains!
for (AtomIterator atom_it = protein.beginAtom(); +atom_it; atom_it++)
{
const String& name = atom_it->getName();
if (name == "N" || name == "O" || name == "CA" || name == "C"
||name == "HA")
{
atom_it->select();
}
}
protein.removeSelected();
GridBasedScoring* gbs = createScoringFunction(&protein, &protein, scoring_type, &constraints, &option);
gbs->setAtomTypeNames(types);
String name = residue->getName()+"_";
name += String((int)it->chi1)+"_";
name += String((int)it->chi2)+"_";
name += String((int)it->chi3)+"_";
name += String((int)it->chi4);
cout<<endl<<"---- Will now precalculate grids for "<<name<<" ... ------------"<<endl<<flush;
// Make sure that atoms lying outside of the grids for flexible side-chains will not be penalized during docking/scoring.
vector<ScoreGridSet*>* gridsets = gbs->getScoreGridSets();
for (Size i = 0; i < gridsets->size(); i++)
{
gridsets->at(i)->setParameters(0, 0, 0);
}
gbs->precalculateGrids();
gbs->saveGridSetsToFile(prefix+name+".bngrd", name);
PDBFile out(prefix+name+".pdb", ios::out);
out << *protein_template; // include backbone atoms into pdb-file, because they will be needed for mapping later
out.close();
delete gbs;
}
delete protein_template;
}
for (list < Constraint* > ::iterator it = constraints.begin(); it != constraints.end(); it++)
{
delete *it;
}
delete sp;
return 0;
}
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