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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 "version.h"
using namespace BALL;
using namespace std;
int main(int argc, char* argv[])
{
CommandlineParser parpars("GridBuilder", "create score-grids for docking", VERSION, String(__DATE__), "Docking");
parpars.registerMandatoryInputFile("rec", "receptor pdb-file");
parpars.registerMandatoryInputFile("rl", "reference-ligand");
parpars.registerMandatoryOutputFile("grd", "ScoreGrid file");
parpars.registerOptionalInputFile("pocket", "configuration file");
parpars.registerOptionalOutputFile("write_ini", "write ini-file w/ default parameters (and don't do anything else)");
String man = "This tool precalculates a score-grid for a binding pocket of a given receptor.\n\nAs input we need:\n\
* a file containing a protonated protein in pdb-format\n\
* a file containing a reference ligand.\n\
This reference ligand should be located in the binding pocket, \n\
so that a grid can be precalculated around it.\n\
Supported formats are mol2, sdf or drf (DockResultFile, xml-based).\n\nOutput of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).";
parpars.setToolManual(man);
parpars.setSupportedFormats("rec","pdb");
parpars.setSupportedFormats("rl",MolFileFactory::getSupportedFormats());
parpars.setSupportedFormats("pocket","ini");
parpars.setSupportedFormats("write_ini","ini");
parpars.setSupportedFormats("grd","grd.gz,grd,bngrd.gz,bngrd");
Options default_options;
ScoringFunction::getDefaultOptions(default_options);
Options* scoring_options = default_options.getSubcategory(ScoringFunction::SUBCATEGORY_NAME);
scoring_options->setDefault("atom_types", "C, H, N, O, P, S, Cl, F, I");
scoring_options->addParameterDescription("atom_types", "elements for which grids should be precalculated", ParamFile::STRING);
parpars.registerAdvancedParameters(default_options);
parpars.setSupportedFormats(ScoringFunction::SUBCATEGORY_NAME, "filename", "ini");
parpars.parse(argc, argv);
String default_inifile = parpars.get("write_ini");
if (default_inifile != CommandlineParser::NOT_FOUND)
{
// if ini-file already exists, read its entries first
list<Constraint*> clist;
if (ifstream(default_inifile.c_str()))
{
DockingAlgorithm::readOptionFile(default_inifile, default_options, clist);
}
scoring_options->setDefault("scoring_type", "GridedMM");
scoring_options->setDefault("scoregrid_resolution", 0.5);
scoring_options->setDefault("nonbonded_cutoff_precalculation", scoring_options->get("nonbonded_cutoff"));
scoring_options->set("nonbonded_cutoff", 3.0);
DockingAlgorithm::writeOptionFile(parpars.get("write_ini"), default_options, clist);
Log << "Ini-file w/ default values has been written to file '"<<default_inifile<<"'. Goodbye!"<<endl;
return 0;
}
Log.setMinLevel(cout, 10);
GenericMolFile* ref_ligand_file = MolFileFactory::open(parpars.get("rl"));
Molecule* ref_ligand = ref_ligand_file->read();
ref_ligand_file->close();
delete ref_ligand_file;
Options option;
parpars.copyAdvancedParametersToOptions(option);
list<Constraint*> constraints;
if (parpars.get("pocket") != CommandlineParser::NOT_FOUND)
{
DockingAlgorithm::readOptionFile(parpars.get("pocket"), option, constraints, ref_ligand);
}
Options* option_category = option.getSubcategory(ScoringFunction::SUBCATEGORY_NAME);
if (!option_category) option_category = &option;
String scoring_type = option_category->setDefault("scoring_type", "GridedMM");
String grid_file = parpars.get("grd");
// Support for using one and the same config-file for grid precalculation and docking
String precalc_nonbonded_cuttoff = option_category->get("nonbonded_cutoff_precalculation");
if (precalc_nonbonded_cuttoff != "")
{
option_category->set("nonbonded_cutoff", precalc_nonbonded_cuttoff);
}
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 par_file = option_category->get("filename");
if (par_file == "") par_file="Amber/amber96-docking.ini";
System receptor;
GenericMolFile* input = MolFileFactory::open(parpars.get("rec"));
if (!input)
{
cerr<<"Format of receptor-file not supported!"<<endl;
return 1;
}
*input >> receptor;
sp->prepare(&receptor, par_file);
delete input;
sp->prepare(ref_ligand, par_file);
GridBasedScoring* gbs = 0;
if (scoring_type == "GridedMM" || scoring_type == "MM")
{
gbs = new GridedMM(receptor, *ref_ligand, option);
}
else if (scoring_type == "GridedPLP" || scoring_type == "PLP")
{
gbs = new GridedPLP(receptor, *ref_ligand, option);
}
else
{
Log.error() << "[Error:] Scoring function '" << scoring_type << "' unknown/unsupported!" << endl;
return 1;
}
for (list < Constraint* > ::iterator it = constraints.begin(); it != constraints.end(); it++)
{
gbs->constraints.push_back(*it);
(*it)->setScoringFunction(gbs);
}
Log.level(10)<<endl<<"-----------------------------------------"<<endl;
Log.level(10)<<"Scores will be calculated as : "<<gbs->getEquation()<<endl;
Log.level(10)<<"-----------------------------------------"<<endl<<endl;
String at = option_category->get("atom_types");
if (!use_PLP && at != "")
{
set<String> types;
Size no = at.countFields(", ");
for (Size i = 0; i < no; i++)
{
String type_i = at.getField(i, ", ");
type_i.trim();
types.insert(type_i);
}
gbs->setAtomTypeNames(types);
}
gbs->precalculateGrids();
gbs->saveGridSetsToFile(grid_file, "GridSets for receptor '"+parpars.get("rec")+"'");
for (list < Constraint* > ::iterator it = constraints.begin(); it != constraints.end(); it++)
{
delete *it;
}
delete gbs;
delete sp;
delete ref_ligand;
return 0;
}
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