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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: global.h,v 1.9 2002/02/27 12:20:31 sturm Exp $
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/SOLVATION/poissonBoltzmann.h>
#include <BALL/STRUCTURE/defaultProcessors.h>
#include <BALL/MOLMEC/COMMON/radiusRuleProcessor.h>
#include <BALL/MOLMEC/COMMON/chargeRuleProcessor.h>
using namespace BALL;
// a pointer to the fragment data base (a pointer since we do
// not need it every time an want to save the loading time)
extern FragmentDB* frag_db;
// the Finite Difference Poisson-Boltzmann object
extern FDPB fdpb;
// the options for the calculation
extern Options options;
// charge and radius assignment processors
extern AssignChargeProcessor charges;
extern AssignRadiusProcessor radii;
extern ClearChargeProcessor clear_charge_proc;
// rule-based assignment processors
extern ChargeRuleProcessor charge_rules;
extern RadiusRuleProcessor radius_rules;
// the system that holds everything
extern System S;
// the name of the dump file
extern String dump_file;
// the default probe sphere radius for surface calculations
extern float probe_radius;
// flags:
// the three main options:
// true, if the solvent excluded surface is to be calculated
extern bool ses_calculation;
// true, if the solvent accessible surface is to be calculated
extern bool sas_calculation;
// true, if a FDPB calculation is to ber performed
extern bool fdpb_calculation;
// the results of the SES and SAS area calculations
extern float total_SAS_area;
extern float total_SAS_volume;
extern float total_SES_area;
extern float total_SES_volume;
// a hash map containing the atom surfaces of the SAS (if calculated)
extern HashMap<const Atom*, float> surface_map;
// true, if timing information and final options should be printed
extern bool verbose;
// true, if the charges should be cleared upon read
extern bool clear_charges;
// true, if the names should be normalized upon read
extern bool normalize_names;
// true, if the bonds should be built upon read
extern bool build_bonds;
// true, if the rule-based assignment is to be used
extern bool use_charge_rules;
extern bool use_radius_rules;
// true, if the solvation free energy is to be calculated
// (difference calculation solvent/vacuum)
extern bool calculate_solvation_energy;
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