BALL: MMFF94.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // $Id: MMFF94.h,v 1.1.8.3 2007/06/15 09:24:20 amoll Exp $ 
00005 //
00006 
00007 // Molecular Mechanics: MMFF94 force field class
00008 
00009 #ifndef BALL_MOLMEC_MMFF94_MMFF94_H
00010 #define BALL_MOLMEC_MMFF94_MMFF94_H
00011 
00012 #ifndef BALL_COMMON_H
00013 # include <BALL/common.h>
00014 #endif
00015 
00016 #ifndef BALL_MOLMEC_COMMON_FORCEFIELD_H
00017 # include <BALL/MOLMEC/COMMON/forceField.h>
00018 #endif
00019 
00020 #ifndef BALL_KERNEL_SYSTEM_H
00021 # include <BALL/KERNEL/system.h>
00022 #endif
00023 
00024 #ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
00025 # include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
00026 #endif
00027 
00028 #ifndef BALL_MOLMEC_MMFF94_MMFF94PROCESSORS_H
00029 # include <BALL/MOLMEC/MMFF94/MMFF94Processors.h>
00030 #endif
00031 
00032 #ifndef BALL_DATATYPE_HASHSET_H
00033 # include <BALL/DATATYPE/hashSet.h>
00034 #endif
00035 
00036 #ifndef BALL_STRUCTURE_KEKULIZER_H
00037 # include <BALL/STRUCTURE/kekulizer.h>
00038 #endif
00039 
00040 #include <vector>
00041 
00042 namespace BALL 
00043 {
00044   using std::vector;
00045 
00049   class BALL_EXPORT MMFF94 
00050     : public ForceField
00051   {
00052     public:
00053 
00057 
00060     struct BALL_EXPORT Option
00061     {
00064       static const char* FOLDER;
00065 
00068       static const char* ASSIGN_CHARGES;
00069 
00072       static const char* ASSIGN_TYPENAMES;
00073 
00076       static const char* ASSIGN_TYPES;
00077 
00080       static const char* OVERWRITE_CHARGES;
00081 
00084       static const char* OVERWRITE_TYPENAMES;
00085 
00090       static const char* NONBONDED_CUTOFF;
00091 
00095       static const char* VDW_CUTOFF;
00096 
00100       static const char* VDW_CUTON;
00101 
00104       static const char* ELECTROSTATIC_CUTOFF;
00105 
00108       static const char* ELECTROSTATIC_CUTON;
00109 
00111       static const char* DISTANCE_DEPENDENT_DIELECTRIC;
00112     };
00113 
00116     struct BALL_EXPORT Default
00117     {
00120       static const char* FOLDER;
00121 
00124       static const bool ASSIGN_CHARGES;
00125 
00128       static const bool ASSIGN_TYPENAMES;
00129 
00132       static const bool ASSIGN_TYPES;
00133 
00136       static const bool OVERWRITE_CHARGES;
00137 
00140       static const bool OVERWRITE_TYPENAMES;
00141 
00144       static const float NONBONDED_CUTOFF;
00145 
00148       static const float VDW_CUTOFF;
00149 
00152       static const float VDW_CUTON;
00153 
00156       static const float ELECTROSTATIC_CUTOFF;
00157 
00160       static const float ELECTROSTATIC_CUTON;
00161 
00163       static const bool DISTANCE_DEPENDENT_DIELECTRIC;
00164     };
00165 
00167 
00170 
00171     BALL_CREATE(MMFF94)
00172 
00173     
00175     MMFF94();
00176 
00179     MMFF94(System& system);
00180 
00183     MMFF94(System& system, const Options& options);
00184  
00187     MMFF94(const MMFF94& force_field);
00188 
00191     virtual ~MMFF94();
00192 
00194 
00197 
00200     const MMFF94& operator = (const MMFF94& force_field)
00201       ;
00202 
00205     virtual void clear()
00206       ;
00207     
00209 
00212 
00215     virtual bool specificSetup()
00216       throw(Exception::TooManyErrors);
00217 
00219 
00222 
00225     double getStretchEnergy() const;
00226 
00229     double getBendEnergy() const;
00230 
00232     double getStretchBendEnergy() const;
00233 
00237     double getTorsionEnergy() const;
00238 
00242     double getNonbondedEnergy() const;
00243 
00246     double getESEnergy() const;
00247 
00250     double getVdWEnergy() const;
00251 
00253     double getPlaneEnergy() const;
00254 
00257     bool hasInitializedParameters() const;
00258 
00262     Size getUpdateFrequency() const;
00263 
00265     virtual String getResults() const
00266       ;
00267 
00269     const vector<Bond*> getBonds() const { return bonds_;}
00270     
00272     const vector<HashSet<Atom*> >& getRings() const { return rings_;}
00273     
00275     const vector<HashSet<Atom*> >& getAromaticRings() const { return aromatic_rings_;}
00276     
00278     bool isInOneAromaticRing(const Bond& bond) const;
00279     
00281     bool assignMMFF94BondType(Bond& bond) const;
00282 
00284     const vector<MMFF94AtomType>& getAtomTypes() const { return atom_types_.getAtomTypes();}
00285 
00287     const MMFF94StretchParameters& getStretchParameters() const { return bond_parameters_;}
00288 
00290     const MMFF94AtomTypeEquivalences & getEquivalences() const { return equivalences_;}
00291 
00293     bool areInOneRing(vector<Atom*> v, Size ring_size = 0) const;
00294     
00296     bool areInOneAromaticRing(const vector<Atom*>& v, Size ring_size = 0) const;
00297 
00301     bool checkAtomType(Atom& atom);
00302 
00304 
00305     protected:
00306 
00307     void insertComponents_();
00308 
00309     void transformAromaticBonds_();
00310     void collectBonds_();
00311     void assignBondTypes_();
00312     void collectRings_();
00313       
00314     String                      folder_;
00315     MMFF94AtomTypes             atom_types_;
00316     MMFF94StretchParameters     bond_parameters_;
00317     MMFF94AtomTypeEquivalences  equivalences_;
00318     MMFF94ESParameters          es_parameters_;
00319     vector<HashSet<Atom*> >     rings_;
00320     vector<HashSet<Atom*> >     aromatic_rings_;
00321     bool                        parameters_initialized_;
00322     vector<Bond*>               bonds_;
00323     MMFF94AtomTyper             atom_typer_;
00324     MMFF94ChargeProcessor       charge_processor_;
00325     Kekuliser                   kekuliser_;
00326     HashSet<Bond*>              aromatic_bonds_;
00327   };
00328 
00329 } // namespace BALL
00330 
00331 #endif // BALL_MOLMEC_MMFF94_H