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9 #ifndef BALL_MOLMEC_MMFF94_MMFF94_H
10 #define BALL_MOLMEC_MMFF94_MMFF94_H
16 #ifndef BALL_MOLMEC_COMMON_FORCEFIELD_H
20 #ifndef BALL_KERNEL_SYSTEM_H
24 #ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
28 #ifndef BALL_MOLMEC_MMFF94_MMFF94PROCESSORS_H
32 #ifndef BALL_DATATYPE_HASHSET_H
36 #ifndef BALL_STRUCTURE_KEKULIZER_H
216 virtual bool specificSetup();
225 double getStretchEnergy()
const;
229 double getBendEnergy()
const;
232 double getStretchBendEnergy()
const;
237 double getTorsionEnergy()
const;
242 double getNonbondedEnergy()
const;
246 double getESEnergy()
const;
250 double getVdWEnergy()
const;
253 double getPlaneEnergy()
const;
257 bool hasInitializedParameters()
const;
262 Size getUpdateFrequency()
const;
265 virtual String getResults()
const
269 const vector<Bond*>
getBonds()
const {
return bonds_;}
272 const vector<HashSet<Atom*> >&
getRings()
const {
return rings_;}
278 bool isInOneAromaticRing(
const Bond& bond)
const;
281 bool assignMMFF94BondType(
Bond& bond)
const;
284 const vector<MMFF94AtomType>&
getAtomTypes()
const {
return atom_types_.getAtomTypes();}
293 bool areInOneRing(vector<Atom*> v,
Size ring_size = 0)
const;
296 bool areInOneAromaticRing(
const vector<Atom*>& v,
Size ring_size = 0)
const;
301 bool checkAtomType(
Atom& atom);
307 void insertComponents_();
309 void transformAromaticBonds_();
310 void collectBonds_();
311 void assignBondTypes_();
312 void collectRings_();
331 #endif // BALL_MOLMEC_MMFF94_H
static const float ELECTROSTATIC_CUTON
static const bool ASSIGN_CHARGES
static const float VDW_CUTON
bool parameters_initialized_
vector< HashSet< Atom * > > aromatic_rings_
static const char * OVERWRITE_CHARGES
static const float ELECTROSTATIC_CUTOFF
static const bool ASSIGN_TYPENAMES
const vector< HashSet< Atom * > > & getRings() const
const MMFF94StretchParameters & getStretchParameters() const
static const char * FOLDER
static const char * DISTANCE_DEPENDENT_DIELECTRIC
MMFF94ESParameters es_parameters_
static const bool DISTANCE_DEPENDENT_DIELECTRIC
Default is false.
static const float NONBONDED_CUTOFF
static const char * FOLDER
static const char * ELECTROSTATIC_CUTOFF
MMFF94AtomTyper atom_typer_
MMFF94AtomTypes atom_types_
static const bool ASSIGN_TYPES
const vector< Bond * > getBonds() const
static const char * VDW_CUTOFF
MMFF94AtomTypeEquivalences equivalences_
static const char * NONBONDED_CUTOFF
MMFF94StretchParameters bond_parameters_
static const char * VDW_CUTON
static const bool OVERWRITE_TYPENAMES
const vector< HashSet< Atom * > > & getAromaticRings() const
static const float VDW_CUTOFF
static const char * OVERWRITE_TYPENAMES
static const bool OVERWRITE_CHARGES
const MMFF94AtomTypeEquivalences & getEquivalences() const
#define BALL_CREATE(name)
static const char * ASSIGN_TYPENAMES
static const char * ELECTROSTATIC_CUTON
MMFF94ChargeProcessor charge_processor_
static const char * ASSIGN_TYPES
HashSet< Bond * > aromatic_bonds_
static const char * ASSIGN_CHARGES
const vector< MMFF94AtomType > & getAtomTypes() const
vector< HashSet< Atom * > > rings_