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9 #ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
10 #define BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
16 #ifndef BALL_DATATYPE_HASHMAP_H
31 class MMFF94AtomTypeEquivalences;
33 #define MMFF94_INVALID_VALUE 99.0
70 virtual bool setup_(
const std::vector<std::vector<String> >&) {
return true;};
109 virtual bool setup_(
const std::vector<std::vector<String> >&);
172 const std::vector<MMFF94AtomType>&
getAtomTypes()
const {
return data_;}
176 virtual bool setup_(
const std::vector<std::vector<String> >&);
245 static double radii[];
246 static double electronegatives[];
250 virtual bool setup_(
const std::vector<std::vector<String> >&);
288 bool assignParameters(
Position bend_type,
290 double& ka,
double& angle)
const;
294 virtual bool setup_(
const std::vector<std::vector<String> >&);
335 bool assignParameters(
Position stretch_bend_type,
const Atom& atom1,
const Atom& atom2,
const Atom& atom3,
336 double& kba_ijk,
double& kba_kji)
const;
347 virtual bool setup_(
const std::vector<std::vector<String> >&);
391 bool assignParameters(
Position type_index,
393 double& v1,
double& v2,
double& v3)
const;
397 virtual bool setup_(
const std::vector<std::vector<String> >&);
443 virtual bool setup_(
const std::vector<std::vector<String> >&);
490 double getR(
Position atom_type)
const;
496 bool assignParameters(
Position at1,
Position at2,
double& rij,
double& rij_7_,
double& eij)
const;
500 virtual bool setup_(
const std::vector<std::vector<String> >&);
506 mutable std::vector<double>
rs_;
509 mutable std::vector<double>
rij_;
513 mutable std::vector<double>
eij_;
556 double getPhi(
Index atom_type)
const;
559 double getPBCI(
Index atom_type)
const;
563 virtual bool setup_(
const std::vector<std::vector<String> >&);
567 std::vector<double> parameters_,
phis_, pbcis_;
573 #endif // BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
Class to store the values of an atom type from MMFFPROP.PAR.
HashMap< Position, EmpiricalBondData > EmpiricalStretchMap
StretchBendMap parameters_
parameters
virtual bool setup_(const std::vector< std::vector< String > > &)
std::vector< bool > calculated_
double kb_sbmb
parameters for optinal single-bond–multiple bond cases (see MMFFPROP.PAR)
bool pilp
has pi lone pair electrons
TorsionsMap parameters_
parameters
HashMap< Position, std::pair< double, double > > StretchBendMap
Map with the force constant and reference angle.
const EmpiricalStretchMap & getEmpiricalParameters() const
HashMap< Position, std::pair< double, double > > BendMap
Map with the force constant and reference angle.
StretchMap buffered_parameters_
EmpiricalStretchMap empirical_parameters_
BendMap parameters_
parameters
std::vector< String > names_
Position getMMFF94Index(Position atom_type1, Position atom_type2)
bool standard_bond_exists
StretchMap parameters_
standard parameters
StretchBendMap buffered_parameters_
const MMFF94AtomTypeEquivalences * equiv_
std::vector< double > rij_7_
std::vector< bool > exists_
const StretchMap & getBondParameters() const
BendMap buffered_parameters_
HashMap< String, double > PlaneMap
Map with the force constant.
PlaneMap buffered_parameters_
Position aspec
atomic number;
const std::vector< MMFF94AtomType > & getAtomTypes() const
HashMap< String, std::vector< double > > TorsionsMap
Map with the force constant and reference angle.
Size MMFF94_number_atom_types
hold the maximum number of MMFF94 atom types + 1 (wildcard)
Size number_expected_fields_
PlaneMap parameters_
parameters
std::vector< double > eij_
std::vector< double > rij_
Position crd
necessary number of bonded neighbours
bool sbmb
can have a delocalized single bond
HashMap< Position, BondData > StretchMap
Position val
number of bonds made to this atom type
std::vector< double > rs_
#define BALL_CREATE(name)
std::vector< VDWEntry > parameters_
parameters
std::vector< MMFF94AtomType > data_
bool valid
Is this a valid MMFF94 atom type?
virtual ~MMFF94ParametersBase()
Destructor.
void setEquivalences(const MMFF94AtomTypeEquivalences &equi)
std::vector< double > phis_
std::vector< std::vector< Position > > equivalences_
TorsionsMap buffered_parameters_
StretchBendMap parameters_by_row_