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MMFF94Parameters.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: MMFF94Parameters.h,v 1.1.8.1 2007/03/25 21:25:17 oliver Exp $
//
// Molecular Mechanics: MMFF94 force field class
#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
#define BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif
#ifndef BALL_DATATYPE_HASHMAP_H
# include <BALL/DATATYPE/hashMap.h>
#endif
namespace BALL
{
class Atom;
class Parameters;
Position getMMFF94Index(Position atom_type1, Position atom_type2);
extern Size MMFF94_number_atom_types;
class MMFF94AtomTypeEquivalences;
#define MMFF94_INVALID_VALUE 99.0
class BALL_EXPORT MMFF94ParametersBase
{
public:
BALL_CREATE(MMFF94ParametersBase)
MMFF94ParametersBase();
virtual ~MMFF94ParametersBase() {};
const MMFF94ParametersBase& operator = (const MMFF94ParametersBase&)
{return *this;};
virtual void clear()
;
bool isInitialized() { return is_initialized_;}
bool readParameters(Parameters& p, const String& section);
void setEquivalences(const MMFF94AtomTypeEquivalences& equi) { equiv_ = &equi;}
protected:
virtual bool setup_(const std::vector<std::vector<String> >&) { return true;};
bool is_initialized_;
// nr of needed fields in parameter files
Size number_expected_fields_;
const MMFF94AtomTypeEquivalences* equiv_;
};
class BALL_EXPORT MMFF94AtomTypeEquivalences:
public MMFF94ParametersBase
{
public:
MMFF94AtomTypeEquivalences();
MMFF94AtomTypeEquivalences(const MMFF94AtomTypeEquivalences& to_copy);
~MMFF94AtomTypeEquivalences();
void clear()
;
Index getEquivalence(Position original, Position number) const;
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
std::vector<std::vector<Position> > equivalences_;
std::vector<String> names_;
std::vector<bool> exists_;
};
struct BALL_EXPORT MMFF94AtomType
{
MMFF94AtomType();
Position aspec;
Position crd;
Position val;
bool pilp;
Position mltb;
bool arom;
bool lin;
bool sbmb;
bool valid;
};
class BALL_EXPORT MMFF94AtomTypes:
public MMFF94ParametersBase
{
public:
MMFF94AtomTypes();
MMFF94AtomTypes(const MMFF94AtomTypes& to_copy);
~MMFF94AtomTypes() {};
const std::vector<MMFF94AtomType>& getAtomTypes() const { return data_;}
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
std::vector<MMFF94AtomType> data_;
};
class BALL_EXPORT MMFF94StretchParameters:
public MMFF94ParametersBase
{
public:
struct BondData
{
BondData();
double kb_normal;
double r0_normal;
bool standard_bond_exists;
double kb_sbmb;
double r0_sbmb;
bool sbmb_exists;
bool empirical;
};
struct EmpiricalBondData
{
double kb;
double r0;
};
typedef HashMap<Position, BondData> StretchMap;
typedef HashMap<Position, EmpiricalBondData> EmpiricalStretchMap;
BALL_CREATE(MMFF94StretchParameters)
MMFF94StretchParameters();
virtual ~MMFF94StretchParameters();
const MMFF94StretchParameters& operator = (const MMFF94StretchParameters& param)
;
virtual void clear()
;
bool assignParameters(Position type1, Position type2, BondData& data) const;
bool readEmpiricalParameters(Parameters& p, const String& section);
const StretchMap& getBondParameters() const { return parameters_;}
const EmpiricalStretchMap& getEmpiricalParameters() const { return empirical_parameters_;}
static double radii[];
static double electronegatives[];
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
StretchMap parameters_;
mutable StretchMap buffered_parameters_;
EmpiricalStretchMap empirical_parameters_;
};
class BALL_EXPORT MMFF94BendParameters
: public MMFF94ParametersBase
{
public:
typedef HashMap<Position, std::pair<double, double> > BendMap;
BALL_CREATE(MMFF94BendParameters)
MMFF94BendParameters();
virtual ~MMFF94BendParameters();
const MMFF94BendParameters& operator = (const MMFF94BendParameters& param)
;
virtual void clear()
;
bool assignParameters(Position bend_type,
Position atom_type1, Position atom_type2, Position atom_type3,
double& ka, double& angle) const;
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
Position getIndex_(Position bend_type, Position atom_type1, Position atom_type2, Position atom_type3) const;
BendMap parameters_;
mutable BendMap buffered_parameters_;
};
class BALL_EXPORT MMFF94StretchBendParameters
: public MMFF94ParametersBase
{
public:
typedef HashMap<Position, std::pair<double, double> > StretchBendMap;
BALL_CREATE(MMFF94StretchBendParameters)
MMFF94StretchBendParameters();
virtual ~MMFF94StretchBendParameters();
const MMFF94StretchBendParameters& operator = (const MMFF94StretchBendParameters& param)
;
virtual void clear()
;
bool assignParameters(Position stretch_bend_type, const Atom& atom1, const Atom& atom2, const Atom& atom3,
double& kba_ijk, double& kba_kji) const;
bool readEmpiricalParameters(Parameters& p, const String& section);
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
Position getIndex_(Position stretch_bend_type,
Position atom_type1, Position atom_type2, Position atom_type3) const;
Position getIndexByRow_(Position r1, Position r2, Position r3) const;
StretchBendMap parameters_;
mutable StretchBendMap buffered_parameters_;
StretchBendMap parameters_by_row_;
};
class BALL_EXPORT MMFF94TorsionParameters
: public MMFF94ParametersBase
{
public:
typedef HashMap<String, std::vector<double> > TorsionsMap;
BALL_CREATE(MMFF94TorsionParameters)
MMFF94TorsionParameters();
virtual ~MMFF94TorsionParameters();
const MMFF94TorsionParameters& operator = (const MMFF94TorsionParameters& param)
;
virtual void clear()
;
bool assignParameters(Position type_index,
Index at1, Index at2, Index at3, Index at4,
double& v1, double& v2, double& v3) const;
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
String getIndex_(Position type, Position atom_type1, Position atom_type2, Position atom_type3, Position atom_type4) const;
TorsionsMap parameters_;
mutable TorsionsMap buffered_parameters_;
static Position ic_[5];
static Position lc_[5];
};
class BALL_EXPORT MMFF94PlaneParameters
: public MMFF94ParametersBase
{
public:
typedef HashMap<String, double> PlaneMap;
BALL_CREATE(MMFF94PlaneParameters)
MMFF94PlaneParameters();
virtual ~MMFF94PlaneParameters();
const MMFF94PlaneParameters& operator = (const MMFF94PlaneParameters& param)
;
virtual void clear()
;
bool assignParameters(Index at1, Index at2, Index at3, Index at4, double& v) const;
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
String getIndex_(Position atom_type1, Position atom_type2, Position atom_type3, Position atom_type4) const;
PlaneMap parameters_;
mutable PlaneMap buffered_parameters_;
};
class BALL_EXPORT MMFF94VDWParameters
: public MMFF94ParametersBase
{
public:
struct VDWEntry
{
double alpha_i;
double ni;
double ai;
double gi;
short donor_acceptor;
bool valid;
};
BALL_CREATE(MMFF94VDWParameters)
MMFF94VDWParameters();
virtual ~MMFF94VDWParameters();
const MMFF94VDWParameters& operator = (const MMFF94VDWParameters& param)
;
virtual void clear()
;
double getR(Position atom_type) const;
const VDWEntry& getParameters(Index at) const;
bool assignParameters(Position at1, Position at2, double& rij, double& rij_7_, double& eij) const;
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
std::vector<VDWEntry> parameters_;
// R star ii for all individual atom types
mutable std::vector<double> rs_;
// R star ij for pairs of atom types
mutable std::vector<double> rij_;
// R star ij ^ 7 for pairs of atom types
mutable std::vector<double> rij_7_;
// R star ij and for pairs of atom types
mutable std::vector<double> eij_;
// bools if indivual value was already calculated
mutable std::vector<bool> calculated_;
};
class BALL_EXPORT MMFF94ESParameters
: public MMFF94ParametersBase
{
public:
BALL_CREATE(MMFF94ESParameters)
MMFF94ESParameters();
virtual ~MMFF94ESParameters();
const MMFF94ESParameters& operator = (const MMFF94ESParameters& param)
;
virtual void clear()
;
double getPartialCharge(Position at1, Position at2, Position bt) const;
bool readEmpiricalParameters(Parameters& p, const String& section);
double getPhi(Index atom_type) const;
double getPBCI(Index atom_type) const;
protected:
virtual bool setup_(const std::vector<std::vector<String> >&);
Position getIndex_(Position at1, Position at2, Position bt) const;
std::vector<double> parameters_, phis_, pbcis_;
};
} // namespace BALL
#endif // BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
BALL::Atom
Definition atom.h:90
BALL::HashMap
HashMap class based on the STL map (containing serveral convenience functions).
Definition hashMap.h:74
BALL::MMFF94AtomTypeEquivalences
Definition MMFF94Parameters.h:85
BALL::MMFF94AtomTypeEquivalences::names_
std::vector< String > names_
Definition MMFF94Parameters.h:111
BALL::MMFF94AtomTypeEquivalences::clear
void clear()
Clear method.
BALL::MMFF94AtomTypeEquivalences::MMFF94AtomTypeEquivalences
MMFF94AtomTypeEquivalences(const MMFF94AtomTypeEquivalences &to_copy)
BALL::MMFF94AtomTypeEquivalences::exists_
std::vector< bool > exists_
Definition MMFF94Parameters.h:112
BALL::MMFF94AtomTypeEquivalences::~MMFF94AtomTypeEquivalences
~MMFF94AtomTypeEquivalences()
BALL::MMFF94AtomTypeEquivalences::equivalences_
std::vector< std::vector< Position > > equivalences_
Definition MMFF94Parameters.h:110
BALL::MMFF94AtomTypeEquivalences::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94AtomTypeEquivalences::MMFF94AtomTypeEquivalences
MMFF94AtomTypeEquivalences()
BALL::MMFF94AtomTypeEquivalences::getEquivalence
Index getEquivalence(Position original, Position number) const
BALL::MMFF94AtomTypes::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94AtomTypes::data_
std::vector< MMFF94AtomType > data_
Definition MMFF94Parameters.h:177
BALL::MMFF94AtomTypes::MMFF94AtomTypes
MMFF94AtomTypes(const MMFF94AtomTypes &to_copy)
BALL::MMFF94AtomTypes::~MMFF94AtomTypes
~MMFF94AtomTypes()
Definition MMFF94Parameters.h:169
BALL::MMFF94AtomTypes::MMFF94AtomTypes
MMFF94AtomTypes()
BALL::MMFF94AtomTypes::getAtomTypes
const std::vector< MMFF94AtomType > & getAtomTypes() const
Definition MMFF94Parameters.h:172
BALL::MMFF94BendParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94BendParameters::buffered_parameters_
BendMap buffered_parameters_
Definition MMFF94Parameters.h:300
BALL::MMFF94BendParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94BendParameters::assignParameters
bool assignParameters(Position bend_type, Position atom_type1, Position atom_type2, Position atom_type3, double &ka, double &angle) const
BALL::MMFF94BendParameters::MMFF94BendParameters
MMFF94BendParameters()
Default constructor.
BALL::MMFF94BendParameters::getIndex_
Position getIndex_(Position bend_type, Position atom_type1, Position atom_type2, Position atom_type3) const
BALL::MMFF94BendParameters::parameters_
BendMap parameters_
parameters
Definition MMFF94Parameters.h:299
BALL::MMFF94BendParameters::BendMap
HashMap< Position, std::pair< double, double > > BendMap
Map with the force constant and reference angle.
Definition MMFF94Parameters.h:269
BALL::MMFF94ESParameters::pbcis_
std::vector< double > pbcis_
Definition MMFF94Parameters.h:567
BALL::MMFF94ESParameters::phis_
std::vector< double > phis_
Definition MMFF94Parameters.h:567
BALL::MMFF94ESParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94ESParameters::getPBCI
double getPBCI(Index atom_type) const
BALL::MMFF94ESParameters::parameters_
std::vector< double > parameters_
parameters
Definition MMFF94Parameters.h:567
BALL::MMFF94ESParameters::getPhi
double getPhi(Index atom_type) const
BALL::MMFF94ESParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94ESParameters::MMFF94ESParameters
MMFF94ESParameters()
Default constructor.
BALL::MMFF94ESParameters::getIndex_
Position getIndex_(Position at1, Position at2, Position bt) const
BALL::MMFF94ESParameters::getPartialCharge
double getPartialCharge(Position at1, Position at2, Position bt) const
BALL::MMFF94ESParameters::readEmpiricalParameters
bool readEmpiricalParameters(Parameters &p, const String &section)
BALL::MMFF94ParametersBase::is_initialized_
bool is_initialized_
Definition MMFF94Parameters.h:72
BALL::MMFF94ParametersBase::readParameters
bool readParameters(Parameters &p, const String &section)
BALL::MMFF94ParametersBase::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
Definition MMFF94Parameters.h:70
BALL::MMFF94ParametersBase::equiv_
const MMFF94AtomTypeEquivalences * equiv_
Definition MMFF94Parameters.h:76
BALL::MMFF94ParametersBase::number_expected_fields_
Size number_expected_fields_
Definition MMFF94Parameters.h:75
BALL::MMFF94ParametersBase::clear
virtual void clear()
Clear method.
BALL::MMFF94ParametersBase::isInitialized
bool isInitialized()
Definition MMFF94Parameters.h:60
BALL::MMFF94ParametersBase::setEquivalences
void setEquivalences(const MMFF94AtomTypeEquivalences &equi)
Definition MMFF94Parameters.h:66
BALL::MMFF94ParametersBase::MMFF94ParametersBase
MMFF94ParametersBase()
Default constructor.
BALL::MMFF94PlaneParameters::getIndex_
String getIndex_(Position atom_type1, Position atom_type2, Position atom_type3, Position atom_type4) const
BALL::MMFF94PlaneParameters::assignParameters
bool assignParameters(Index at1, Index at2, Index at3, Index at4, double &v) const
BALL::MMFF94PlaneParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94PlaneParameters::buffered_parameters_
PlaneMap buffered_parameters_
Definition MMFF94Parameters.h:449
BALL::MMFF94PlaneParameters::MMFF94PlaneParameters
MMFF94PlaneParameters()
Default constructor.
BALL::MMFF94PlaneParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94PlaneParameters::PlaneMap
HashMap< String, double > PlaneMap
Map with the force constant.
Definition MMFF94Parameters.h:420
BALL::MMFF94PlaneParameters::parameters_
PlaneMap parameters_
parameters
Definition MMFF94Parameters.h:448
BALL::MMFF94StretchBendParameters::assignParameters
bool assignParameters(Position stretch_bend_type, const Atom &atom1, const Atom &atom2, const Atom &atom3, double &kba_ijk, double &kba_kji) const
BALL::MMFF94StretchBendParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94StretchBendParameters::parameters_
StretchBendMap parameters_
parameters
Definition MMFF94Parameters.h:355
BALL::MMFF94StretchBendParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94StretchBendParameters::getIndexByRow_
Position getIndexByRow_(Position r1, Position r2, Position r3) const
BALL::MMFF94StretchBendParameters::StretchBendMap
HashMap< Position, std::pair< double, double > > StretchBendMap
Map with the force constant and reference angle.
Definition MMFF94Parameters.h:316
BALL::MMFF94StretchBendParameters::MMFF94StretchBendParameters
MMFF94StretchBendParameters()
Default constructor.
BALL::MMFF94StretchBendParameters::buffered_parameters_
StretchBendMap buffered_parameters_
Definition MMFF94Parameters.h:356
BALL::MMFF94StretchBendParameters::getIndex_
Position getIndex_(Position stretch_bend_type, Position atom_type1, Position atom_type2, Position atom_type3) const
BALL::MMFF94StretchBendParameters::readEmpiricalParameters
bool readEmpiricalParameters(Parameters &p, const String &section)
BALL::MMFF94StretchBendParameters::parameters_by_row_
StretchBendMap parameters_by_row_
Definition MMFF94Parameters.h:357
BALL::MMFF94StretchParameters::buffered_parameters_
StretchMap buffered_parameters_
Definition MMFF94Parameters.h:254
BALL::MMFF94StretchParameters::assignParameters
bool assignParameters(Position type1, Position type2, BondData &data) const
BALL::MMFF94StretchParameters::electronegatives
static double electronegatives[]
Definition MMFF94Parameters.h:246
BALL::MMFF94StretchParameters::readEmpiricalParameters
bool readEmpiricalParameters(Parameters &p, const String &section)
BALL::MMFF94StretchParameters::empirical_parameters_
EmpiricalStretchMap empirical_parameters_
Definition MMFF94Parameters.h:255
BALL::MMFF94StretchParameters::StretchMap
HashMap< Position, BondData > StretchMap
Definition MMFF94Parameters.h:214
BALL::MMFF94StretchParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94StretchParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94StretchParameters::MMFF94StretchParameters
MMFF94StretchParameters()
Default constructor.
BALL::MMFF94StretchParameters::getBondParameters
const StretchMap & getBondParameters() const
Definition MMFF94Parameters.h:240
BALL::MMFF94StretchParameters::getEmpiricalParameters
const EmpiricalStretchMap & getEmpiricalParameters() const
Definition MMFF94Parameters.h:243
BALL::MMFF94StretchParameters::EmpiricalStretchMap
HashMap< Position, EmpiricalBondData > EmpiricalStretchMap
Definition MMFF94Parameters.h:215
BALL::MMFF94StretchParameters::radii
static double radii[]
Definition MMFF94Parameters.h:245
BALL::MMFF94StretchParameters::parameters_
StretchMap parameters_
standard parameters
Definition MMFF94Parameters.h:253
BALL::MMFF94TorsionParameters::buffered_parameters_
TorsionsMap buffered_parameters_
Definition MMFF94Parameters.h:403
BALL::MMFF94TorsionParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94TorsionParameters::getIndex_
String getIndex_(Position type, Position atom_type1, Position atom_type2, Position atom_type3, Position atom_type4) const
BALL::MMFF94TorsionParameters::MMFF94TorsionParameters
MMFF94TorsionParameters()
Default constructor.
BALL::MMFF94TorsionParameters::lc_
static Position lc_[5]
Definition MMFF94Parameters.h:405
BALL::MMFF94TorsionParameters::assignParameters
bool assignParameters(Position type_index, Index at1, Index at2, Index at3, Index at4, double &v1, double &v2, double &v3) const
BALL::MMFF94TorsionParameters::ic_
static Position ic_[5]
Definition MMFF94Parameters.h:404
BALL::MMFF94TorsionParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94TorsionParameters::parameters_
TorsionsMap parameters_
parameters
Definition MMFF94Parameters.h:402
BALL::MMFF94TorsionParameters::TorsionsMap
HashMap< String, std::vector< double > > TorsionsMap
Map with the force constant and reference angle.
Definition MMFF94Parameters.h:372
BALL::MMFF94VDWParameters::getR
double getR(Position atom_type) const
BALL::MMFF94VDWParameters::eij_
std::vector< double > eij_
Definition MMFF94Parameters.h:513
BALL::MMFF94VDWParameters::MMFF94VDWParameters
MMFF94VDWParameters()
Default constructor.
BALL::MMFF94VDWParameters::rs_
std::vector< double > rs_
Definition MMFF94Parameters.h:506
BALL::MMFF94VDWParameters::clear
virtual void clear()
Clear method.
BALL::MMFF94VDWParameters::setup_
virtual bool setup_(const std::vector< std::vector< String > > &)
BALL::MMFF94VDWParameters::parameters_
std::vector< VDWEntry > parameters_
parameters
Definition MMFF94Parameters.h:503
BALL::MMFF94VDWParameters::rij_
std::vector< double > rij_
Definition MMFF94Parameters.h:509
BALL::MMFF94VDWParameters::rij_7_
std::vector< double > rij_7_
Definition MMFF94Parameters.h:511
BALL::MMFF94VDWParameters::assignParameters
bool assignParameters(Position at1, Position at2, double &rij, double &rij_7_, double &eij) const
BALL::MMFF94VDWParameters::calculated_
std::vector< bool > calculated_
Definition MMFF94Parameters.h:515
BALL::MMFF94VDWParameters::getParameters
const VDWEntry & getParameters(Index at) const
Retrieve vdW parameters for a single atom type.
BALL::Parameters
Definition parameters.h:25
BALL::String
Definition string.h:57
common.h
BALL_CREATE
#define BALL_CREATE(name)
Definition create.h:62
hashMap.h
BALL
Definition constants.h:13
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114
BALL::MMFF94_number_atom_types
Size MMFF94_number_atom_types
hold the maximum number of MMFF94 atom types + 1 (wildcard)
BALL::Position
BALL_SIZE_TYPE Position
Definition COMMON/global.h:140
BALL::getMMFF94Index
Position getMMFF94Index(Position atom_type1, Position atom_type2)
BALL::Index
BALL_INDEX_TYPE Index
Definition COMMON/global.h:105
std
STL namespace.
BALL::MMFF94AtomType::mltb
Position mltb
Definition MMFF94Parameters.h:137
BALL::MMFF94AtomType::arom
bool arom
is aromatic
Definition MMFF94Parameters.h:140
BALL::MMFF94AtomType::valid
bool valid
Is this a valid MMFF94 atom type?
Definition MMFF94Parameters.h:149
BALL::MMFF94AtomType::lin
bool lin
has linear bond
Definition MMFF94Parameters.h:143
BALL::MMFF94AtomType::aspec
Position aspec
atomic number;
Definition MMFF94Parameters.h:123
BALL::MMFF94AtomType::val
Position val
number of bonds made to this atom type
Definition MMFF94Parameters.h:129
BALL::MMFF94AtomType::MMFF94AtomType
MMFF94AtomType()
BALL::MMFF94AtomType::sbmb
bool sbmb
can have a delocalized single bond
Definition MMFF94Parameters.h:146
BALL::MMFF94AtomType::pilp
bool pilp
has pi lone pair electrons
Definition MMFF94Parameters.h:132
BALL::MMFF94AtomType::crd
Position crd
necessary number of bonded neighbours
Definition MMFF94Parameters.h:126
BALL::MMFF94StretchParameters::BondData
Definition MMFF94Parameters.h:192
BALL::MMFF94StretchParameters::BondData::BondData
BondData()
BALL::MMFF94StretchParameters::BondData::r0_normal
double r0_normal
Definition MMFF94Parameters.h:196
BALL::MMFF94StretchParameters::BondData::sbmb_exists
bool sbmb_exists
Definition MMFF94Parameters.h:202
BALL::MMFF94StretchParameters::BondData::standard_bond_exists
bool standard_bond_exists
Definition MMFF94Parameters.h:197
BALL::MMFF94StretchParameters::BondData::r0_sbmb
double r0_sbmb
Definition MMFF94Parameters.h:201
BALL::MMFF94StretchParameters::BondData::kb_normal
double kb_normal
Definition MMFF94Parameters.h:195
BALL::MMFF94StretchParameters::BondData::empirical
bool empirical
Definition MMFF94Parameters.h:203
BALL::MMFF94StretchParameters::BondData::kb_sbmb
double kb_sbmb
parameters for optinal single-bond–multiple bond cases (see MMFFPROP.PAR)
Definition MMFF94Parameters.h:200
BALL::MMFF94StretchParameters::EmpiricalBondData
Definition MMFF94Parameters.h:208
BALL::MMFF94StretchParameters::EmpiricalBondData::kb
double kb
Definition MMFF94Parameters.h:209
BALL::MMFF94StretchParameters::EmpiricalBondData::r0
double r0
Definition MMFF94Parameters.h:210
BALL::MMFF94VDWParameters::VDWEntry
Definition MMFF94Parameters.h:464
BALL::MMFF94VDWParameters::VDWEntry::valid
bool valid
Definition MMFF94Parameters.h:470
BALL::MMFF94VDWParameters::VDWEntry::alpha_i
double alpha_i
Definition MMFF94Parameters.h:465
BALL::MMFF94VDWParameters::VDWEntry::ai
double ai
Definition MMFF94Parameters.h:467
BALL::MMFF94VDWParameters::VDWEntry::donor_acceptor
short donor_acceptor
Definition MMFF94Parameters.h:469
BALL::MMFF94VDWParameters::VDWEntry::gi
double gi
Definition MMFF94Parameters.h:468
BALL::MMFF94VDWParameters::VDWEntry::ni
double ni
Definition MMFF94Parameters.h:466