/usr/include/BALL/MOLMEC/MMFF94/MMFF94StretchBend.h is in libball1.4-dev 1.4.3~beta1-4.
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//
// $Id: MMFF94StretchBend.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $
//
#ifndef BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
#define BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
#ifndef BALL_MOLMEC_COMMON_FORCEFIELDCOMPONENT_H
# include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
#endif
#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
# include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
#endif
namespace BALL
{
class MMFF94;
/** MMFF94 bond stretch component
\ingroup MMFF94
*/
class BALL_EXPORT MMFF94StretchBend
: public ForceFieldComponent
{
public:
struct BALL_EXPORT StretchBend
{
double kba_ijk;
double kba_kji;
double energy; // debug
Index sbtijk;
Index stretch_i_j, stretch_j_k;
Index bend_index;
};
/// see MMFFANG.PAR
struct BALL_EXPORT Bend
{
Bend();
double theta0;
double delta_theta;
double theta;
double ka;
Atom* atom1;
Atom* atom2;
Atom* atom3;
bool is_linear;
Position ATIJK;
double energy; // debug
bool emperical; // debug
TVector3<double> n1, n2;
};
///
struct BALL_EXPORT Stretch
{
Atom* atom1;
Atom* atom2;
double kb;
double r0;
double delta_r;
bool sbmb;
bool emperical;
Vector3 n;
};
/// flag to enable BENDS
#define MMFF94_BENDS_ENABLED "enable Bends"
/// flag to enable Stretches
#define MMFF94_STRETCHES_ENABLED "enable Stretches"
/// flag to enable StretchBends
#define MMFF94_STRETCHBENDS_ENABLED "enable StrechBends"
BALL_CREATE(MMFF94StretchBend)
/** Default constructor.
*/
MMFF94StretchBend();
/** Constructor.
*/
MMFF94StretchBend(ForceField& force_field);
/** Copy constructor
*/
MMFF94StretchBend(const MMFF94StretchBend& to_copy);
/** Destructor.
*/
virtual ~MMFF94StretchBend();
/** Setup method.
*/
virtual bool setup()
throw(Exception::TooManyErrors);
/// Calculates and returns the component's energy.
virtual double updateEnergy();
///
virtual double updateBendEnergy();
///
virtual double updateStretchEnergy();
///
virtual double updateStretchBendEnergy();
///
double getStretchEnergy() const;
///
double getBendEnergy() const;
///
double getStretchBendEnergy() const;
/// Calculates and returns the component's forces.
virtual void updateForces();
///
virtual void updateBendForces();
///
virtual void updateStretchForces();
///
virtual void updateStretchBendForces();
///
const vector<Bend>& getBends() const { return bends_;}
///
const vector<Stretch>& getStretches() const { return stretches_;}
///
const vector<StretchBend>& getStretchBends() const { return stretch_bends_;}
///
Index calculateSBTIJK(Position angle_type,
bool bond_type1,
bool bond_type2);
///
Position getBendType(const Bond& bond1, const Bond& bond2,
Atom& atom1, Atom& atom2, Atom& atom3) const;
/// Bend emperical reference angle
double calculateBendEmpiricalReferenceAngle(Atom& atom1, Atom& atom2, Atom& atom3) const;
/// Bend emperical force constant
double calculateBendEmpiricalForceConstant(Atom& atom1, Atom& atom2, Atom& atom3, double angle_0) const;
/// Calculate the radius value per Schomaker-Stevenson Rule
double calculateStretchR0(const Bond& bond);
///
double calculateStretchConstant(const Bond& bond, double r0);
private:
inline void AddDV3_(Vector3& f3, const TVector3<double> d3);
void calculateDeltas_();
bool setupBends_();
bool setupStretches_();
bool setupStretchBends_();
void errorOccured_(const String& string,
const Atom& a1, const Atom& a2, const Atom& a3);
vector<Bend> bends_;
vector<Stretch> stretches_;
vector<StretchBend> stretch_bends_;
const MMFF94StretchParameters* stretch_parameters_;
MMFF94BendParameters bend_parameters_;
MMFF94StretchBendParameters sb_parameters_;
static double bend_z_[];
static double bend_c_[];
static String bend_elements_[];
double stretch_energy_;
double bend_energy_;
double stretch_bend_energy_;
MMFF94* mmff94_;
bool stretch_enabled_, bend_enabled_, stretchbend_enabled_;
};
} // namespace BALL
#endif // BALL_MOLMEC_MMFF94_MMFF94STRETCHBEND_H
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