OBFFConstraints Class Reference

Internal class for OBForceField to handle constraints. More...

#include <openbabel/forcefield.h>

List of all members.

Public Member Functions

 OBFFConstraints ()
 ~OBFFConstraints ()
void Clear ()
double GetConstraintEnergy ()
vector3 GetGradient (int a)
OBFFConstraints & operator= (const OBFFConstraints &ai)
void Setup (OBMol &mol)
Methods to set constraints
void SetFactor (double factor)
void AddIgnore (int a)
void AddAtomConstraint (int a)
void AddAtomXConstraint (int a)
void AddAtomYConstraint (int a)
void AddAtomZConstraint (int a)
void AddDistanceConstraint (int a, int b, double length)
void AddAngleConstraint (int a, int b, int c, double angle)
void AddTorsionConstraint (int a, int b, int c, int d, double torsion)
void DeleteConstraint (int index)
Methods to get information about set constraints
double GetFactor ()
int Size () const
int GetConstraintType (int index) const
double GetConstraintValue (int index) const
int GetConstraintAtomA (int index) const
int GetConstraintAtomB (int index) const
int GetConstraintAtomC (int index) const
int GetConstraintAtomD (int index) const
bool IsIgnored (int a)
bool IsFixed (int a)
bool IsXFixed (int a)
bool IsYFixed (int a)
bool IsZFixed (int a)
OBBitVec GetIgnoredBitVec ()

Detailed Description

Internal class for OBForceField to handle constraints.

Since:
version 2.2

Constructor & Destructor Documentation

OBFFConstraints (  ) 

Constructor.

~OBFFConstraints (  )  [inline]

Destructor.

Member Function Documentation

void Clear ( void   ) 

Clear all constraints.

double GetConstraintEnergy (  ) 

Get the constraint energy.

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::LineSearch(), OBForceField::Newton2NumLineSearch(), OBForceField::SteepestDescentInitialize(), and OBForceField::SteepestDescentTakeNSteps().

vector3 GetGradient ( int  a  ) 

Get the constraint gradient for atom with index a.

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::MolecularDynamicsTakeNSteps(), and OBForceField::SteepestDescentTakeNSteps().

OBFFConstraints& operator= ( const OBFFConstraints &  ai  )  [inline]

Get the constrain gradient for the atom.

void Setup ( OBMol &  mol  ) 

Translate indices to OBAtom* objects, this function is called from OBForceField::Setup, this function doesn't have to be called from anywhere else.

Referenced by OBForceField::SetConstraints(), and OBForceField::Setup().

void SetFactor ( double  factor  ) 

Set Constraint factor.

void AddIgnore ( int  a  ) 

Ignore the atom while setting up calculations.

void AddAtomConstraint ( int  a  ) 

Fix the position of an atom.

void AddAtomXConstraint ( int  a  ) 

Fix the x coordinate of the atom position.

void AddAtomYConstraint ( int  a  ) 

Fix the y coordinate of the atom position.

void AddAtomZConstraint ( int  a  ) 

Fix the z coordinate of the atom position.

void AddDistanceConstraint ( int  a,
int  b,
double  length 
)

Constrain the bond length a-b.

void AddAngleConstraint ( int  a,
int  b,
int  c,
double  angle 
)

Constrain the angle a-b-c.

void AddTorsionConstraint ( int  a,
int  b,
int  c,
int  d,
double  torsion 
)

Constrain the torsion angle a-b-c-d.

void DeleteConstraint ( int  index  ) 

Delete a constraint

index constraint index

double GetFactor (  ) 

Get Constraint factor.

int Size (  )  const

Returns:
the number of set constraints

Referenced by OBForceField::Setup().

int GetConstraintType ( int  index  )  const

The following constraint types are known: OBFF_CONST_IGNORE (ignore the atom while setting up calculations, forcefield implementations need to check this value in their setup function), OBFF_CONST_ATOM (fix atom position), OBFF_CONST_ATOM_X (fix x coordinate), OBFF_CONST_ATOM_Y (fix y coordinate), OBFF_CONST_ATOM_Z (fix z coordinate), OBFF_CONST_BOND (constrain bond length), OBFF_CONST_ANGLE (constrain angle), OBFF_CONST_TORSION (constrain torsion angle)

Returns:
the constraint type

double GetConstraintValue ( int  index  )  const

Returns:
The constraint value, this can be a bond length, angle or torsion angle depending on the constraint type.

int GetConstraintAtomA ( int  index  )  const

Returns:
The constraint atom a (or fixed atom)
index constraint index

int GetConstraintAtomB ( int  index  )  const

Returns:
The constraint atom b
index constraint index

int GetConstraintAtomC ( int  index  )  const

Returns:
The constraint atom c
index constraint index

int GetConstraintAtomD ( int  index  )  const

Returns:
The constraint atom d
index constraint index

bool IsIgnored ( int  a  ) 

Returns:
true if this atom is ignored
a atom index

bool IsFixed ( int  a  ) 

Returns:
true if this atom is fixed
a atom index

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::GenerateVelocities(), OBForceField::MolecularDynamicsTakeNSteps(), and OBForceField::SteepestDescentTakeNSteps().

bool IsXFixed ( int  a  ) 

Returns:
true if the x coordinate for this atom is fixed
a atom index

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::GenerateVelocities(), and OBForceField::SteepestDescentTakeNSteps().

bool IsYFixed ( int  a  ) 

Returns:
true if the y coordinate for this atom is fixed
a atom index

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::GenerateVelocities(), and OBForceField::SteepestDescentTakeNSteps().

bool IsZFixed ( int  a  ) 

Returns:
true if the z coordinate for this atom is fixed
a atom index

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::GenerateVelocities(), and OBForceField::SteepestDescentTakeNSteps().

OBBitVec GetIgnoredBitVec (  )  [inline]

Returns:
the ignored atom indexes as bitvec. (used in OBForceField::Setup() to determine if a call to OBForceField::SetupCalculations() is needed)

Referenced by OBForceField::SetConstraints(), and OBForceField::Setup().

The documentation for this class was generated from the following files: