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 ()
OBBitVec	GetFixedBitVec ()

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Detailed Description

Internal class for OBForceField to handle constraints.

Since:

version 2.2

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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().

OBBitVec GetFixedBitVec

(

)

[inline]

Returns:

the fixed atom indexes as bitvec. (used in OBForceField::SystematicRotorSearch() and similar)

Referenced by OBForceField::RandomRotorSearchInitialize(), OBForceField::SystematicRotorSearchInitialize(), and OBForceField::WeightedRotorSearch().

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

• forcefield.h
• forcefield.cpp