forcefield.h File Reference

Handle forcefields. More...

#include <vector>
#include <string>
#include <map>
#include <list>
#include <set>
#include <openbabel/babelconfig.h>
#include <openbabel/base.h>
#include <openbabel/mol.h>
#include <openbabel/plugin.h>
#include <openbabel/grid.h>
#include <openbabel/griddata.h>
#include <float.h>

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Namespaces
namespace	OpenBabel
Classes
struct	LineSearchType
	The type of line search to be used for optimization -- simple or Newton numeric. More...
class	OBFFParameter
	Internal class for OBForceField to hold forcefield parameters. More...
class	OBFFCalculation2
	Internal class for OBForceField to hold energy and gradient calculations on specific force fields. More...
class	OBFFCalculation3
	Internal class for OBForceField to hold energy and gradient calculations on specific force fields. More...
class	OBFFCalculation4
	Internal class for OBForceField to hold energy and gradient calculations on specific force fields. More...
class	OBFFConstraint
	Internal class for OBForceField to hold constraints. More...
class	OBFFConstraints
	Internal class for OBForceField to handle constraints. More...
class	OBForceField
	Base class for molecular mechanics force fields. More...
Defines
#define	OBFF_LOGLVL_NONE   0
#define	OBFF_LOGLVL_LOW   1
#define	OBFF_LOGLVL_MEDIUM   2
#define	OBFF_LOGLVL_HIGH   3
#define	OBFF_ENERGY   (1 << 0)
#define	OBFF_EBOND   (1 << 1)
#define	OBFF_EANGLE   (1 << 2)
#define	OBFF_ESTRBND   (1 << 3)
#define	OBFF_ETORSION   (1 << 4)
#define	OBFF_EOOP   (1 << 5)
#define	OBFF_EVDW   (1 << 6)
#define	OBFF_EELECTROSTATIC   (1 << 7)
#define	OBFF_CONST_IGNORE   (1 << 0)
#define	OBFF_CONST_ATOM   (1 << 1)
#define	OBFF_CONST_ATOM_X   (1 << 2)
#define	OBFF_CONST_ATOM_Y   (1 << 3)
#define	OBFF_CONST_ATOM_Z   (1 << 4)
#define	OBFF_CONST_DISTANCE   (1 << 5)
#define	OBFF_CONST_ANGLE   (1 << 6)
#define	OBFF_CONST_TORSION   (1 << 7)
#define	OBFF_CONST_CHIRAL   (1 << 8)
#define	OBFF_NUMERICAL_GRADIENT   (1 << 0)
#define	OBFF_ANALYTICAL_GRADIENT   (1 << 1)
#define	KCAL_TO_KJ   4.1868
#define	IF_OBFF_LOGLVL_LOW   if(_loglvl >= OBFF_LOGLVL_LOW)
#define	IF_OBFF_LOGLVL_MEDIUM   if(_loglvl >= OBFF_LOGLVL_MEDIUM)
#define	IF_OBFF_LOGLVL_HIGH   if(_loglvl >= OBFF_LOGLVL_HIGH)

---

Detailed Description

Handle forcefields.

---

Define Documentation

#define OBFF_LOGLVL_NONE   0

no output

Referenced by OBForceField::RandomRotorSearchInitialize(), OBForceField::RandomRotorSearchNextConformer(), OBForceField::SystematicRotorSearchNextConformer(), and OBForceField::WeightedRotorSearch().

#define OBFF_LOGLVL_LOW   1

SteepestDescent progress... (no output from Energy()).

#define OBFF_LOGLVL_MEDIUM   2

individual energy terms

#define OBFF_LOGLVL_HIGH   3

individual calculations and parameters

#define OBFF_ENERGY   (1 << 0)

all terms

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_EBOND   (1 << 1)

bond term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_EANGLE   (1 << 2)

angle term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_ESTRBND   (1 << 3)

strbnd term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_ETORSION   (1 << 4)

torsion term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_EOOP   (1 << 5)

oop term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_EVDW   (1 << 6)

vdw term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_EELECTROSTATIC   (1 << 7)

electrostatic term

Referenced by OBForceField::NumericalDerivative(), and OBForceField::NumericalSecondDerivative().

#define OBFF_CONST_IGNORE   (1 << 0)

ignore the atom while setting up calculations

Referenced by OBFFConstraints::AddIgnore(), and OBFFConstraints::DeleteConstraint().

#define OBFF_CONST_ATOM   (1 << 1)

fix the atom position

Referenced by OBFFConstraints::AddAtomConstraint(), and OBFFConstraints::DeleteConstraint().

#define OBFF_CONST_ATOM_X   (1 << 2)

fix the x coordinate of the atom position

Referenced by OBFFConstraints::AddAtomXConstraint(), and OBFFConstraints::DeleteConstraint().

#define OBFF_CONST_ATOM_Y   (1 << 3)

fix the y coordinate of the atom position

Referenced by OBFFConstraints::AddAtomYConstraint(), and OBFFConstraints::DeleteConstraint().

#define OBFF_CONST_ATOM_Z   (1 << 4)

fix the z coordinate of the atom position

Referenced by OBFFConstraints::AddAtomZConstraint(), and OBFFConstraints::DeleteConstraint().

#define OBFF_CONST_DISTANCE   (1 << 5)

constrain distance length

Referenced by OBFFConstraints::AddDistanceConstraint(), and OBFFConstraints::GetConstraintEnergy().

#define OBFF_CONST_ANGLE   (1 << 6)

constrain angle

Referenced by OBFFConstraints::AddAngleConstraint(), and OBFFConstraints::GetConstraintEnergy().

#define OBFF_CONST_TORSION   (1 << 7)

constrain torsion

Referenced by OBFFConstraints::AddTorsionConstraint(), and OBFFConstraints::GetConstraintEnergy().

#define OBFF_CONST_CHIRAL   (1 << 8)

constrain chiral volume

#define OBFF_NUMERICAL_GRADIENT   (1 << 0)

use numerical gradients

#define OBFF_ANALYTICAL_GRADIENT   (1 << 1)

use analytical gradients

#define KCAL_TO_KJ   4.1868

Referenced by OBForceField::CorrectVelocities(), OBForceField::GenerateVelocities(), and OBForceField::MolecularDynamicsTakeNSteps().

#define IF_OBFF_LOGLVL_LOW   if(_loglvl >= OBFF_LOGLVL_LOW)

Referenced by OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBForceField::DistanceGeometry(), OBForceField::PrintFormalCharges(), OBForceField::PrintPartialCharges(), OBForceField::PrintTypes(), OBForceField::PrintVelocities(), OBForceField::RandomRotorSearchInitialize(), OBForceField::RandomRotorSearchNextConformer(), OBForceField::SteepestDescentInitialize(), OBForceField::SteepestDescentTakeNSteps(), OBForceField::SystematicRotorSearchInitialize(), OBForceField::SystematicRotorSearchNextConformer(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateSteepestDescent(), and OBForceField::WeightedRotorSearch().

#define IF_OBFF_LOGLVL_MEDIUM   if(_loglvl >= OBFF_LOGLVL_MEDIUM)

#define IF_OBFF_LOGLVL_HIGH   if(_loglvl >= OBFF_LOGLVL_HIGH)

Referenced by OBForceField::WeightedRotorSearch().