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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Go to the source code of this file.

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().