CDPL::ConfGen::StructureGeneratorSettings Class Reference

Bundle of configuration parameters for single 3D structure generation via class ConfGen::StructureGenerator. More...

#include <StructureGeneratorSettings.hpp>

Public Member Functions
	StructureGeneratorSettings ()
	Constructs the StructureGeneratorSettings instance with default configuration parameter values. More...
void	setGenerationMode (unsigned int mode)
	Sets the structure generation mode (see ConfGen::StructureGenerationMode). More...
unsigned int	getGenerationMode () const
	Returns the currently configured structure generation mode. More...
void	generateCoordinatesFromScratch (bool generate)
	Specifies whether 3D coordinates should be generated from scratch (vs. reusing existing input coordinates). More...
bool	generateCoordinatesFromScratch () const
	Tells whether 3D coordinates are generated from scratch. More...
void	sampleAngleToleranceRanges (bool sample)
	Specifies whether torsion-angle tolerance ranges are sampled during structure generation. More...
bool	sampleAngleToleranceRanges () const
	Tells whether torsion-angle tolerance ranges are sampled during structure generation. More...
void	setTimeout (std::size_t mil_secs)
	Sets the timeout for the structure generation pipeline. More...
std::size_t	getTimeout () const
	Returns the currently configured timeout in milliseconds. More...
void	setFragmentModeForceFieldType (unsigned int type)
	Sets the MMFF94 force field variant used for fragment-mode structure generation (see ForceField::MMFF94 variants). More...
unsigned int	getFragmentModeForceFieldType () const
	Returns the currently configured fragment-mode force field type. More...
void	setDGModeForceFieldType (unsigned int type)
	Sets the MMFF94 force field variant used for DG-mode structure generation. More...
unsigned int	getDGModeForceFieldType () const
	Returns the currently configured DG-mode force field type. More...
void	strictForceFieldParameterization (bool strict)
	Specifies whether force field parameterization should be strict (missing parameters cause failure). More...
bool	strictForceFieldParameterization () const
	Tells whether force field parameterization is strict. More...
void	setDielectricConstant (double de_const)
	Sets the dielectric constant used in the electrostatic energy term. More...
double	getDielectricConstant () const
	Returns the currently configured dielectric constant. More...
void	setDistanceExponent (double exponent)
	Sets the distance exponent used in the electrostatic energy term. More...
double	getDistanceExponent () const
	Returns the currently configured distance exponent. More...
void	setMaxNumRefinementIterations (std::size_t max_iter)
	Sets the maximum number of iterations of the force field-based coordinate refinement step. More...
std::size_t	getMaxNumRefinementIterations () const
	Returns the currently configured maximum number of refinement iterations. More...
void	setRefinementTolerance (double tol)
	Sets the convergence tolerance of the force field-based coordinate refinement step. More...
double	getRefinementTolerance () const
	Returns the currently configured refinement tolerance. More...
void	setMaxNumSampledConformers (std::size_t max_num)
	Sets the maximum number of conformers sampled during structure generation. More...
std::size_t	getMaxNumSampledConformers () const
	Returns the currently configured maximum number of sampled conformers. More...
void	setConvergenceCheckCycleSize (std::size_t size)
	Sets the cycle size for the convergence check of the structure-sampling loop. More...
std::size_t	getConvergenceCheckCycleSize () const
	Returns the currently configured convergence check cycle size. More...
void	setMacrocycleRotorBondCountThreshold (std::size_t min_count)
	Sets the minimum number of rotatable bonds in a macrocycle for it to be considered as flexible. More...
std::size_t	getMacrocycleRotorBondCountThreshold () const
	Returns the currently configured flexible macrocycle rotor bond count threshold. More...
FragmentConformerGeneratorSettings &	getFragmentBuildSettings ()
	Returns the embedded fragment-build settings (mutable). More...
const FragmentConformerGeneratorSettings &	getFragmentBuildSettings () const
	Returns the embedded fragment-build settings. More...

Static Public Attributes
static const StructureGeneratorSettings	DEFAULT
	A static instance providing configuration parameter default values. More...

Detailed Description

Bundle of configuration parameters for single 3D structure generation via class ConfGen::StructureGenerator.

Constructor & Destructor Documentation

StructureGeneratorSettings()

CDPL::ConfGen::StructureGeneratorSettings::StructureGeneratorSettings

(

)

Constructs the StructureGeneratorSettings instance with default configuration parameter values.

Member Function Documentation

setGenerationMode()

void CDPL::ConfGen::StructureGeneratorSettings::setGenerationMode

(

unsigned int

mode

)

Sets the structure generation mode (see ConfGen::StructureGenerationMode).

Parameters

mode	The new generation mode.

getGenerationMode()

unsigned int CDPL::ConfGen::StructureGeneratorSettings::getGenerationMode

(

)

const

Returns the currently configured structure generation mode.

Returns

The current generation mode.

generateCoordinatesFromScratch() [1/2]

void CDPL::ConfGen::StructureGeneratorSettings::generateCoordinatesFromScratch

(

bool

generate

)

Specifies whether 3D coordinates should be generated from scratch (vs. reusing existing input coordinates).

Parameters

generate

true to generate coordinates from scratch, and false to keep existing input coordinates.

generateCoordinatesFromScratch() [2/2]

bool CDPL::ConfGen::StructureGeneratorSettings::generateCoordinatesFromScratch

(

)

const

Tells whether 3D coordinates are generated from scratch.

Returns

true if coordinates are generated from scratch, and false otherwise.

sampleAngleToleranceRanges() [1/2]

void CDPL::ConfGen::StructureGeneratorSettings::sampleAngleToleranceRanges

(

bool

sample

)

Specifies whether torsion-angle tolerance ranges are sampled during structure generation.

Parameters

sample

true to enable sampling, and false to disable it.

sampleAngleToleranceRanges() [2/2]

bool CDPL::ConfGen::StructureGeneratorSettings::sampleAngleToleranceRanges

(

)

const

Tells whether torsion-angle tolerance ranges are sampled during structure generation.

Returns

true if sampling is enabled, and false otherwise.

setTimeout()

void CDPL::ConfGen::StructureGeneratorSettings::setTimeout

(

std::size_t

mil_secs

)

Sets the timeout for the structure generation pipeline.

Parameters

mil_secs

The new timeout in milliseconds (0 disables the timeout).

getTimeout()

std::size_t CDPL::ConfGen::StructureGeneratorSettings::getTimeout

(

)

const

Returns the currently configured timeout in milliseconds.

Returns

The timeout in milliseconds.

setFragmentModeForceFieldType()

void CDPL::ConfGen::StructureGeneratorSettings::setFragmentModeForceFieldType

(

unsigned int

type

)

Sets the MMFF94 force field variant used for fragment-mode structure generation (see ForceField::MMFF94 variants).

Parameters

type	The new force field type.

getFragmentModeForceFieldType()

unsigned int CDPL::ConfGen::StructureGeneratorSettings::getFragmentModeForceFieldType

(

)

const

Returns the currently configured fragment-mode force field type.

Returns

The current force field type.

setDGModeForceFieldType()

void CDPL::ConfGen::StructureGeneratorSettings::setDGModeForceFieldType

(

unsigned int

type

)

Sets the MMFF94 force field variant used for DG-mode structure generation.

Parameters

type	The new force field type.

getDGModeForceFieldType()

unsigned int CDPL::ConfGen::StructureGeneratorSettings::getDGModeForceFieldType

(

)

const

Returns the currently configured DG-mode force field type.

Returns

The force field type identifier.

strictForceFieldParameterization() [1/2]

void CDPL::ConfGen::StructureGeneratorSettings::strictForceFieldParameterization

(

bool

strict

)

Specifies whether force field parameterization should be strict (missing parameters cause failure).

Parameters

strict

true to enable strict parameterization, and false to tolerate missing parameters.

strictForceFieldParameterization() [2/2]

bool CDPL::ConfGen::StructureGeneratorSettings::strictForceFieldParameterization

(

)

const

Tells whether force field parameterization is strict.

Returns

true if strict parameterization is enabled, and false otherwise.

setDielectricConstant()

void CDPL::ConfGen::StructureGeneratorSettings::setDielectricConstant

(

double

de_const

)

Sets the dielectric constant used in the electrostatic energy term.

Parameters

de_const

The new dielectric constant.

getDielectricConstant()

double CDPL::ConfGen::StructureGeneratorSettings::getDielectricConstant

(

)

const

Returns the currently configured dielectric constant.

Returns

The dielectric constant.

setDistanceExponent()

void CDPL::ConfGen::StructureGeneratorSettings::setDistanceExponent

(

double

exponent

)

Sets the distance exponent used in the electrostatic energy term.

Parameters

exponent

The new distance exponent.

getDistanceExponent()

double CDPL::ConfGen::StructureGeneratorSettings::getDistanceExponent

(

)

const

Returns the currently configured distance exponent.

Returns

The distance exponent.

setMaxNumRefinementIterations()

void CDPL::ConfGen::StructureGeneratorSettings::setMaxNumRefinementIterations

(

std::size_t

max_iter

)

Sets the maximum number of iterations of the force field-based coordinate refinement step.

Parameters

max_iter

The new maximum number of iterations.

getMaxNumRefinementIterations()

std::size_t CDPL::ConfGen::StructureGeneratorSettings::getMaxNumRefinementIterations

(

)

const

Returns the currently configured maximum number of refinement iterations.

Returns

The maximum number of iterations.

setRefinementTolerance()

void CDPL::ConfGen::StructureGeneratorSettings::setRefinementTolerance

(

double

tol

)

Sets the convergence tolerance of the force field-based coordinate refinement step.

Parameters

tol	The new refinement tolerance.

getRefinementTolerance()

double CDPL::ConfGen::StructureGeneratorSettings::getRefinementTolerance

(

)

const

Returns the currently configured refinement tolerance.

Returns

The refinement tolerance.

setMaxNumSampledConformers()

void CDPL::ConfGen::StructureGeneratorSettings::setMaxNumSampledConformers

(

std::size_t

max_num

)

Sets the maximum number of conformers sampled during structure generation.

Parameters

max_num

The new maximum number of sampled conformers.

getMaxNumSampledConformers()

std::size_t CDPL::ConfGen::StructureGeneratorSettings::getMaxNumSampledConformers

(

)

const

Returns the currently configured maximum number of sampled conformers.

Returns

The maximum number of sampled conformers.

setConvergenceCheckCycleSize()

void CDPL::ConfGen::StructureGeneratorSettings::setConvergenceCheckCycleSize

(

std::size_t

size

)

Sets the cycle size for the convergence check of the structure-sampling loop.

Parameters

size	The new convergence check cycle size.

getConvergenceCheckCycleSize()

std::size_t CDPL::ConfGen::StructureGeneratorSettings::getConvergenceCheckCycleSize

(

)

const

Returns the currently configured convergence check cycle size.

Returns

The convergence check cycle size.

setMacrocycleRotorBondCountThreshold()

void CDPL::ConfGen::StructureGeneratorSettings::setMacrocycleRotorBondCountThreshold

(

std::size_t

min_count

)

Sets the minimum number of rotatable bonds in a macrocycle for it to be considered as flexible.

Parameters

min_count

The new threshold.

getMacrocycleRotorBondCountThreshold()

std::size_t CDPL::ConfGen::StructureGeneratorSettings::getMacrocycleRotorBondCountThreshold

(

)

const

Returns the currently configured flexible macrocycle rotor bond count threshold.

Returns

The threshold.

getFragmentBuildSettings() [1/2]

FragmentConformerGeneratorSettings& CDPL::ConfGen::StructureGeneratorSettings::getFragmentBuildSettings

(

)

Returns the embedded fragment-build settings (mutable).

Returns

A reference to the fragment-build settings.

getFragmentBuildSettings() [2/2]

const FragmentConformerGeneratorSettings& CDPL::ConfGen::StructureGeneratorSettings::getFragmentBuildSettings

(

)

const

Returns the embedded fragment-build settings.

Returns

A const reference to the fragment-build settings.

Member Data Documentation

DEFAULT

const StructureGeneratorSettings CDPL::ConfGen::StructureGeneratorSettings::DEFAULT

static

A static instance providing configuration parameter default values.

---

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

• StructureGeneratorSettings.hpp