Bundle of configuration parameters for conformer ensemble generation via class ConfGen::ConformerGenerator. More...

#include <ConformerGeneratorSettings.hpp>

Public Member Functions
	ConformerGeneratorSettings ()
	Constructs the `ConformerGeneratorSettings` instance with default configuration parameter values. More...

void	setSamplingMode (unsigned int mode)
	Specifies the conformer-sampling strategy to use. More...

unsigned int	getSamplingMode () const
	Returns the currently configured conformer-sampling strategy. More...

void	sampleHeteroAtomHydrogens (bool sample)
	Specifies whether torsions of heteroatom hydrogen rotors shall be sampled. More...

bool	sampleHeteroAtomHydrogens () const
	Tells whether torsions of heteroatom hydrogen rotors are sampled. More...

void	sampleAngleToleranceRanges (bool sample)
	Specifies whether additional torsion samples within the tolerance ranges defined by the torsion library entries shall be generated. More...

bool	sampleAngleToleranceRanges () const
	Tells whether tolerance-range sampling is enabled. More...

void	enumerateRings (bool enumerate)
	Specifies whether ring conformations shall be enumerated. More...

bool	enumerateRings () const
	Tells whether ring conformations are enumerated. More...

void	setNitrogenEnumerationMode (unsigned int mode)
	Sets the enumeration mode for stereogenic nitrogen centers. More...

unsigned int	getNitrogenEnumerationMode () const
	Returns the currently configured nitrogen enumeration mode. More...

void	generateCoordinatesFromScratch (bool generate)
	Specifies whether 3D coordinates shall be generated from scratch (ignoring any 3D input). More...

bool	generateCoordinatesFromScratch () const
	Tells whether 3D coordinates are generated from scratch. More...

void	includeInputCoordinates (bool include)
	Specifies whether the input conformation shall be included in the output conformer ensemble. More...

bool	includeInputCoordinates () const
	Tells whether the input coordinates are included in the output conformer ensemble. More...

void	setEnergyWindow (double win_size)
	Sets the energy window size (in kcal/mol) above the found global minimum within which conformers are kept. More...

double	getEnergyWindow () const
	Returns the configured energy window size. More...

double	getEnergyWindow (std::size_t num_rot_bonds) const
	Returns the energy window size that applies for molecules with num_rot_bonds rotatable bonds. More...

void	clearEnergyWindowRanges ()
	Removes all registered rotatable bond count-dependent energy window overrides. More...

void	addEnergyWindowRange (std::size_t num_rot_bonds, double win_size)
	Registers an energy window override that applies up to and including num_rot_bonds rotatable bonds. More...

void	setMaxPoolSize (std::size_t max_size)
	Sets the maximum number of conformers to keep in the internal candidate pool. More...

std::size_t	getMaxPoolSize () const
	Returns the maximum number of conformers kept in the internal candidate pool. More...

void	setMaxRotatableBondCount (long max_count)
	Sets the upper limit on the number of rotatable bonds an input molecule may have to be processed. More...

long	getMaxRotatableBondCount () const
	Returns the rotatable bond count limit above which input molecules are rejected. More...

void	setTimeout (std::size_t mil_secs)
	Sets the maximum allowed wall clock processing time per molecule. More...

std::size_t	getTimeout () const
	Returns the configured per-molecule wall clock time limit. More...

void	setForceFieldTypeSystematic (unsigned int type)
	Sets the force field type used by the systematic sampling pipeline. More...

unsigned int	getForceFieldTypeSystematic () const
	Returns the force field type used by the systematic sampling pipeline. More...

void	setForceFieldTypeStochastic (unsigned int type)
	Sets the force field type used by the stochastic sampling pipeline. More...

unsigned int	getForceFieldTypeStochastic () const
	Returns the force field type used by the stochastic sampling pipeline. More...

void	strictForceFieldParameterization (bool strict)
	Specifies whether strict MMFF94 parameterization is required. More...

bool	strictForceFieldParameterization () const
	Tells whether strict MMFF94 parameterization is required. More...

void	setDielectricConstant (double de_const)
	Sets the dielectric constant used by the MMFF94 electrostatic interactions. More...

double	getDielectricConstant () const
	Returns the dielectric constant used by the MMFF94 electrostatic interactions. More...

void	setDistanceExponent (double exponent)
	Sets the exponent of the MMFF94 distance-dependent electrostatic term. More...

double	getDistanceExponent () const
	Returns the exponent of the MMFF94 distance-dependent electrostatic term. More...

void	setMaxNumOutputConformers (std::size_t max_num)
	Sets the maximum number of output conformers per molecule. More...

std::size_t	getMaxNumOutputConformers () const
	Returns the configured maximum number of output conformers. More...

std::size_t	getMaxNumOutputConformers (std::size_t num_rot_bonds) const
	Returns the maximum number of output conformers that applies for molecules with num_rot_bonds rotatable bonds. More...

void	clearMaxNumOutputConformersRanges ()
	Removes all registered rotatable bond count-dependent output conformer overrides. More...

void	addMaxNumOutputConformersRange (std::size_t num_rot_bonds, std::size_t max_num)
	Registers an output conformer limit override that applies up to and including num_rot_bonds rotatable bonds. More...

void	setMinRMSD (double min_rmsd)
	Sets the minimum pairwise heavy atom RMSD that conformers in the output ensemble must keep. More...

double	getMinRMSD () const
	Returns the globally configured minimum RMSD threshold. More...

double	getMinRMSD (std::size_t num_rot_bonds) const
	Returns the minimum RMSD threshold that applies for molecules with num_rot_bonds rotatable bonds. More...

void	clearMinRMSDRanges ()
	Removes all registered rotatable bond count-dependent minimum RMSD overrides. More...

void	addMinRMSDRange (std::size_t num_rot_bonds, double min_rmsd)
	Registers a minimum RMSD override that applies up to and including num_rot_bonds rotatable bonds. More...

void	setMaxNumRefinementIterations (std::size_t max_iter)
	Sets the maximum number of MMFF94 energy minimization iterations per conformer. More...

std::size_t	getMaxNumRefinementIterations () const
	Returns the maximum number of MMFF94 energy minimization iterations per conformer. More...

void	setRefinementTolerance (double tol)
	Sets the convergence tolerance of the MMFF94 energy minimization step. More...

double	getRefinementTolerance () const
	Returns the convergence tolerance of the MMFF94 energy minimization step. More...

void	setMaxNumSampledConformers (std::size_t max_num)
	Sets the upper bound on the number of trial conformations produced by the stochastic sampler. More...

std::size_t	getMaxNumSampledConformers () const
	Returns the upper bound on the number of trial conformations produced by the stochastic sampler. More...

void	setConvergenceCheckCycleSize (std::size_t size)
	Sets the cycle size (in trial conformations) at which the stochastic sampler tests for convergence. More...

std::size_t	getConvergenceCheckCycleSize () const
	Returns the cycle size at which the stochastic sampler tests for convergence. More...

void	setMacrocycleRotorBondCountThreshold (std::size_t min_count)
	Sets the minimum number of rotatable bonds a ring must contain to be considered as a flexible macrocycle. More...

std::size_t	getMacrocycleRotorBondCountThreshold () const
	Returns the flexible macrocycle rotatable bond count threshold. More...

FragmentConformerGeneratorSettings &	getFragmentBuildSettings ()
	Returns a reference to the nested fragment conformer build settings. More...

const FragmentConformerGeneratorSettings &	getFragmentBuildSettings () const
	Returns a `const` reference to the nested fragment conformer build settings. More...

Static Public Attributes
static const ConformerGeneratorSettings	DEFAULT
	Instance providing configuration parameter default values. More...

static const ConformerGeneratorSettings	SMALL_SET_DIVERSE
	Preset producing a small, diversity-optimized conformer ensemble. More...

static const ConformerGeneratorSettings	MEDIUM_SET_DIVERSE
	Preset producing a medium-sized, diversity-optimized conformer ensemble. More...

static const ConformerGeneratorSettings	LARGE_SET_DIVERSE
	Preset producing a large, diversity-optimized conformer ensemble. More...

static const ConformerGeneratorSettings	SMALL_SET_DENSE
	Preset producing a small, dense conformer ensemble (tight RMSD threshold). More...

static const ConformerGeneratorSettings	MEDIUM_SET_DENSE
	Preset producing a medium-sized, dense conformer ensemble (tight RMSD threshold). More...

static const ConformerGeneratorSettings	LARGE_SET_DENSE
	Preset producing a large, dense conformer ensemble (tight RMSD threshold). More...

Detailed Description

Bundle of configuration parameters for conformer ensemble generation via class ConfGen::ConformerGenerator.

Constructor & Destructor Documentation

◆ ConformerGeneratorSettings()

CDPL::ConfGen::ConformerGeneratorSettings::ConformerGeneratorSettings ( )

Constructs the ConformerGeneratorSettings instance with default configuration parameter values.

Member Function Documentation

◆ setSamplingMode()

void CDPL::ConfGen::ConformerGeneratorSettings::setSamplingMode ( unsigned int mode )

Specifies the conformer-sampling strategy to use.

Parameters

mode	One of the ConfGen::ConformerSamplingMode values.

◆ getSamplingMode()

unsigned int CDPL::ConfGen::ConformerGeneratorSettings::getSamplingMode ( ) const

Returns the currently configured conformer-sampling strategy.

Returns: One of the ConfGen::ConformerSamplingMode values.

◆ sampleHeteroAtomHydrogens() [1/2]

void CDPL::ConfGen::ConformerGeneratorSettings::sampleHeteroAtomHydrogens ( bool sample )

Specifies whether torsions of heteroatom hydrogen rotors shall be sampled.

Parameters

sample If true, such torsions are sampled.

◆ sampleHeteroAtomHydrogens() [2/2]

bool CDPL::ConfGen::ConformerGeneratorSettings::sampleHeteroAtomHydrogens ( ) const

Tells whether torsions of heteroatom hydrogen rotors are sampled.

Returns: true if sampling is enabled, and false otherwise.

◆ sampleAngleToleranceRanges() [1/2]

void CDPL::ConfGen::ConformerGeneratorSettings::sampleAngleToleranceRanges ( bool sample )

Specifies whether additional torsion samples within the tolerance ranges defined by the torsion library entries shall be generated.

Parameters

sample If true, tolerance-range sampling is enabled.

◆ sampleAngleToleranceRanges() [2/2]

bool CDPL::ConfGen::ConformerGeneratorSettings::sampleAngleToleranceRanges ( ) const

Tells whether tolerance-range sampling is enabled.

Returns: true if tolerance-range sampling is enabled, and false otherwise.

◆ enumerateRings() [1/2]

void CDPL::ConfGen::ConformerGeneratorSettings::enumerateRings ( bool enumerate )

Specifies whether ring conformations shall be enumerated.

Parameters

enumerate If true, ring conformations are enumerated.

◆ enumerateRings() [2/2]

bool CDPL::ConfGen::ConformerGeneratorSettings::enumerateRings ( ) const

Tells whether ring conformations are enumerated.

Returns: true if ring conformations are enumerated, and false otherwise.

◆ setNitrogenEnumerationMode()

void CDPL::ConfGen::ConformerGeneratorSettings::setNitrogenEnumerationMode ( unsigned int mode )

Sets the enumeration mode for stereogenic nitrogen centers.

Parameters

mode	One of the ConfGen::NitrogenEnumerationMode values.

◆ getNitrogenEnumerationMode()

unsigned int CDPL::ConfGen::ConformerGeneratorSettings::getNitrogenEnumerationMode ( ) const

Returns the currently configured nitrogen enumeration mode.

Returns: One of the ConfGen::NitrogenEnumerationMode values.

◆ generateCoordinatesFromScratch() [1/2]

void CDPL::ConfGen::ConformerGeneratorSettings::generateCoordinatesFromScratch ( bool generate )

Specifies whether 3D coordinates shall be generated from scratch (ignoring any 3D input).

Parameters

generate If true, 3D coordinates are always generated from scratch.

◆ generateCoordinatesFromScratch() [2/2]

bool CDPL::ConfGen::ConformerGeneratorSettings::generateCoordinatesFromScratch ( ) const

Tells whether 3D coordinates are generated from scratch.

Returns: true if 3D coordinates are always regenerated, and false otherwise.

◆ includeInputCoordinates() [1/2]

void CDPL::ConfGen::ConformerGeneratorSettings::includeInputCoordinates ( bool include )

Specifies whether the input conformation shall be included in the output conformer ensemble.

Parameters

include If true, the input coordinates become part of the output ensemble.

◆ includeInputCoordinates() [2/2]

bool CDPL::ConfGen::ConformerGeneratorSettings::includeInputCoordinates ( ) const

Tells whether the input coordinates are included in the output conformer ensemble.

Returns: true if the input coordinates are included, and false otherwise.

◆ setEnergyWindow()

void CDPL::ConfGen::ConformerGeneratorSettings::setEnergyWindow ( double win_size )

Sets the energy window size (in kcal/mol) above the found global minimum within which conformers are kept.

Parameters

win_size The new energy window size in kcal/mol.

◆ getEnergyWindow() [1/2]

double CDPL::ConfGen::ConformerGeneratorSettings::getEnergyWindow ( ) const

Returns the configured energy window size.

Returns: The energy window size in kcal/mol.

◆ getEnergyWindow() [2/2]

double CDPL::ConfGen::ConformerGeneratorSettings::getEnergyWindow ( std::size_t num_rot_bonds ) const

Returns the energy window size that applies for molecules with num_rot_bonds rotatable bonds.

If a rotatable bond-specific range was registered via addEnergyWindowRange(), the matching value is returned; otherwise the global window from getEnergyWindow() is used.

Parameters

num_rot_bonds The rotatable bond count.

Returns: The energy window size in kcal/mol.

Since: 1.1

◆ clearEnergyWindowRanges()

void CDPL::ConfGen::ConformerGeneratorSettings::clearEnergyWindowRanges ( )

Removes all registered rotatable bond count-dependent energy window overrides.

Since: 1.1

◆ addEnergyWindowRange()

void CDPL::ConfGen::ConformerGeneratorSettings::addEnergyWindowRange	(	std::size_t	num_rot_bonds,
		double	win_size
	)

Registers an energy window override that applies up to and including num_rot_bonds rotatable bonds.

Parameters

num_rot_bonds	The upper-bound rotatable bond count to which win_size applies.
win_size	The energy window size (in kcal/mol).

Since: 1.1

◆ setMaxPoolSize()

void CDPL::ConfGen::ConformerGeneratorSettings::setMaxPoolSize ( std::size_t max_size )

Sets the maximum number of conformers to keep in the internal candidate pool.

Parameters

max_size The new maximum pool size.

◆ getMaxPoolSize()

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getMaxPoolSize ( ) const

Returns the maximum number of conformers kept in the internal candidate pool.

Returns: The maximum pool size.

◆ setMaxRotatableBondCount()

void CDPL::ConfGen::ConformerGeneratorSettings::setMaxRotatableBondCount ( long max_count )

Sets the upper limit on the number of rotatable bonds an input molecule may have to be processed.

Parameters

max_count The new rotatable bond count limit (-1 disables the limit).

Since: 1.1

◆ getMaxRotatableBondCount()

long CDPL::ConfGen::ConformerGeneratorSettings::getMaxRotatableBondCount ( ) const

Returns the rotatable bond count limit above which input molecules are rejected.

Returns: The rotatable bond count limit (-1 disables the limit).

Since: 1.1

◆ setTimeout()

void CDPL::ConfGen::ConformerGeneratorSettings::setTimeout ( std::size_t mil_secs )

Sets the maximum allowed wall clock processing time per molecule.

Parameters

mil_secs The new time limit in milliseconds (zero disables the limit).

◆ getTimeout()

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getTimeout ( ) const

Returns the configured per-molecule wall clock time limit.

Returns: The time limit in milliseconds (zero if disabled).

◆ setForceFieldTypeSystematic()

void CDPL::ConfGen::ConformerGeneratorSettings::setForceFieldTypeSystematic ( unsigned int type )

Sets the force field type used by the systematic sampling pipeline.

Parameters

type	One of the ConfGen::ForceFieldType values.

◆ getForceFieldTypeSystematic()

unsigned int CDPL::ConfGen::ConformerGeneratorSettings::getForceFieldTypeSystematic ( ) const

Returns the force field type used by the systematic sampling pipeline.

Returns: One of the ConfGen::ForceFieldType values.

◆ setForceFieldTypeStochastic()

void CDPL::ConfGen::ConformerGeneratorSettings::setForceFieldTypeStochastic ( unsigned int type )

Sets the force field type used by the stochastic sampling pipeline.

Parameters

type	One of the ConfGen::ForceFieldType values.

◆ getForceFieldTypeStochastic()

unsigned int CDPL::ConfGen::ConformerGeneratorSettings::getForceFieldTypeStochastic ( ) const

Returns the force field type used by the stochastic sampling pipeline.

Returns: One of the ConfGen::ForceFieldType values.

◆ strictForceFieldParameterization() [1/2]

void CDPL::ConfGen::ConformerGeneratorSettings::strictForceFieldParameterization ( bool strict )

Specifies whether strict MMFF94 parameterization is required.

Parameters

strict If true, missing/ambiguous parameters cause a generation failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

◆ strictForceFieldParameterization() [2/2]

bool CDPL::ConfGen::ConformerGeneratorSettings::strictForceFieldParameterization ( ) const

Tells whether strict MMFF94 parameterization is required.

Returns: true if strict parameterization is required, and false otherwise.

◆ setDielectricConstant()

void CDPL::ConfGen::ConformerGeneratorSettings::setDielectricConstant ( double de_const )

Sets the dielectric constant used by the MMFF94 electrostatic interactions.

Parameters

de_const The new dielectric constant.

◆ getDielectricConstant()

double CDPL::ConfGen::ConformerGeneratorSettings::getDielectricConstant ( ) const

Returns the dielectric constant used by the MMFF94 electrostatic interactions.

Returns: The dielectric constant.

◆ setDistanceExponent()

void CDPL::ConfGen::ConformerGeneratorSettings::setDistanceExponent ( double exponent )

Sets the exponent of the MMFF94 distance-dependent electrostatic term.

Parameters

exponent The new distance exponent.

◆ getDistanceExponent()

double CDPL::ConfGen::ConformerGeneratorSettings::getDistanceExponent ( ) const

Returns the exponent of the MMFF94 distance-dependent electrostatic term.

Returns: The distance exponent.

◆ setMaxNumOutputConformers()

void CDPL::ConfGen::ConformerGeneratorSettings::setMaxNumOutputConformers ( std::size_t max_num )

Sets the maximum number of output conformers per molecule.

Parameters

max_num The new output conformer count limit.

◆ getMaxNumOutputConformers() [1/2]

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumOutputConformers ( ) const

Returns the configured maximum number of output conformers.

Returns: The output conformer count limit.

◆ getMaxNumOutputConformers() [2/2]

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumOutputConformers ( std::size_t num_rot_bonds ) const

Returns the maximum number of output conformers that applies for molecules with num_rot_bonds rotatable bonds.

If a rotatable bond-specific range was registered via addMaxNumOutputConformersRange(), the matching value is returned; otherwise the global limit from getMaxNumOutputConformers() is used.

Parameters

num_rot_bonds The rotatable bond count.

Returns: The output conformer limit.

Since: 1.1

◆ clearMaxNumOutputConformersRanges()

void CDPL::ConfGen::ConformerGeneratorSettings::clearMaxNumOutputConformersRanges ( )

Removes all registered rotatable bond count-dependent output conformer overrides.

Since: 1.1

◆ addMaxNumOutputConformersRange()

void CDPL::ConfGen::ConformerGeneratorSettings::addMaxNumOutputConformersRange	(	std::size_t	num_rot_bonds,
		std::size_t	max_num
	)

Registers an output conformer limit override that applies up to and including num_rot_bonds rotatable bonds.

Parameters

num_rot_bonds	The upper-bound rotatable bond count to which max_num applies.
max_num	The output conformer limit used for matching molecules.

Since: 1.1

◆ setMinRMSD()

void CDPL::ConfGen::ConformerGeneratorSettings::setMinRMSD ( double min_rmsd )

Sets the minimum pairwise heavy atom RMSD that conformers in the output ensemble must keep.

Parameters

min_rmsd The new minimum RMSD threshold (in Å).

◆ getMinRMSD() [1/2]

double CDPL::ConfGen::ConformerGeneratorSettings::getMinRMSD ( ) const

Returns the globally configured minimum RMSD threshold.

Returns: The minimum RMSD threshold (in Å).

◆ getMinRMSD() [2/2]

double CDPL::ConfGen::ConformerGeneratorSettings::getMinRMSD ( std::size_t num_rot_bonds ) const

Returns the minimum RMSD threshold that applies for molecules with num_rot_bonds rotatable bonds.

If a rotatable bond-specific range was registered via addMinRMSDRange(), the matching value is returned; otherwise the global threshold from getMinRMSD() is used.

Parameters

num_rot_bonds The rotatable bond count.

Returns: The minimum RMSD threshold (in Å).

Since: 1.1

◆ clearMinRMSDRanges()

void CDPL::ConfGen::ConformerGeneratorSettings::clearMinRMSDRanges ( )

Removes all registered rotatable bond count-dependent minimum RMSD overrides.

Since: 1.1

◆ addMinRMSDRange()

void CDPL::ConfGen::ConformerGeneratorSettings::addMinRMSDRange	(	std::size_t	num_rot_bonds,
		double	min_rmsd
	)

Registers a minimum RMSD override that applies up to and including num_rot_bonds rotatable bonds.

Parameters

num_rot_bonds	The upper-bound rotatable bond count to which min_rmsd applies.
min_rmsd	The minimum RMSD threshold used for matching molecules.

Since: 1.1

◆ setMaxNumRefinementIterations()

void CDPL::ConfGen::ConformerGeneratorSettings::setMaxNumRefinementIterations ( std::size_t max_iter )

Sets the maximum number of MMFF94 energy minimization iterations per conformer.

Parameters

max_iter The new iteration limit (zero disables refinement).

◆ getMaxNumRefinementIterations()

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumRefinementIterations ( ) const

Returns the maximum number of MMFF94 energy minimization iterations per conformer.

Returns: The iteration limit (zero if refinement is disabled).

◆ setRefinementTolerance()

void CDPL::ConfGen::ConformerGeneratorSettings::setRefinementTolerance ( double tol )

Sets the convergence tolerance of the MMFF94 energy minimization step.

Parameters

tol	The new convergence tolerance.

◆ getRefinementTolerance()

double CDPL::ConfGen::ConformerGeneratorSettings::getRefinementTolerance ( ) const

Returns the convergence tolerance of the MMFF94 energy minimization step.

Returns: The convergence tolerance.

◆ setMaxNumSampledConformers()

void CDPL::ConfGen::ConformerGeneratorSettings::setMaxNumSampledConformers ( std::size_t max_num )

Sets the upper bound on the number of trial conformations produced by the stochastic sampler.

Parameters

max_num The new sampled conformer limit.

◆ getMaxNumSampledConformers()

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumSampledConformers ( ) const

Returns the upper bound on the number of trial conformations produced by the stochastic sampler.

Returns: The sampled conformer limit.

◆ setConvergenceCheckCycleSize()

void CDPL::ConfGen::ConformerGeneratorSettings::setConvergenceCheckCycleSize ( std::size_t size )

Sets the cycle size (in trial conformations) at which the stochastic sampler tests for convergence.

Parameters

size	The new convergence check cycle size.

◆ getConvergenceCheckCycleSize()

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getConvergenceCheckCycleSize ( ) const

Returns the cycle size at which the stochastic sampler tests for convergence.

Returns: The convergence check cycle size.

◆ setMacrocycleRotorBondCountThreshold()

void CDPL::ConfGen::ConformerGeneratorSettings::setMacrocycleRotorBondCountThreshold ( std::size_t min_count )

Sets the minimum number of rotatable bonds a ring must contain to be considered as a flexible macrocycle.

Parameters

min_count The new flexible macrocycle rotatable bond count threshold.

◆ getMacrocycleRotorBondCountThreshold()

std::size_t CDPL::ConfGen::ConformerGeneratorSettings::getMacrocycleRotorBondCountThreshold ( ) const

Returns the flexible macrocycle rotatable bond count threshold.

Returns: The threshold.

◆ getFragmentBuildSettings() [1/2]

FragmentConformerGeneratorSettings& CDPL::ConfGen::ConformerGeneratorSettings::getFragmentBuildSettings ( )

Returns a reference to the nested fragment conformer build settings.

Returns: A reference to the build settings.

◆ getFragmentBuildSettings() [2/2]

const FragmentConformerGeneratorSettings& CDPL::ConfGen::ConformerGeneratorSettings::getFragmentBuildSettings ( ) const

Returns a const reference to the nested fragment conformer build settings.

Returns: A const reference to the build settings.

Member Data Documentation

◆ DEFAULT

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::DEFAULT

static

Instance providing configuration parameter default values.

◆ SMALL_SET_DIVERSE

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::SMALL_SET_DIVERSE

static

Preset producing a small, diversity-optimized conformer ensemble.

◆ MEDIUM_SET_DIVERSE

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::MEDIUM_SET_DIVERSE

static

Preset producing a medium-sized, diversity-optimized conformer ensemble.

◆ LARGE_SET_DIVERSE

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::LARGE_SET_DIVERSE

static

Preset producing a large, diversity-optimized conformer ensemble.

◆ SMALL_SET_DENSE

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::SMALL_SET_DENSE

static

Preset producing a small, dense conformer ensemble (tight RMSD threshold).

◆ MEDIUM_SET_DENSE

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::MEDIUM_SET_DENSE

static

Preset producing a medium-sized, dense conformer ensemble (tight RMSD threshold).

◆ LARGE_SET_DENSE

const ConformerGeneratorSettings CDPL::ConfGen::ConformerGeneratorSettings::LARGE_SET_DENSE

static

Preset producing a large, dense conformer ensemble (tight RMSD threshold).

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

ConformerGeneratorSettings.hpp

Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ConformerGeneratorSettings()

Member Function Documentation

◆ setSamplingMode()

◆ getSamplingMode()

◆ sampleHeteroAtomHydrogens() [1/2]

◆ sampleHeteroAtomHydrogens() [2/2]

◆ sampleAngleToleranceRanges() [1/2]

◆ sampleAngleToleranceRanges() [2/2]

◆ enumerateRings() [1/2]

◆ enumerateRings() [2/2]

◆ setNitrogenEnumerationMode()

◆ getNitrogenEnumerationMode()

◆ generateCoordinatesFromScratch() [1/2]

◆ generateCoordinatesFromScratch() [2/2]

◆ includeInputCoordinates() [1/2]

◆ includeInputCoordinates() [2/2]

◆ setEnergyWindow()

◆ getEnergyWindow() [1/2]

◆ getEnergyWindow() [2/2]

◆ clearEnergyWindowRanges()

◆ addEnergyWindowRange()

◆ setMaxPoolSize()

◆ getMaxPoolSize()

◆ setMaxRotatableBondCount()

◆ getMaxRotatableBondCount()

◆ setTimeout()

◆ getTimeout()

◆ setForceFieldTypeSystematic()

◆ getForceFieldTypeSystematic()

◆ setForceFieldTypeStochastic()

◆ getForceFieldTypeStochastic()

◆ strictForceFieldParameterization() [1/2]

◆ strictForceFieldParameterization() [2/2]

◆ setDielectricConstant()

◆ getDielectricConstant()

◆ setDistanceExponent()

◆ getDistanceExponent()

◆ setMaxNumOutputConformers()

◆ getMaxNumOutputConformers() [1/2]

◆ getMaxNumOutputConformers() [2/2]

◆ clearMaxNumOutputConformersRanges()

◆ addMaxNumOutputConformersRange()

◆ setMinRMSD()

◆ getMinRMSD() [1/2]

◆ getMinRMSD() [2/2]

◆ clearMinRMSDRanges()

◆ addMinRMSDRange()

◆ setMaxNumRefinementIterations()

◆ getMaxNumRefinementIterations()

◆ setRefinementTolerance()

◆ getRefinementTolerance()

◆ setMaxNumSampledConformers()

◆ getMaxNumSampledConformers()

◆ setConvergenceCheckCycleSize()

◆ getConvergenceCheckCycleSize()

◆ setMacrocycleRotorBondCountThreshold()

◆ getMacrocycleRotorBondCountThreshold()

◆ getFragmentBuildSettings() [1/2]

◆ getFragmentBuildSettings() [2/2]

Member Data Documentation

◆ DEFAULT

◆ SMALL_SET_DIVERSE

◆ MEDIUM_SET_DIVERSE

◆ LARGE_SET_DIVERSE

◆ SMALL_SET_DENSE

◆ MEDIUM_SET_DENSE

◆ LARGE_SET_DENSE