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

#include <FragmentConformerGeneratorSettings.hpp>

Classes
class	FragmentSettings
	Per-fragment-class settings (separate parameters for chain, small ring system and macrocycle fragments). More...

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

virtual	~FragmentConformerGeneratorSettings ()
	Destructor. More...

void	preserveInputBondingGeometries (bool preserve)
	Specifies whether the bonding geometries (bond lengths and angles) of the input fragment shall be preserved. More...

bool	preserveInputBondingGeometries () const
	Tells whether the bonding geometries of the input fragment are preserved. More...

void	setForceFieldType (unsigned int type)
	Sets the force field type used for fragment conformer minimization. More...

unsigned int	getForceFieldType () const
	Returns the force field type used for fragment conformer minimization. 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	setMaxNumRefinementIterations (std::size_t max_iter)
	Sets the maximum number of MMFF94 energy-minimization iterations per fragment conformer. More...

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

void	setRefinementStopGradient (double grad_norm)
	Sets the gradient-norm threshold at which fragment conformer refinement is considered converged. More...

double	getRefinementStopGradient () const
	Returns the gradient-norm threshold used to terminate refinement. More...

void	setMacrocycleRotorBondCountThreshold (std::size_t min_count)
	Sets the minimum number of rotatable bonds a macrocyclic 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...

FragmentSettings &	getChainSettings ()
	Returns a reference to the per-fragment-class settings used for chain fragments. More...

const FragmentSettings &	getChainSettings () const
	Returns a `const` reference to the per-fragment-class settings used for chain fragments. More...

FragmentSettings &	getMacrocycleSettings ()
	Returns a reference to the per-fragment-class settings used for flexible macrocyclic ring systems. More...

const FragmentSettings &	getMacrocycleSettings () const
	Returns a `const` reference to the per-fragment-class settings used for flexible macrocyclic ring systems. More...

FragmentSettings &	getSmallRingSystemSettings ()
	Returns a reference to the per-fragment-class settings used for small ring systems. More...

const FragmentSettings &	getSmallRingSystemSettings () const
	Returns a `const` reference to the per-fragment-class settings used for small ring systems. More...

void	setSmallRingSystemSamplingFactor (std::size_t factor)
	Sets a multiplicative factor scaling the sampling effort for small ring systems. More...

std::size_t	getSmallRingSystemSamplingFactor () const
	Returns the multiplicative factor scaling the sampling effort for small ring systems. More...

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

static const FragmentConformerGeneratorSettings	FAST
	A static instance preconfigured for fast (less thorough) conformer generation. More...

static const FragmentConformerGeneratorSettings	THOROUGH
	A static instance preconfigured for thorough (slower) conformer generation. More...

Detailed Description

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

Constructor & Destructor Documentation

◆ FragmentConformerGeneratorSettings()

CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentConformerGeneratorSettings ( )

Constructs the % FragmentConformerGeneratorSettings instance with default configuration parameter values.

◆ ~FragmentConformerGeneratorSettings()

virtual CDPL::ConfGen::FragmentConformerGeneratorSettings::~FragmentConformerGeneratorSettings ( )

inlinevirtual

Destructor.

Member Function Documentation

◆ preserveInputBondingGeometries() [1/2]

void CDPL::ConfGen::FragmentConformerGeneratorSettings::preserveInputBondingGeometries ( bool preserve )

Specifies whether the bonding geometries (bond lengths and angles) of the input fragment shall be preserved.

Parameters

preserve If true, the bonding geometry of the input is reused; otherwise it is rebuilt.

◆ preserveInputBondingGeometries() [2/2]

bool CDPL::ConfGen::FragmentConformerGeneratorSettings::preserveInputBondingGeometries ( ) const

Tells whether the bonding geometries of the input fragment are preserved.

Returns: true if the input bonding geometry is reused, and false otherwise.

◆ setForceFieldType()

void CDPL::ConfGen::FragmentConformerGeneratorSettings::setForceFieldType ( unsigned int type )

Sets the force field type used for fragment conformer minimization.

Parameters

type	One of the ConfGen::ForceFieldType values.

◆ getForceFieldType()

unsigned int CDPL::ConfGen::FragmentConformerGeneratorSettings::getForceFieldType ( ) const

Returns the force field type used for fragment conformer minimization.

Returns: One of the ConfGen::ForceFieldType values.

◆ strictForceFieldParameterization() [1/2]

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

Specifies whether strict MMFF94 parameterization is required.

Parameters

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

◆ strictForceFieldParameterization() [2/2]

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

Tells whether strict MMFF94 parameterization is required.

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

◆ setDielectricConstant()

void CDPL::ConfGen::FragmentConformerGeneratorSettings::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::FragmentConformerGeneratorSettings::getDielectricConstant ( ) const

Returns the dielectric constant used by the MMFF94 electrostatic interactions.

Returns: The dielectric constant.

◆ setDistanceExponent()

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

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

Parameters

exponent The new distance exponent.

◆ getDistanceExponent()

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

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

Returns: The distance exponent.

◆ setMaxNumRefinementIterations()

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

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

Parameters

max_iter The new iteration limit (zero disables refinement).

◆ getMaxNumRefinementIterations()

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

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

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

◆ setRefinementStopGradient()

void CDPL::ConfGen::FragmentConformerGeneratorSettings::setRefinementStopGradient ( double grad_norm )

Sets the gradient-norm threshold at which fragment conformer refinement is considered converged.

Parameters

grad_norm The new stop-gradient threshold.

◆ getRefinementStopGradient()

double CDPL::ConfGen::FragmentConformerGeneratorSettings::getRefinementStopGradient ( ) const

Returns the gradient-norm threshold used to terminate refinement.

Returns: The stop-gradient threshold.

◆ setMacrocycleRotorBondCountThreshold()

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

Sets the minimum number of rotatable bonds a macrocyclic 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::FragmentConformerGeneratorSettings::getMacrocycleRotorBondCountThreshold ( ) const

Returns the flexible macrocycle rotatable bond count threshold.

Returns: The current threshold.

◆ getChainSettings() [1/2]

FragmentSettings& CDPL::ConfGen::FragmentConformerGeneratorSettings::getChainSettings ( )

Returns a reference to the per-fragment-class settings used for chain fragments.

Returns: A reference to the chain-fragment settings.

◆ getChainSettings() [2/2]

const FragmentSettings& CDPL::ConfGen::FragmentConformerGeneratorSettings::getChainSettings ( ) const

Returns a const reference to the per-fragment-class settings used for chain fragments.

Returns: A const reference to the chain-fragment settings.

◆ getMacrocycleSettings() [1/2]

FragmentSettings& CDPL::ConfGen::FragmentConformerGeneratorSettings::getMacrocycleSettings ( )

Returns a reference to the per-fragment-class settings used for flexible macrocyclic ring systems.

Returns: A reference to the macrocycle settings.

◆ getMacrocycleSettings() [2/2]

const FragmentSettings& CDPL::ConfGen::FragmentConformerGeneratorSettings::getMacrocycleSettings ( ) const

Returns a const reference to the per-fragment-class settings used for flexible macrocyclic ring systems.

Returns: A const reference to the macrocycle settings.

◆ getSmallRingSystemSettings() [1/2]

FragmentSettings& CDPL::ConfGen::FragmentConformerGeneratorSettings::getSmallRingSystemSettings ( )

Returns a reference to the per-fragment-class settings used for small ring systems.

Returns: A reference to the small ring system settings.

◆ getSmallRingSystemSettings() [2/2]

const FragmentSettings& CDPL::ConfGen::FragmentConformerGeneratorSettings::getSmallRingSystemSettings ( ) const

Returns a const reference to the per-fragment-class settings used for small ring systems.

Returns: A const reference to the small ring system settings.

◆ setSmallRingSystemSamplingFactor()

void CDPL::ConfGen::FragmentConformerGeneratorSettings::setSmallRingSystemSamplingFactor ( std::size_t factor )

Sets a multiplicative factor scaling the sampling effort for small ring systems.

Parameters

factor The new sampling-effort multiplier.

◆ getSmallRingSystemSamplingFactor()

std::size_t CDPL::ConfGen::FragmentConformerGeneratorSettings::getSmallRingSystemSamplingFactor ( ) const

Returns the multiplicative factor scaling the sampling effort for small ring systems.

Returns: The sampling-effort multiplier.

Member Data Documentation

◆ DEFAULT

const FragmentConformerGeneratorSettings CDPL::ConfGen::FragmentConformerGeneratorSettings::DEFAULT

static

A static instance providing configuration parameter default values.

◆ FAST

const FragmentConformerGeneratorSettings CDPL::ConfGen::FragmentConformerGeneratorSettings::FAST

static

A static instance preconfigured for fast (less thorough) conformer generation.

◆ THOROUGH

const FragmentConformerGeneratorSettings CDPL::ConfGen::FragmentConformerGeneratorSettings::THOROUGH

static

A static instance preconfigured for thorough (slower) conformer generation.

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

FragmentConformerGeneratorSettings.hpp

Classes

Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FragmentConformerGeneratorSettings()

◆ ~FragmentConformerGeneratorSettings()

Member Function Documentation

◆ preserveInputBondingGeometries() [1/2]

◆ preserveInputBondingGeometries() [2/2]

◆ setForceFieldType()

◆ getForceFieldType()

◆ strictForceFieldParameterization() [1/2]

◆ strictForceFieldParameterization() [2/2]

◆ setDielectricConstant()

◆ getDielectricConstant()

◆ setDistanceExponent()

◆ getDistanceExponent()

◆ setMaxNumRefinementIterations()

◆ getMaxNumRefinementIterations()

◆ setRefinementStopGradient()

◆ getRefinementStopGradient()

◆ setMacrocycleRotorBondCountThreshold()

◆ getMacrocycleRotorBondCountThreshold()

◆ getChainSettings() [1/2]

◆ getChainSettings() [2/2]

◆ getMacrocycleSettings() [1/2]

◆ getMacrocycleSettings() [2/2]

◆ getSmallRingSystemSettings() [1/2]

◆ getSmallRingSystemSettings() [2/2]

◆ setSmallRingSystemSamplingFactor()

◆ getSmallRingSystemSamplingFactor()

Member Data Documentation

◆ DEFAULT

◆ FAST

◆ THOROUGH