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

Inheritance diagram for CDPL.ConfGen.ConformerGeneratorSettings:

Public Member Functions
None	__init__ ()
	Constructs the `ConformerGeneratorSettings` instance with default configuration parameter values.

None	__init__ (ConformerGeneratorSettings settings)
	Initializes a copy of the `ConformerGeneratorSettings` instance settings. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

ConformerGeneratorSettings	assign (ConformerGeneratorSettings settings)
	Replaces the current state of self with a copy of the state of the `ConformerGeneratorSettings` instance settings. More...

None	setSamplingMode (int mode)
	Specifies the conformer-sampling strategy to use. More...

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

None	sampleHeteroAtomHydrogens (bool sample)
	Specifies whether torsions of heteroatom hydrogen rotors shall be sampled. More...

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

None	sampleAngleToleranceRanges (bool sample)
	Specifies whether additional torsion samples within the tolerance ranges defined by the torsion library entries shall be generated. More...

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

None	enumerateRings (bool enumerate)
	Specifies whether ring conformations shall be enumerated. More...

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

None	setNitrogenEnumerationMode (int mode)
	Sets the enumeration mode for stereogenic nitrogen centers. More...

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

None	generateCoordinatesFromScratch (bool generate)
	Specifies whether 3D coordinates shall be generated from scratch (ignoring any 3D input). More...

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

None	includeInputCoordinates (bool include)
	Specifies whether the input conformation shall be included in the output conformer ensemble. More...

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

None	setEnergyWindow (float win_size)
	Sets the energy window size (in kcal/mol) above the found global minimum within which conformers are kept. More...

float	getEnergyWindow ()
	Returns the configured energy window size. More...

float	getEnergyWindow (int num_rot_bonds)
	Returns the energy window size that applies for molecules with num_rot_bonds rotatable bonds. More...

None	clearEnergyWindowRanges ()
	Removes all registered rotatable bond count-dependent energy window overrides. More...

None	addEnergyWindowRange (int num_rot_bonds, float win_size)
	Registers an energy window override that applies up to and including num_rot_bonds rotatable bonds. More...

None	setMaxPoolSize (int max_size)
	Sets the maximum number of conformers to keep in the internal candidate pool. More...

int	getMaxPoolSize ()
	Returns the maximum number of conformers kept in the internal candidate pool. More...

None	setMaxRotatableBondCount (int max_count)
	Sets the upper limit on the number of rotatable bonds an input molecule may have to be processed. More...

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

None	setTimeout (int mil_secs)
	Sets the maximum allowed wall clock processing time per molecule. More...

int	getTimeout ()
	Returns the configured per-molecule wall clock time limit. More...

None	setForceFieldTypeSystematic (int type)
	Sets the force field type used by the systematic sampling pipeline. More...

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

None	setForceFieldTypeStochastic (int type)
	Sets the force field type used by the stochastic sampling pipeline. More...

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

None	strictForceFieldParameterization (bool strict)
	Specifies whether strict MMFF94 parameterization is required. More...

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

None	setDielectricConstant (float de_const)
	Sets the dielectric constant used by the MMFF94 electrostatic interactions. More...

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

None	setDistanceExponent (float dist_expo)

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

None	setMaxNumOutputConformers (int max_num)
	Sets the maximum number of output conformers per molecule. More...

int	getMaxNumOutputConformers ()
	Returns the configured maximum number of output conformers. More...

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

None	clearMaxNumOutputConformersRanges ()
	Removes all registered rotatable bond count-dependent output conformer overrides. More...

None	addMaxNumOutputConformersRange (int num_rot_bonds, int max_num)
	Registers an output conformer limit override that applies up to and including num_rot_bonds rotatable bonds. More...

None	setMinRMSD (float min_rmsd)
	Sets the minimum pairwise heavy atom RMSD that conformers in the output ensemble must keep. More...

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

float	getMinRMSD (int num_rot_bonds)
	Returns the minimum RMSD threshold that applies for molecules with num_rot_bonds rotatable bonds. More...

None	clearMinRMSDRanges ()
	Removes all registered rotatable bond count-dependent minimum RMSD overrides. More...

None	addMinRMSDRange (int num_rot_bonds, float min_rmsd)
	Registers a minimum RMSD override that applies up to and including num_rot_bonds rotatable bonds. More...

None	setMaxNumRefinementIterations (int max_num)

int	getMaxNumRefinementIterations ()
	Returns the maximum number of MMFF94 energy minimization iterations per conformer. More...

None	setRefinementStopGradient (float tol)

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

None	setMaxNumSampledConformers (int max_num)
	Sets the upper bound on the number of trial conformations produced by the stochastic sampler. More...

int	getMaxNumSampledConformers ()
	Returns the upper bound on the number of trial conformations produced by the stochastic sampler. More...

None	setConvergenceCheckCycleSize (int size)
	Sets the cycle size (in trial conformations) at which the stochastic sampler tests for convergence. More...

int	getConvergenceCheckCycleSize ()
	Returns the cycle size at which the stochastic sampler tests for convergence. More...

None	setMacrocycleRotorBondCountThreshold (int max_size)

int	getMacrocycleRotorBondCountThreshold ()
	Returns the flexible macrocycle rotatable bond count threshold. More...

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

Static Public Attributes
	DEFAULT = _HIDDEN_VALUE_
	Instance providing configuration parameter default values.

	SMALL_SET_DIVERSE = _HIDDEN_VALUE_
	Preset producing a small, diversity-optimized conformer ensemble.

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

	LARGE_SET_DIVERSE = _HIDDEN_VALUE_
	Preset producing a large, diversity-optimized conformer ensemble.

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

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

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

Properties
	objectID = property(getObjectID)

	samplingMode = property(getSamplingMode, setSamplingMode)

	sampleHetAtomHydrogens = property(sampleHeteroAtomHydrogens, sampleHeteroAtomHydrogens)

	sampleAngleTolRanges = property(sampleAngleToleranceRanges, sampleAngleToleranceRanges)

	enumRings = property(enumerateRings, enumerateRings)

	nitrogenEnumMode = property(getNitrogenEnumerationMode, setNitrogenEnumerationMode)

	genCoordsFromScratch = property(generateCoordinatesFromScratch, generateCoordinatesFromScratch)

	includeInputCoords = property(includeInputCoordinates, includeInputCoordinates)

	energyWindow = property(getEnergyWindow, setEnergyWindow)

	maxPoolSize = property(getMaxPoolSize, setMaxPoolSize)

	maxRotatableBondCount = property(getMaxRotatableBondCount, setMaxRotatableBondCount)

	timeout = property(getTimeout, setTimeout)

	forceFieldTypeSystematic = property(getForceFieldTypeSystematic, setForceFieldTypeSystematic)

	forceFieldTypeStochastic = property(getForceFieldTypeStochastic, setForceFieldTypeStochastic)

	strictForceFieldParam = property(strictForceFieldParameterization, strictForceFieldParameterization)

	dielectricConstant = property(getDielectricConstant, setDielectricConstant)

	distanceExponent = property(getDistanceExponent, setDistanceExponent)

	maxNumOutputConformers = property(getMaxNumOutputConformers, setMaxNumOutputConformers)

	minRMSD = property(getMinRMSD, setMinRMSD)

	maxNumRefinementIterations = property(getMaxNumRefinementIterations, setMaxNumRefinementIterations)

	refinementTolerance = property(getRefinementTolerance, setRefinementTolerance)

	maxNumSampledConformers = property(getMaxNumSampledConformers, setMaxNumSampledConformers)

	convCheckCycleSize = property(getConvergenceCheckCycleSize, setConvergenceCheckCycleSize)

	macrocycleRotorBondCountThresh = property(getMacrocycleRotorBondCountThreshold, setMacrocycleRotorBondCountThreshold)

	fragmentBuildSettings = property(getFragmentBuildSettings)

Detailed Description

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

Constructor & Destructor Documentation

◆ init()

None CDPL.ConfGen.ConformerGeneratorSettings.__init__ ( ConformerGeneratorSettings settings )

Initializes a copy of the ConformerGeneratorSettings instance settings.

Parameters

settings The ConformerGeneratorSettings instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.ConfGen.ConformerGeneratorSettings.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python ConformerGeneratorSettings instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two ConformerGeneratorSettings instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ assign()

ConformerGeneratorSettings CDPL.ConfGen.ConformerGeneratorSettings.assign ( ConformerGeneratorSettings settings )

Replaces the current state of self with a copy of the state of the ConformerGeneratorSettings instance settings.

Parameters

settings The ConformerGeneratorSettings instance to copy.

Returns: self

◆ setSamplingMode()

None CDPL.ConfGen.ConformerGeneratorSettings.setSamplingMode ( int mode )

Specifies the conformer-sampling strategy to use.

Parameters

mode	One of the ConfGen.ConformerSamplingMode values.

◆ getSamplingMode()

int CDPL.ConfGen.ConformerGeneratorSettings.getSamplingMode ( )

Returns the currently configured conformer-sampling strategy.

Returns: One of the ConfGen.ConformerSamplingMode values.

◆ sampleHeteroAtomHydrogens() [1/2]

None 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 ( )

Tells whether torsions of heteroatom hydrogen rotors are sampled.

Returns: True if sampling is enabled, and False otherwise.

◆ sampleAngleToleranceRanges() [1/2]

None 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 ( )

Tells whether tolerance-range sampling is enabled.

Returns: True if tolerance-range sampling is enabled, and False otherwise.

◆ enumerateRings() [1/2]

None 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 ( )

Tells whether ring conformations are enumerated.

Returns: True if ring conformations are enumerated, and False otherwise.

◆ setNitrogenEnumerationMode()

None CDPL.ConfGen.ConformerGeneratorSettings.setNitrogenEnumerationMode ( int mode )

Sets the enumeration mode for stereogenic nitrogen centers.

Parameters

mode	One of the ConfGen.NitrogenEnumerationMode values.

◆ getNitrogenEnumerationMode()

int CDPL.ConfGen.ConformerGeneratorSettings.getNitrogenEnumerationMode ( )

Returns the currently configured nitrogen enumeration mode.

Returns: One of the ConfGen.NitrogenEnumerationMode values.

◆ generateCoordinatesFromScratch() [1/2]

None 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 ( )

Tells whether 3D coordinates are generated from scratch.

Returns: True if 3D coordinates are always regenerated, and False otherwise.

◆ includeInputCoordinates() [1/2]

None 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 ( )

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

Returns: True if the input coordinates are included, and False otherwise.

◆ setEnergyWindow()

None CDPL.ConfGen.ConformerGeneratorSettings.setEnergyWindow ( float 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]

float CDPL.ConfGen.ConformerGeneratorSettings.getEnergyWindow ( )

Returns the configured energy window size.

Returns: The energy window size in kcal/mol.

◆ getEnergyWindow() [2/2]

float CDPL.ConfGen.ConformerGeneratorSettings.getEnergyWindow ( int num_rot_bonds )

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()

None CDPL.ConfGen.ConformerGeneratorSettings.clearEnergyWindowRanges ( )

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

Since: 1.1

◆ addEnergyWindowRange()

None CDPL.ConfGen.ConformerGeneratorSettings.addEnergyWindowRange	(	int	num_rot_bonds,
		float	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()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxPoolSize ( int max_size )

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

Parameters

max_size The new maximum pool size.

◆ getMaxPoolSize()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxPoolSize ( )

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

Returns: The maximum pool size.

◆ setMaxRotatableBondCount()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxRotatableBondCount ( int 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()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxRotatableBondCount ( )

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()

None CDPL.ConfGen.ConformerGeneratorSettings.setTimeout ( int 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()

int CDPL.ConfGen.ConformerGeneratorSettings.getTimeout ( )

Returns the configured per-molecule wall clock time limit.

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

◆ setForceFieldTypeSystematic()

None CDPL.ConfGen.ConformerGeneratorSettings.setForceFieldTypeSystematic ( int type )

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

Parameters

type	One of the ConfGen.ForceFieldType values.

◆ getForceFieldTypeSystematic()

int CDPL.ConfGen.ConformerGeneratorSettings.getForceFieldTypeSystematic ( )

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

Returns: One of the ConfGen.ForceFieldType values.

◆ setForceFieldTypeStochastic()

None CDPL.ConfGen.ConformerGeneratorSettings.setForceFieldTypeStochastic ( int type )

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

Parameters

type	One of the ConfGen.ForceFieldType values.

◆ getForceFieldTypeStochastic()

int CDPL.ConfGen.ConformerGeneratorSettings.getForceFieldTypeStochastic ( )

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

Returns: One of the ConfGen.ForceFieldType values.

◆ strictForceFieldParameterization() [1/2]

None 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 ( )

Tells whether strict MMFF94 parameterization is required.

Returns: True if strict parameterization is required, and False otherwise.

◆ setDielectricConstant()

None CDPL.ConfGen.ConformerGeneratorSettings.setDielectricConstant ( float de_const )

Sets the dielectric constant used by the MMFF94 electrostatic interactions.

Parameters

de_const The new dielectric constant.

◆ getDielectricConstant()

float CDPL.ConfGen.ConformerGeneratorSettings.getDielectricConstant ( )

Returns the dielectric constant used by the MMFF94 electrostatic interactions.

Returns: The dielectric constant.

◆ setDistanceExponent()

None CDPL.ConfGen.ConformerGeneratorSettings.setDistanceExponent ( float dist_expo )

Parameters

dist_expo

◆ getDistanceExponent()

float CDPL.ConfGen.ConformerGeneratorSettings.getDistanceExponent ( )

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

Returns: The distance exponent.

◆ setMaxNumOutputConformers()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxNumOutputConformers ( int max_num )

Sets the maximum number of output conformers per molecule.

Parameters

max_num The new output conformer count limit.

◆ getMaxNumOutputConformers() [1/2]

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumOutputConformers ( )

Returns the configured maximum number of output conformers.

Returns: The output conformer count limit.

◆ getMaxNumOutputConformers() [2/2]

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumOutputConformers ( int num_rot_bonds )

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()

None CDPL.ConfGen.ConformerGeneratorSettings.clearMaxNumOutputConformersRanges ( )

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

Since: 1.1

◆ addMaxNumOutputConformersRange()

None CDPL.ConfGen.ConformerGeneratorSettings.addMaxNumOutputConformersRange	(	int	num_rot_bonds,
		int	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()

None CDPL.ConfGen.ConformerGeneratorSettings.setMinRMSD ( float 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]

float CDPL.ConfGen.ConformerGeneratorSettings.getMinRMSD ( )

Returns the globally configured minimum RMSD threshold.

Returns: The minimum RMSD threshold (in Å).

◆ getMinRMSD() [2/2]

float CDPL.ConfGen.ConformerGeneratorSettings.getMinRMSD ( int num_rot_bonds )

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()

None CDPL.ConfGen.ConformerGeneratorSettings.clearMinRMSDRanges ( )

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

Since: 1.1

◆ addMinRMSDRange()

None CDPL.ConfGen.ConformerGeneratorSettings.addMinRMSDRange	(	int	num_rot_bonds,
		float	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()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxNumRefinementIterations ( int max_num )

Parameters

max_num

◆ getMaxNumRefinementIterations()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumRefinementIterations ( )

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

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

◆ setRefinementStopGradient()

None CDPL.ConfGen.ConformerGeneratorSettings.setRefinementStopGradient ( float tol )

Parameters

tol

◆ getRefinementTolerance()

float CDPL.ConfGen.ConformerGeneratorSettings.getRefinementTolerance ( )

Returns the convergence tolerance of the MMFF94 energy minimization step.

Returns: The convergence tolerance.

◆ setMaxNumSampledConformers()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxNumSampledConformers ( int 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()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumSampledConformers ( )

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

Returns: The sampled conformer limit.

◆ setConvergenceCheckCycleSize()

None CDPL.ConfGen.ConformerGeneratorSettings.setConvergenceCheckCycleSize ( int 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()

int CDPL.ConfGen.ConformerGeneratorSettings.getConvergenceCheckCycleSize ( )

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

Returns: The convergence check cycle size.

◆ setMacrocycleRotorBondCountThreshold()

None CDPL.ConfGen.ConformerGeneratorSettings.setMacrocycleRotorBondCountThreshold ( int max_size )

Parameters

max_size

◆ getMacrocycleRotorBondCountThreshold()

int CDPL.ConfGen.ConformerGeneratorSettings.getMacrocycleRotorBondCountThreshold ( )

Returns the flexible macrocycle rotatable bond count threshold.

Returns: The threshold.

◆ getFragmentBuildSettings()

FragmentConformerGeneratorSettings CDPL.ConfGen.ConformerGeneratorSettings.getFragmentBuildSettings ( )

Returns a reference to the nested fragment conformer build settings.

Returns: A reference to the build settings.

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ 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()

◆ setRefinementStopGradient()

◆ getRefinementTolerance()

◆ setMaxNumSampledConformers()

◆ getMaxNumSampledConformers()

◆ setConvergenceCheckCycleSize()

◆ getConvergenceCheckCycleSize()

◆ setMacrocycleRotorBondCountThreshold()

◆ getMacrocycleRotorBondCountThreshold()

◆ getFragmentBuildSettings()

◆ init()