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

Inheritance diagram for CDPL.ConfGen.StructureGeneratorSettings:

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

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

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

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

None	setGenerationMode (int mode)
	Sets the structure generation mode (see ConfGen.StructureGenerationMode). More...

int	getGenerationMode ()
	Returns the currently configured structure generation mode. More...

None	generateCoordinatesFromScratch (bool generate)
	Specifies whether 3D coordinates should be generated from scratch (vs. More...

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

None	sampleAngleToleranceRanges (bool sample)
	Specifies whether torsion-angle tolerance ranges are sampled during structure generation. More...

bool	sampleAngleToleranceRanges ()
	Tells whether torsion-angle tolerance ranges are sampled during structure generation. More...

None	setTimeout (int mil_secs)
	Sets the timeout for the structure generation pipeline. More...

int	getTimeout ()
	Returns the currently configured timeout in milliseconds. More...

None	setFragmentModeForceFieldType (int type)
	Sets the MMFF94 force field variant used for fragment-mode structure generation (see ForceField.MMFF94 variants). More...

int	getFragmentModeForceFieldType ()
	Returns the currently configured fragment-mode force field type. More...

None	setDGModeForceFieldType (int type)
	Sets the MMFF94 force field variant used for DG-mode structure generation. More...

int	getDGModeForceFieldType ()
	Returns the currently configured DG-mode force field type. More...

None	strictForceFieldParameterization (bool strict)
	Specifies whether force field parameterization should be strict (missing parameters cause failure). More...

bool	strictForceFieldParameterization ()
	Tells whether force field parameterization is strict. More...

None	setDielectricConstant (float de_const)
	Sets the dielectric constant used in the electrostatic energy term. More...

float	getDielectricConstant ()
	Returns the currently configured dielectric constant. More...

None	setDistanceExponent (float dist_expo)

float	getDistanceExponent ()
	Returns the currently configured distance exponent. More...

None	setMaxNumRefinementIterations (int max_num)

int	getMaxNumRefinementIterations ()
	Returns the currently configured maximum number of refinement iterations. More...

None	setRefinementTolerance (float tol)
	Sets the convergence tolerance of the force field-based coordinate refinement step. More...

float	getRefinementTolerance ()
	Returns the currently configured refinement tolerance. More...

None	setMacrocycleRotorBondCountThreshold (int max_size)

int	getMacrocycleRotorBondCountThreshold ()
	Returns the currently configured flexible macrocycle rotor bond count threshold. More...

None	setMaxNumSampledConformers (int max_num)
	Sets the maximum number of conformers sampled during structure generation. More...

int	getMaxNumSampledConformers ()
	Returns the currently configured maximum number of sampled conformers. More...

None	setConvergenceCheckCycleSize (int size)
	Sets the cycle size for the convergence check of the structure-sampling loop. More...

int	getConvergenceCheckCycleSize ()
	Returns the currently configured convergence check cycle size. More...

FragmentConformerGeneratorSettings	getFragmentBuildSettings ()
	Returns the embedded fragment-build settings. More...

Static Public Attributes
	DEFAULT = _HIDDEN_VALUE_
	A static instance providing configuration parameter default values.

Properties
	objectID = property(getObjectID)

	generationMode = property(getGenerationMode, setGenerationMode)

	genCoordsFromScratch = property(generateCoordinatesFromScratch, generateCoordinatesFromScratch)

	sampleAngleTolRanges = property(sampleAngleToleranceRanges, sampleAngleToleranceRanges)

	timeout = property(getTimeout, setTimeout)

	fragModeForceFieldType = property(getFragmentModeForceFieldType, setFragmentModeForceFieldType)

	dgModeForceFieldType = property(getDGModeForceFieldType, setDGModeForceFieldType)

	strictForceFieldParam = property(strictForceFieldParameterization, strictForceFieldParameterization)

	dielectricConstant = property(getDielectricConstant, setDielectricConstant)

	distanceExponent = property(getDistanceExponent, setDistanceExponent)

	maxNumRefinementIterations = property(getMaxNumRefinementIterations, setMaxNumRefinementIterations)

	refinementTolerance = property(getRefinementTolerance, setRefinementTolerance)

	macrocycleRotorBondCountThresh = property(getMacrocycleRotorBondCountThreshold, setMacrocycleRotorBondCountThreshold)

	maxNumSampledConformers = property(getMaxNumSampledConformers, setMaxNumSampledConformers)

	convCheckCycleSize = property(getConvergenceCheckCycleSize, setConvergenceCheckCycleSize)

	fragmentBuildSettings = property(getFragmentBuildSettings)

Detailed Description

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

Constructor & Destructor Documentation

◆ init()

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

Initializes a copy of the StructureGeneratorSettings instance settings.

Parameters

settings The StructureGeneratorSettings instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.ConfGen.StructureGeneratorSettings.getObjectID ( )

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

Different Python StructureGeneratorSettings 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 StructureGeneratorSettings 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()

StructureGeneratorSettings CDPL.ConfGen.StructureGeneratorSettings.assign ( StructureGeneratorSettings settings )

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

Parameters

settings The StructureGeneratorSettings instance to copy.

Returns: self

◆ setGenerationMode()

None CDPL.ConfGen.StructureGeneratorSettings.setGenerationMode ( int mode )

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

Parameters

mode	The new generation mode.

◆ getGenerationMode()

int CDPL.ConfGen.StructureGeneratorSettings.getGenerationMode ( )

Returns the currently configured structure generation mode.

Returns: The current generation mode.

◆ generateCoordinatesFromScratch() [1/2]

None 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 ( )

Tells whether 3D coordinates are generated from scratch.

Returns: True if coordinates are generated from scratch, and False otherwise.

◆ sampleAngleToleranceRanges() [1/2]

None 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 ( )

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

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

◆ setTimeout()

None CDPL.ConfGen.StructureGeneratorSettings.setTimeout ( int mil_secs )

Sets the timeout for the structure generation pipeline.

Parameters

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

◆ getTimeout()

int CDPL.ConfGen.StructureGeneratorSettings.getTimeout ( )

Returns the currently configured timeout in milliseconds.

Returns: The timeout in milliseconds.

◆ setFragmentModeForceFieldType()

None CDPL.ConfGen.StructureGeneratorSettings.setFragmentModeForceFieldType ( 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()

int CDPL.ConfGen.StructureGeneratorSettings.getFragmentModeForceFieldType ( )

Returns the currently configured fragment-mode force field type.

Returns: The current force field type.

◆ setDGModeForceFieldType()

None CDPL.ConfGen.StructureGeneratorSettings.setDGModeForceFieldType ( int type )

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

Parameters

type	The new force field type.

◆ getDGModeForceFieldType()

int CDPL.ConfGen.StructureGeneratorSettings.getDGModeForceFieldType ( )

Returns the currently configured DG-mode force field type.

Returns: The force field type identifier.

◆ strictForceFieldParameterization() [1/2]

None 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 ( )

Tells whether force field parameterization is strict.

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

◆ setDielectricConstant()

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

Sets the dielectric constant used in the electrostatic energy term.

Parameters

de_const The new dielectric constant.

◆ getDielectricConstant()

float CDPL.ConfGen.StructureGeneratorSettings.getDielectricConstant ( )

Returns the currently configured dielectric constant.

Returns: The dielectric constant.

◆ setDistanceExponent()

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

Parameters

dist_expo

◆ getDistanceExponent()

float CDPL.ConfGen.StructureGeneratorSettings.getDistanceExponent ( )

Returns the currently configured distance exponent.

Returns: The distance exponent.

◆ setMaxNumRefinementIterations()

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

Parameters

max_num

◆ getMaxNumRefinementIterations()

int CDPL.ConfGen.StructureGeneratorSettings.getMaxNumRefinementIterations ( )

Returns the currently configured maximum number of refinement iterations.

Returns: The maximum number of iterations.

◆ setRefinementTolerance()

None CDPL.ConfGen.StructureGeneratorSettings.setRefinementTolerance ( float tol )

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

Parameters

tol	The new refinement tolerance.

◆ getRefinementTolerance()

float CDPL.ConfGen.StructureGeneratorSettings.getRefinementTolerance ( )

Returns the currently configured refinement tolerance.

Returns: The refinement tolerance.

◆ setMacrocycleRotorBondCountThreshold()

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

Parameters

max_size

◆ getMacrocycleRotorBondCountThreshold()

int CDPL.ConfGen.StructureGeneratorSettings.getMacrocycleRotorBondCountThreshold ( )

Returns the currently configured flexible macrocycle rotor bond count threshold.

Returns: The threshold.

◆ setMaxNumSampledConformers()

None CDPL.ConfGen.StructureGeneratorSettings.setMaxNumSampledConformers ( int max_num )

Sets the maximum number of conformers sampled during structure generation.

Parameters

max_num The new maximum number of sampled conformers.

◆ getMaxNumSampledConformers()

int CDPL.ConfGen.StructureGeneratorSettings.getMaxNumSampledConformers ( )

Returns the currently configured maximum number of sampled conformers.

Returns: The maximum number of sampled conformers.

◆ setConvergenceCheckCycleSize()

None CDPL.ConfGen.StructureGeneratorSettings.setConvergenceCheckCycleSize ( int size )

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

Parameters

size	The new convergence check cycle size.

◆ getConvergenceCheckCycleSize()

int CDPL.ConfGen.StructureGeneratorSettings.getConvergenceCheckCycleSize ( )

Returns the currently configured convergence check cycle size.

Returns: The convergence check cycle size.

◆ getFragmentBuildSettings()

FragmentConformerGeneratorSettings CDPL.ConfGen.StructureGeneratorSettings.getFragmentBuildSettings ( )

Returns the embedded fragment-build settings.

Returns: A reference to the fragment-build settings.

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ setGenerationMode()

◆ getGenerationMode()

◆ generateCoordinatesFromScratch() [1/2]

◆ generateCoordinatesFromScratch() [2/2]

◆ sampleAngleToleranceRanges() [1/2]

◆ sampleAngleToleranceRanges() [2/2]

◆ setTimeout()

◆ getTimeout()

◆ setFragmentModeForceFieldType()

◆ getFragmentModeForceFieldType()

◆ setDGModeForceFieldType()

◆ getDGModeForceFieldType()

◆ strictForceFieldParameterization() [1/2]

◆ strictForceFieldParameterization() [2/2]

◆ setDielectricConstant()

◆ getDielectricConstant()

◆ setDistanceExponent()

◆ getDistanceExponent()

◆ setMaxNumRefinementIterations()

◆ getMaxNumRefinementIterations()

◆ setRefinementTolerance()

◆ getRefinementTolerance()

◆ setMacrocycleRotorBondCountThreshold()

◆ getMacrocycleRotorBondCountThreshold()

◆ setMaxNumSampledConformers()

◆ getMaxNumSampledConformers()

◆ setConvergenceCheckCycleSize()

◆ getConvergenceCheckCycleSize()

◆ getFragmentBuildSettings()

◆ init()