CDPL.ConfGen.ConformerGeneratorSettings Class Reference

Inheritance diagram for CDPL.ConfGen.ConformerGeneratorSettings:

Public Member Functions
None	__init__ ()
	Initializes the ConformerGeneratorSettings instance.
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)
int	getSamplingMode ()
None	sampleHeteroAtomHydrogens (bool sample)
bool	sampleHeteroAtomHydrogens ()
None	sampleAngleToleranceRanges (bool sample)
bool	sampleAngleToleranceRanges ()
None	enumerateRings (bool enumerate)
bool	enumerateRings ()
None	setNitrogenEnumerationMode (int mode)
int	getNitrogenEnumerationMode ()
None	generateCoordinatesFromScratch (bool generate)
bool	generateCoordinatesFromScratch ()
None	includeInputCoordinates (bool include)
bool	includeInputCoordinates ()
None	setEnergyWindow (float win_size)
float	getEnergyWindow ()
float	getEnergyWindow (int num_rot_bonds)
None	clearEnergyWindowRanges ()
None	addEnergyWindowRange (int num_rot_bonds, float win_size)
None	setMaxPoolSize (int max_size)
int	getMaxPoolSize ()
None	setMaxRotatableBondCount (int max_count)
int	getMaxRotatableBondCount ()
None	setTimeout (int mil_secs)
int	getTimeout ()
None	setForceFieldTypeSystematic (int type)
int	getForceFieldTypeSystematic ()
None	setForceFieldTypeStochastic (int type)
int	getForceFieldTypeStochastic ()
None	strictForceFieldParameterization (bool strict)
bool	strictForceFieldParameterization ()
None	setDielectricConstant (float de_const)
float	getDielectricConstant ()
None	setDistanceExponent (float dist_expo)
float	getDistanceExponent ()
None	setMaxNumOutputConformers (int max_num)
int	getMaxNumOutputConformers ()
int	getMaxNumOutputConformers (int num_rot_bonds)
None	clearMaxNumOutputConformersRanges ()
None	addMaxNumOutputConformersRange (int num_rot_bonds, int max_num)
None	setMinRMSD (float min_rmsd)
float	getMinRMSD ()
float	getMinRMSD (int num_rot_bonds)
None	clearMinRMSDRanges ()
None	addMinRMSDRange (int num_rot_bonds, float min_rmsd)
None	setMaxNumRefinementIterations (int max_num)
int	getMaxNumRefinementIterations ()
None	setRefinementStopGradient (float tol)
float	getRefinementTolerance ()
None	setMaxNumSampledConformers (int max_num)
int	getMaxNumSampledConformers ()
None	setConvergenceCheckCycleSize (int size)
int	getConvergenceCheckCycleSize ()
None	setMacrocycleRotorBondCountThreshold (int max_size)
int	getMacrocycleRotorBondCountThreshold ()
FragmentConformerGeneratorSettings	getFragmentBuildSettings ()

Static Public Attributes
	DEFAULT = _HIDDEN_VALUE_
	SMALL_SET_DIVERSE = _HIDDEN_VALUE_
	MEDIUM_SET_DIVERSE = _HIDDEN_VALUE_
	LARGE_SET_DIVERSE = _HIDDEN_VALUE_
	SMALL_SET_DENSE = _HIDDEN_VALUE_
	MEDIUM_SET_DENSE = _HIDDEN_VALUE_
	LARGE_SET_DENSE = _HIDDEN_VALUE_

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)

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

)

Parameters

mode

getSamplingMode()

int CDPL.ConfGen.ConformerGeneratorSettings.getSamplingMode

(

)

Returns

sampleHeteroAtomHydrogens() [1/2]

None CDPL.ConfGen.ConformerGeneratorSettings.sampleHeteroAtomHydrogens

(

bool

sample

)

Parameters

sample

sampleHeteroAtomHydrogens() [2/2]

bool CDPL.ConfGen.ConformerGeneratorSettings.sampleHeteroAtomHydrogens

(

)

Returns

sampleAngleToleranceRanges() [1/2]

None CDPL.ConfGen.ConformerGeneratorSettings.sampleAngleToleranceRanges

(

bool

sample

)

Parameters

sample

sampleAngleToleranceRanges() [2/2]

bool CDPL.ConfGen.ConformerGeneratorSettings.sampleAngleToleranceRanges

(

)

Returns

enumerateRings() [1/2]

None CDPL.ConfGen.ConformerGeneratorSettings.enumerateRings

(

bool

enumerate

)

Parameters

enumerate

enumerateRings() [2/2]

bool CDPL.ConfGen.ConformerGeneratorSettings.enumerateRings

(

)

Returns

setNitrogenEnumerationMode()

None CDPL.ConfGen.ConformerGeneratorSettings.setNitrogenEnumerationMode

(

int

mode

)

Parameters

mode

getNitrogenEnumerationMode()

int CDPL.ConfGen.ConformerGeneratorSettings.getNitrogenEnumerationMode

(

)

Returns

generateCoordinatesFromScratch() [1/2]

None CDPL.ConfGen.ConformerGeneratorSettings.generateCoordinatesFromScratch

(

bool

generate

)

Parameters

generate

generateCoordinatesFromScratch() [2/2]

bool CDPL.ConfGen.ConformerGeneratorSettings.generateCoordinatesFromScratch

(

)

Returns

includeInputCoordinates() [1/2]

None CDPL.ConfGen.ConformerGeneratorSettings.includeInputCoordinates

(

bool

include

)

Parameters

include

includeInputCoordinates() [2/2]

bool CDPL.ConfGen.ConformerGeneratorSettings.includeInputCoordinates

(

)

Returns

setEnergyWindow()

None CDPL.ConfGen.ConformerGeneratorSettings.setEnergyWindow

(

float

win_size

)

Parameters

win_size

getEnergyWindow() [1/2]

float CDPL.ConfGen.ConformerGeneratorSettings.getEnergyWindow

(

)

Returns

getEnergyWindow() [2/2]

float CDPL.ConfGen.ConformerGeneratorSettings.getEnergyWindow

(

int

num_rot_bonds

)

Parameters

num_rot_bonds

Returns

addEnergyWindowRange()

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

Parameters

num_rot_bonds
win_size

setMaxPoolSize()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxPoolSize

(

int

max_size

)

Parameters

max_size

getMaxPoolSize()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxPoolSize

(

)

Returns

setMaxRotatableBondCount()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxRotatableBondCount

(

int

max_count

)

Parameters

max_count

getMaxRotatableBondCount()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxRotatableBondCount

(

)

Returns

setTimeout()

None CDPL.ConfGen.ConformerGeneratorSettings.setTimeout

(

int

mil_secs

)

Parameters

mil_secs

getTimeout()

int CDPL.ConfGen.ConformerGeneratorSettings.getTimeout

(

)

Returns

setForceFieldTypeSystematic()

None CDPL.ConfGen.ConformerGeneratorSettings.setForceFieldTypeSystematic

(

int

type

)

Parameters

type

getForceFieldTypeSystematic()

int CDPL.ConfGen.ConformerGeneratorSettings.getForceFieldTypeSystematic

(

)

Returns

setForceFieldTypeStochastic()

None CDPL.ConfGen.ConformerGeneratorSettings.setForceFieldTypeStochastic

(

int

type

)

Parameters

type

getForceFieldTypeStochastic()

int CDPL.ConfGen.ConformerGeneratorSettings.getForceFieldTypeStochastic

(

)

Returns

strictForceFieldParameterization() [1/2]

None CDPL.ConfGen.ConformerGeneratorSettings.strictForceFieldParameterization

(

bool

strict

)

Parameters

strict

strictForceFieldParameterization() [2/2]

bool CDPL.ConfGen.ConformerGeneratorSettings.strictForceFieldParameterization

(

)

Returns

setDielectricConstant()

None CDPL.ConfGen.ConformerGeneratorSettings.setDielectricConstant

(

float

de_const

)

Parameters

de_const

getDielectricConstant()

float CDPL.ConfGen.ConformerGeneratorSettings.getDielectricConstant

(

)

Returns

setDistanceExponent()

None CDPL.ConfGen.ConformerGeneratorSettings.setDistanceExponent

(

float

dist_expo

)

Parameters

dist_expo

getDistanceExponent()

float CDPL.ConfGen.ConformerGeneratorSettings.getDistanceExponent

(

)

Returns

setMaxNumOutputConformers()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxNumOutputConformers

(

int

max_num

)

Parameters

max_num

getMaxNumOutputConformers() [1/2]

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumOutputConformers

(

)

Returns

getMaxNumOutputConformers() [2/2]

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumOutputConformers

(

int

num_rot_bonds

)

Parameters

num_rot_bonds

Returns

addMaxNumOutputConformersRange()

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

Parameters

num_rot_bonds
max_num

setMinRMSD()

None CDPL.ConfGen.ConformerGeneratorSettings.setMinRMSD

(

float

min_rmsd

)

Parameters

min_rmsd

getMinRMSD() [1/2]

float CDPL.ConfGen.ConformerGeneratorSettings.getMinRMSD

(

)

Returns

getMinRMSD() [2/2]

float CDPL.ConfGen.ConformerGeneratorSettings.getMinRMSD

(

int

num_rot_bonds

)

Parameters

num_rot_bonds

Returns

addMinRMSDRange()

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

Parameters

num_rot_bonds
min_rmsd

setMaxNumRefinementIterations()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxNumRefinementIterations

(

int

max_num

)

Parameters

max_num

getMaxNumRefinementIterations()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumRefinementIterations

(

)

Returns

setRefinementStopGradient()

None CDPL.ConfGen.ConformerGeneratorSettings.setRefinementStopGradient

(

float

tol

)

Parameters

tol

getRefinementTolerance()

float CDPL.ConfGen.ConformerGeneratorSettings.getRefinementTolerance

(

)

Returns

setMaxNumSampledConformers()

None CDPL.ConfGen.ConformerGeneratorSettings.setMaxNumSampledConformers

(

int

max_num

)

Parameters

max_num

getMaxNumSampledConformers()

int CDPL.ConfGen.ConformerGeneratorSettings.getMaxNumSampledConformers

(

)

Returns

setConvergenceCheckCycleSize()

None CDPL.ConfGen.ConformerGeneratorSettings.setConvergenceCheckCycleSize

(

int

size

)

Parameters

size

getConvergenceCheckCycleSize()

int CDPL.ConfGen.ConformerGeneratorSettings.getConvergenceCheckCycleSize

(

)

Returns

setMacrocycleRotorBondCountThreshold()

None CDPL.ConfGen.ConformerGeneratorSettings.setMacrocycleRotorBondCountThreshold

(

int

max_size

)

Parameters

max_size

getMacrocycleRotorBondCountThreshold()

int CDPL.ConfGen.ConformerGeneratorSettings.getMacrocycleRotorBondCountThreshold

(

)

Returns

getFragmentBuildSettings()

FragmentConformerGeneratorSettings CDPL.ConfGen.ConformerGeneratorSettings.getFragmentBuildSettings

(

)

Returns