CDPL.ConfGen.FragmentConformerGeneratorSettings Class Reference

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

Inheritance diagram for CDPL.ConfGen.FragmentConformerGeneratorSettings:

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

Public Member Functions
None	__init__ ()
	Constructs the % FragmentConformerGeneratorSettings instance with default configuration parameter values.
None	__init__ (FragmentConformerGeneratorSettings settings)
	Initializes a copy of the FragmentConformerGeneratorSettings instance settings. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
FragmentConformerGeneratorSettings	assign (FragmentConformerGeneratorSettings settings)
	Replaces the current state of self with a copy of the state of the FragmentConformerGeneratorSettings instance settings. More...
None	preserveInputBondingGeometries (bool preserve)
	Specifies whether the bonding geometries (bond lengths and angles) of the input fragment shall be preserved. More...
bool	preserveInputBondingGeometries ()
	Tells whether the bonding geometries of the input fragment are preserved. More...
None	setForceFieldType (int type)
	Sets the force field type used for fragment conformer minimization. More...
int	getForceFieldType ()
	Returns the force field type used for fragment conformer minimization. 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	setMaxNumRefinementIterations (int max_num)
int	getMaxNumRefinementIterations ()
	Returns the maximum number of MMFF94 energy-minimization iterations per fragment conformer. More...
None	setRefinementStopGradient (float grad_norm)
	Sets the gradient-norm threshold at which fragment conformer refinement is considered converged. More...
float	getRefinementStopGradient ()
	Returns the gradient-norm threshold used to terminate refinement. More...
None	setMacrocycleRotorBondCountThreshold (int max_size)
int	getMacrocycleRotorBondCountThreshold ()
	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...
FragmentSettings	getMacrocycleSettings ()
	Returns a 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...
None	setSmallRingSystemSamplingFactor (int min_rmsd)
int	getSmallRingSystemSamplingFactor ()
	Returns the multiplicative factor scaling the sampling effort for small ring systems. More...

Static Public Attributes
	DEFAULT = _HIDDEN_VALUE_
	A static instance providing configuration parameter default values.
	FAST = _HIDDEN_VALUE_
	A static instance preconfigured for fast (less thorough) conformer generation.
	THOROUGH = _HIDDEN_VALUE_
	A static instance preconfigured for thorough (slower) conformer generation.

Properties
	objectID = property(getObjectID)
	preserveInputBondingGeom = property(preserveInputBondingGeometries, preserveInputBondingGeometries)
	forceFieldType = property(getForceFieldType, setForceFieldType)
	strictForceFieldParam = property(strictForceFieldParameterization, strictForceFieldParameterization)
	dielectricConstant = property(getDielectricConstant, setDielectricConstant)
	distanceExponent = property(getDistanceExponent, setDistanceExponent)
	maxNumRefinementIterations = property(getMaxNumRefinementIterations, setMaxNumRefinementIterations)
	refinementStopGradient = property(getRefinementStopGradient, setRefinementStopGradient)
	macrocycleRotorBondCountThresh = property(getMacrocycleRotorBondCountThreshold, setMacrocycleRotorBondCountThreshold)
	chainSettings = property(getChainSettings)
	macrocycleSettings = property(getMacrocycleSettings)
	smallRingSysSettings = property(getSmallRingSystemSettings)
	smallRingSysSamplingFactor = property(getSmallRingSystemSamplingFactor, setSmallRingSystemSamplingFactor)

Detailed Description

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

Constructor & Destructor Documentation

__init__()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.__init__

(

FragmentConformerGeneratorSettings

settings

)

Initializes a copy of the FragmentConformerGeneratorSettings instance settings.

Parameters

settings

The FragmentConformerGeneratorSettings instance to copy.

Member Function Documentation

getObjectID()

int CDPL.ConfGen.FragmentConformerGeneratorSettings.getObjectID

(

)

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

Different Python FragmentConformerGeneratorSettings 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 FragmentConformerGeneratorSettings 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()

FragmentConformerGeneratorSettings CDPL.ConfGen.FragmentConformerGeneratorSettings.assign

(

FragmentConformerGeneratorSettings

settings

)

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

Parameters

settings

The FragmentConformerGeneratorSettings instance to copy.

Returns

self

preserveInputBondingGeometries() [1/2]

None 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

(

)

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

Returns

True if the input bonding geometry is reused, and False otherwise.

setForceFieldType()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.setForceFieldType

(

int

type

)

Sets the force field type used for fragment conformer minimization.

Parameters

type	One of the ConfGen.ForceFieldType values.

getForceFieldType()

int CDPL.ConfGen.FragmentConformerGeneratorSettings.getForceFieldType

(

)

Returns the force field type used for fragment conformer minimization.

Returns

One of the ConfGen.ForceFieldType values.

strictForceFieldParameterization() [1/2]

None 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

(

)

Tells whether strict MMFF94 parameterization is required.

Returns

True if strict parameterization is required, and False otherwise.

setDielectricConstant()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.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.FragmentConformerGeneratorSettings.getDielectricConstant

(

)

Returns the dielectric constant used by the MMFF94 electrostatic interactions.

Returns

The dielectric constant.

setDistanceExponent()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.setDistanceExponent

(

float

dist_expo

)

Parameters

dist_expo

getDistanceExponent()

float CDPL.ConfGen.FragmentConformerGeneratorSettings.getDistanceExponent

(

)

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

Returns

The distance exponent.

setMaxNumRefinementIterations()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.setMaxNumRefinementIterations

(

int

max_num

)

Parameters

max_num

getMaxNumRefinementIterations()

int CDPL.ConfGen.FragmentConformerGeneratorSettings.getMaxNumRefinementIterations

(

)

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

Returns

The iteration limit (zero if refinement is disabled).

setRefinementStopGradient()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.setRefinementStopGradient

(

float

grad_norm

)

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

Parameters

grad_norm

The new stop-gradient threshold.

getRefinementStopGradient()

float CDPL.ConfGen.FragmentConformerGeneratorSettings.getRefinementStopGradient

(

)

Returns the gradient-norm threshold used to terminate refinement.

Returns

The stop-gradient threshold.

setMacrocycleRotorBondCountThreshold()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.setMacrocycleRotorBondCountThreshold

(

int

max_size

)

Parameters

max_size

getMacrocycleRotorBondCountThreshold()

int CDPL.ConfGen.FragmentConformerGeneratorSettings.getMacrocycleRotorBondCountThreshold

(

)

Returns the flexible macrocycle rotatable bond count threshold.

Returns

The current threshold.

getChainSettings()

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.

getMacrocycleSettings()

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.

getSmallRingSystemSettings()

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.

setSmallRingSystemSamplingFactor()

None CDPL.ConfGen.FragmentConformerGeneratorSettings.setSmallRingSystemSamplingFactor

(

int

min_rmsd

)

Parameters

min_rmsd

getSmallRingSystemSamplingFactor()

int CDPL.ConfGen.FragmentConformerGeneratorSettings.getSmallRingSystemSamplingFactor

(

)

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

Returns

The sampling-effort multiplier.