Chemical Data Processing Library Python API - Version 1.1.1
Classes | Public Member Functions | Static Public Attributes | Properties | List of all members
CDPL.Shape.GaussianShapeFunctionAlignment Class Reference
+ Inheritance diagram for CDPL.Shape.GaussianShapeFunctionAlignment:

Classes

class  Result
 

Public Member Functions

None __init__ ()
 Initializes the GaussianShapeFunctionAlignment instance.
 
None __init__ (GaussianShapeFunction ref_func, int sym_class)
 Initializes the GaussianShapeFunctionAlignment instance. More...
 
int getObjectID ()
 Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
 
None setOverlapFunction (GaussianShapeOverlapFunction func)
 
GaussianShapeOverlapFunction getOverlapFunction ()
 
FastGaussianShapeOverlapFunction getDefaultOverlapFunction ()
 
None setReference (GaussianShapeFunction func, int sym_class)
 
GaussianShapeFunction getReference ()
 
None setStartGenerator (GaussianShapeAlignmentStartGenerator gen)
 
GaussianShapeAlignmentStartGenerator getStartGenerator ()
 
PrincipalAxesAlignmentStartGenerator getDefaultStartGenerator ()
 
None setColorMatchFunction (Pharm.BoolSizeType2Functor func)
 
Pharm.BoolSizeType2Functor getColorMatchFunction ()
 
None setColorFilterFunction (BoolSizeTypeFunctor func)
 
BoolSizeTypeFunctor getColorFilterFunction ()
 
None performAlignment (bool perf_align)
 
bool performAlignment ()
 
None setMaxNumOptimizationIterations (int max_iter)
 
int getMaxNumOptimizationIterations ()
 
None setOptimizationStopGradient (float grad_norm)
 
float getOptimizationStopGradient ()
 
None optimizeOverlap (bool optimize)
 
bool optimizeOverlap ()
 
None greedyOptimization (bool greedy)
 
bool greedyOptimization ()
 
int setupReference (GaussianShapeFunction func, Math.Matrix4D xform)
 
int setupAligned (GaussianShapeFunction func, Math.Matrix4D xform)
 
float calcSelfOverlap (GaussianShapeFunction calc)
 
float calcColorSelfOverlap (GaussianShapeFunction calc)
 
None calcColorOverlaps (bool calc)
 
bool calcColorOverlaps ()
 
bool align (GaussianShapeFunction func, int sym_class)
 
int getNumResults ()
 
Result getResult (int idx)
 
int __len__ ()
 
Result __getitem__ (int idx)
 

Static Public Attributes

float DEF_OPTIMIZATION_STOP_GRADIENT = 1.0
 
int DEF_MAX_OPTIMIZATION_ITERATIONS = 20
 

Properties

 objectID = property(getObjectID)
 
 numResults = property(getNumResults)
 
 overlapFunction = property(getOverlapFunction, setOverlapFunction)
 
 defaultOverlapFunction = property(getDefaultOverlapFunction)
 
 reference = property(getReference, setReference)
 
 startGenerator = property(getStartGenerator, setStartGenerator)
 
 defaultStartGenerator = property(getDefaultStartGenerator)
 
 colorMatchFunction = property(getColorMatchFunction, setColorMatchFunction)
 
 colorFilterFunction = property(getColorFilterFunction, setColorFilterFunction)
 
 perfAlignment = property(performAlignment, performAlignment)
 
 maxNumOptIterations = property(getMaxNumOptimizationIterations, setMaxNumOptimizationIterations)
 
 optStopGradient = property(getOptimizationStopGradient, setOptimizationStopGradient)
 
 optOverlap = property(optimizeOverlap, optimizeOverlap)
 
 greedyOpt = property(greedyOptimization, greedyOptimization)
 
 colorOverlaps = property(calcColorOverlaps, calcColorOverlaps)
 

Constructor & Destructor Documentation

◆ __init__()

None CDPL.Shape.GaussianShapeFunctionAlignment.__init__ ( GaussianShapeFunction  ref_func,
int  sym_class 
)

Initializes the GaussianShapeFunctionAlignment instance.

Parameters
ref_func
sym_class

Member Function Documentation

◆ getObjectID()

int CDPL.Shape.GaussianShapeFunctionAlignment.getObjectID ( )

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

Different Python GaussianShapeFunctionAlignment 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 GaussianShapeFunctionAlignment 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.

◆ setOverlapFunction()

None CDPL.Shape.GaussianShapeFunctionAlignment.setOverlapFunction ( GaussianShapeOverlapFunction  func)
Parameters
func

◆ getOverlapFunction()

GaussianShapeOverlapFunction CDPL.Shape.GaussianShapeFunctionAlignment.getOverlapFunction ( )
Returns

◆ getDefaultOverlapFunction()

FastGaussianShapeOverlapFunction CDPL.Shape.GaussianShapeFunctionAlignment.getDefaultOverlapFunction ( )
Returns

◆ setReference()

None CDPL.Shape.GaussianShapeFunctionAlignment.setReference ( GaussianShapeFunction  func,
int  sym_class 
)
Parameters
func
sym_class

◆ getReference()

GaussianShapeFunction CDPL.Shape.GaussianShapeFunctionAlignment.getReference ( )
Returns

◆ setStartGenerator()

None CDPL.Shape.GaussianShapeFunctionAlignment.setStartGenerator ( GaussianShapeAlignmentStartGenerator  gen)
Parameters
gen

◆ getStartGenerator()

GaussianShapeAlignmentStartGenerator CDPL.Shape.GaussianShapeFunctionAlignment.getStartGenerator ( )
Returns

◆ getDefaultStartGenerator()

PrincipalAxesAlignmentStartGenerator CDPL.Shape.GaussianShapeFunctionAlignment.getDefaultStartGenerator ( )
Returns

◆ setColorMatchFunction()

None CDPL.Shape.GaussianShapeFunctionAlignment.setColorMatchFunction ( Pharm.BoolSizeType2Functor  func)
Parameters
func

◆ getColorMatchFunction()

Pharm.BoolSizeType2Functor CDPL.Shape.GaussianShapeFunctionAlignment.getColorMatchFunction ( )
Returns

◆ setColorFilterFunction()

None CDPL.Shape.GaussianShapeFunctionAlignment.setColorFilterFunction ( BoolSizeTypeFunctor  func)
Parameters
func

◆ getColorFilterFunction()

BoolSizeTypeFunctor CDPL.Shape.GaussianShapeFunctionAlignment.getColorFilterFunction ( )
Returns

◆ performAlignment() [1/2]

None CDPL.Shape.GaussianShapeFunctionAlignment.performAlignment ( bool  perf_align)
Parameters
perf_align

◆ performAlignment() [2/2]

bool CDPL.Shape.GaussianShapeFunctionAlignment.performAlignment ( )
Returns

◆ setMaxNumOptimizationIterations()

None CDPL.Shape.GaussianShapeFunctionAlignment.setMaxNumOptimizationIterations ( int  max_iter)
Parameters
max_iter

◆ getMaxNumOptimizationIterations()

int CDPL.Shape.GaussianShapeFunctionAlignment.getMaxNumOptimizationIterations ( )
Returns

◆ setOptimizationStopGradient()

None CDPL.Shape.GaussianShapeFunctionAlignment.setOptimizationStopGradient ( float  grad_norm)
Parameters
grad_norm

◆ getOptimizationStopGradient()

float CDPL.Shape.GaussianShapeFunctionAlignment.getOptimizationStopGradient ( )
Returns

◆ optimizeOverlap() [1/2]

None CDPL.Shape.GaussianShapeFunctionAlignment.optimizeOverlap ( bool  optimize)
Parameters
optimize

◆ optimizeOverlap() [2/2]

bool CDPL.Shape.GaussianShapeFunctionAlignment.optimizeOverlap ( )
Returns

◆ greedyOptimization() [1/2]

None CDPL.Shape.GaussianShapeFunctionAlignment.greedyOptimization ( bool  greedy)
Parameters
greedy

◆ greedyOptimization() [2/2]

bool CDPL.Shape.GaussianShapeFunctionAlignment.greedyOptimization ( )
Returns

◆ setupReference()

int CDPL.Shape.GaussianShapeFunctionAlignment.setupReference ( GaussianShapeFunction  func,
Math.Matrix4D  xform 
)
Parameters
func
xform
Returns

◆ setupAligned()

int CDPL.Shape.GaussianShapeFunctionAlignment.setupAligned ( GaussianShapeFunction  func,
Math.Matrix4D  xform 
)
Parameters
func
xform
Returns

◆ calcSelfOverlap()

float CDPL.Shape.GaussianShapeFunctionAlignment.calcSelfOverlap ( GaussianShapeFunction  calc)
Parameters
calc
Returns

◆ calcColorSelfOverlap()

float CDPL.Shape.GaussianShapeFunctionAlignment.calcColorSelfOverlap ( GaussianShapeFunction  calc)
Parameters
calc
Returns

◆ calcColorOverlaps() [1/2]

None CDPL.Shape.GaussianShapeFunctionAlignment.calcColorOverlaps ( bool  calc)
Parameters
calc

◆ calcColorOverlaps() [2/2]

bool CDPL.Shape.GaussianShapeFunctionAlignment.calcColorOverlaps ( )
Returns

◆ align()

bool CDPL.Shape.GaussianShapeFunctionAlignment.align ( GaussianShapeFunction  func,
int  sym_class 
)
Parameters
func
sym_class
Returns

◆ getNumResults()

int CDPL.Shape.GaussianShapeFunctionAlignment.getNumResults ( )
Returns

◆ getResult()

Result CDPL.Shape.GaussianShapeFunctionAlignment.getResult ( int  idx)
Parameters
idx
Returns

◆ __len__()

int CDPL.Shape.GaussianShapeFunctionAlignment.__len__ ( )
Returns

◆ __getitem__()

Result CDPL.Shape.GaussianShapeFunctionAlignment.__getitem__ ( int  idx)
Parameters
idx
Returns
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