Chemical Data Processing Library Python API - Version 1.1.1
Public Member Functions | Static Public Attributes | Properties | List of all members
CDPL.GRAIL.GRAILDataSetGenerator Class Reference

GRAILDataSetGenerator. More...

+ Inheritance diagram for CDPL.GRAIL.GRAILDataSetGenerator:

Public Member Functions

None __init__ ()
 Initializes the GRAILDataSetGenerator instance.
 
None __init__ (GRAILDataSetGenerator gen)
 Initializes a copy of the GRAILDataSetGenerator instance gen. More...
 
int getObjectID ()
 Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
 
GRAILDataSetGenerator assign (GRAILDataSetGenerator gen)
 Replaces the current state of self with a copy of the state of the GRAILDataSetGenerator instance gen. More...
 
None setScoringFunction (int ftr_type, int tgt_ftr_type, DoubleVector3DFeatureFunctor func)
 
None removeScoringFunction (int ftr_type, int tgt_ftr_type)
 
DoubleVector3DFeatureFunctor getScoringFunction (int ftr_type, int tgt_ftr_type)
 
None setGridName (int ftr_type, int tgt_ftr_type, str name)
 
None removeGridName (int ftr_type, int tgt_ftr_type)
 
str getGridName (int ftr_type, int tgt_ftr_type)
 
None enableInteraction (int ftr_type, int tgt_ftr_type, bool enable)
 
bool isInteractionEnabled (int ftr_type, int tgt_ftr_type)
 
bool clearEnabledInteractions (int arg2, int self)
 
None setScoreCombinationFunction (Math.DoubleDVectorFunctor func)
 
Math.DoubleDVectorFunctor getScoreCombinationFunction ()
 
None normalizeScores (bool normalize)
 
bool scoresNormalized ()
 
None diminishScoresByAtomDensity (bool diminish)
 
bool scoresDiminishedByAtomDensity ()
 
None storeEnvironmentAtomDensityGrid (bool store)
 
bool environmentAtomDensityGridStored ()
 
None setEnvironmentAtomDensityGridName ()
 
str getEnvironmentAtomDensityGridName ()
 
float getGridStepSize ()
 
None setGridStepSize (float size)
 
int getGridXSize ()
 
None setGridXSize (int size)
 
int getGridYSize ()
 
None setGridYSize (int size)
 
int getGridZSize ()
 
None setGridZSize (int size)
 
Math.Matrix4D getGridTransform ()
 
None setGridTransform (Math.Matrix4D xform)
 
None setGridParamsForBoundingBox (Math.Vector3D bbox_min, Math.Vector3D bbox_max, float step_size=0.5)
 
Pharm.DefaultPharmacophoreGenerator getPharmacophoreGenerator ()
 
None setPharmacophoreProcessingFunction (VoidPharmacophoreFunctor func)
 
VoidPharmacophoreFunctor getPharmacophoreProcessingFunction ()
 
None calcInteractionGrids (Chem.MolecularGraph tgt_env, Chem.Atom3DCoordinatesFunction coords_func, Grid.DRegularGridSet grid_set, bool append=False)
 
Grid.DRegularGrid calcAtomDensityGrid (Chem.AtomContainer atoms, Chem.Atom3DCoordinatesFunction coords_func, str grid_name)
 

Static Public Attributes

float DEF_GRID_STEP_SIZE = 0.5
 

Properties

 objectID = property(getObjectID)
 
 normalizedScores = property(scoresNormalized, normalizeScores)
 
 scoreCombinationFunction = property(getScoreCombinationFunction, setScoreCombinationFunction)
 
 pharmProcessingFunction = property(getPharmacophoreProcessingFunction, setPharmacophoreProcessingFunction)
 
 gridStepSize = property(getGridStepSize, setGridStepSize)
 
 gridXSize = property(getGridXSize, setGridXSize)
 
 gridYSize = property(getGridYSize, setGridYSize)
 
 gridZSize = property(getGridZSize, setGridZSize)
 
 gridTransform = property(getGridTransform, setGridTransform)
 
 pharmGenerator = property(getPharmacophoreGenerator)
 
 dimScoresByAtomDensity = property(scoresDiminishedByAtomDensity, diminishScoresByAtomDensity)
 
 storeEnvAtomDensityGrid = property(environmentAtomDensityGridStored, storeEnvironmentAtomDensityGrid)
 
 envAtomDensityGridName = property(getEnvironmentAtomDensityGridName, setEnvironmentAtomDensityGridName)
 

Detailed Description

GRAILDataSetGenerator.

See also
[GRAIL]

Constructor & Destructor Documentation

◆ __init__()

None CDPL.GRAIL.GRAILDataSetGenerator.__init__ ( GRAILDataSetGenerator  gen)

Initializes a copy of the GRAILDataSetGenerator instance gen.

Parameters
genThe GRAILDataSetGenerator instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.GRAIL.GRAILDataSetGenerator.getObjectID ( )

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

Different Python GRAILDataSetGenerator 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 GRAILDataSetGenerator 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()

GRAILDataSetGenerator CDPL.GRAIL.GRAILDataSetGenerator.assign ( GRAILDataSetGenerator  gen)

Replaces the current state of self with a copy of the state of the GRAILDataSetGenerator instance gen.

Parameters
genThe GRAILDataSetGenerator instance to copy.
Returns
self

◆ setScoringFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setScoringFunction ( int  ftr_type,
int  tgt_ftr_type,
DoubleVector3DFeatureFunctor  func 
)
Parameters
ftr_type
tgt_ftr_type
func

◆ removeScoringFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.removeScoringFunction ( int  ftr_type,
int  tgt_ftr_type 
)
Parameters
ftr_type
tgt_ftr_type

◆ getScoringFunction()

DoubleVector3DFeatureFunctor CDPL.GRAIL.GRAILDataSetGenerator.getScoringFunction ( int  ftr_type,
int  tgt_ftr_type 
)
Parameters
ftr_type
tgt_ftr_type
Returns

◆ setGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridName ( int  ftr_type,
int  tgt_ftr_type,
str  name 
)
Parameters
ftr_type
tgt_ftr_type
name

◆ removeGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.removeGridName ( int  ftr_type,
int  tgt_ftr_type 
)
Parameters
ftr_type
tgt_ftr_type

◆ getGridName()

str CDPL.GRAIL.GRAILDataSetGenerator.getGridName ( int  ftr_type,
int  tgt_ftr_type 
)
Parameters
ftr_type
tgt_ftr_type
Returns

◆ enableInteraction()

None CDPL.GRAIL.GRAILDataSetGenerator.enableInteraction ( int  ftr_type,
int  tgt_ftr_type,
bool  enable 
)
Parameters
ftr_type
tgt_ftr_type
enable

◆ isInteractionEnabled()

bool CDPL.GRAIL.GRAILDataSetGenerator.isInteractionEnabled ( int  ftr_type,
int  tgt_ftr_type 
)
Parameters
ftr_type
tgt_ftr_type
Returns

◆ clearEnabledInteractions()

bool CDPL.GRAIL.GRAILDataSetGenerator.clearEnabledInteractions ( int  arg2,
int  self 
)
Parameters
arg1
arg2
Returns

◆ setScoreCombinationFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setScoreCombinationFunction ( Math.DoubleDVectorFunctor  func)
Parameters
func

◆ getScoreCombinationFunction()

Math.DoubleDVectorFunctor CDPL.GRAIL.GRAILDataSetGenerator.getScoreCombinationFunction ( )
Returns

◆ normalizeScores()

None CDPL.GRAIL.GRAILDataSetGenerator.normalizeScores ( bool  normalize)
Parameters
normalize

◆ scoresNormalized()

bool CDPL.GRAIL.GRAILDataSetGenerator.scoresNormalized ( )
Returns

◆ diminishScoresByAtomDensity()

None CDPL.GRAIL.GRAILDataSetGenerator.diminishScoresByAtomDensity ( bool  diminish)
Parameters
diminish

◆ scoresDiminishedByAtomDensity()

bool CDPL.GRAIL.GRAILDataSetGenerator.scoresDiminishedByAtomDensity ( )
Returns

◆ storeEnvironmentAtomDensityGrid()

None CDPL.GRAIL.GRAILDataSetGenerator.storeEnvironmentAtomDensityGrid ( bool  store)
Parameters
store

◆ environmentAtomDensityGridStored()

bool CDPL.GRAIL.GRAILDataSetGenerator.environmentAtomDensityGridStored ( )
Returns

◆ setEnvironmentAtomDensityGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.setEnvironmentAtomDensityGridName ( )
Parameters
<br>

◆ getEnvironmentAtomDensityGridName()

str CDPL.GRAIL.GRAILDataSetGenerator.getEnvironmentAtomDensityGridName ( )
Returns

◆ getGridStepSize()

float CDPL.GRAIL.GRAILDataSetGenerator.getGridStepSize ( )
Returns

◆ setGridStepSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridStepSize ( float  size)
Parameters
size

◆ getGridXSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridXSize ( )
Returns

◆ setGridXSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridXSize ( int  size)
Parameters
size

◆ getGridYSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridYSize ( )
Returns

◆ setGridYSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridYSize ( int  size)
Parameters
size

◆ getGridZSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridZSize ( )
Returns

◆ setGridZSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridZSize ( int  size)
Parameters
size

◆ getGridTransform()

Math.Matrix4D CDPL.GRAIL.GRAILDataSetGenerator.getGridTransform ( )
Returns

◆ setGridTransform()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridTransform ( Math.Matrix4D  xform)
Parameters
xform

◆ setGridParamsForBoundingBox()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridParamsForBoundingBox ( Math.Vector3D  bbox_min,
Math.Vector3D  bbox_max,
float   step_size = 0.5 
)
Parameters
bbox_min
bbox_max
step_size

◆ getPharmacophoreGenerator()

Pharm.DefaultPharmacophoreGenerator CDPL.GRAIL.GRAILDataSetGenerator.getPharmacophoreGenerator ( )
Returns

◆ setPharmacophoreProcessingFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setPharmacophoreProcessingFunction ( VoidPharmacophoreFunctor  func)
Parameters
func

◆ getPharmacophoreProcessingFunction()

VoidPharmacophoreFunctor CDPL.GRAIL.GRAILDataSetGenerator.getPharmacophoreProcessingFunction ( )
Returns

◆ calcInteractionGrids()

None CDPL.GRAIL.GRAILDataSetGenerator.calcInteractionGrids ( Chem.MolecularGraph  tgt_env,
Chem.Atom3DCoordinatesFunction  coords_func,
Grid.DRegularGridSet  grid_set,
bool   append = False 
)
Parameters
tgt_env
coords_func
grid_set
append

◆ calcAtomDensityGrid()

Grid.DRegularGrid CDPL.GRAIL.GRAILDataSetGenerator.calcAtomDensityGrid ( Chem.AtomContainer  atoms,
Chem.Atom3DCoordinatesFunction  coords_func,
str  grid_name 
)
Parameters
atoms
coords_func
grid_name
Returns