 |
Chemical Data Processing Library Python API - Version 1.4.0
|
|
Chemical Data Processing Library Python API - Version 1.4.0
|
Generator that produces alignment starting transformations by aligning the principal axes of the aligned shape to those of the reference shape. More...
Inheritance diagram for CDPL.Shape.PrincipalAxesAlignmentStartGenerator:Public Member Functions | |
| None | __init__ () |
Constructs the PrincipalAxesAlignmentStartGenerator instance. | |
| None | __init__ (PrincipalAxesAlignmentStartGenerator gen) |
Initializes a copy of the PrincipalAxesAlignmentStartGenerator instance gen. More... | |
| None | setSymmetryThreshold (float thresh) |
| Sets the relative threshold for treating two principal moments as equal. More... | |
| float | getSymmetryThreshold () |
| Returns the currently configured symmetry threshold. More... | |
| None | genShapeCenterStarts (bool generate) |
| Enables or disables the generation of a starting transformation at the shape centroid. More... | |
| bool | genShapeCenterStarts () |
| Tells whether a starting transformation at the shape centroid is generated. More... | |
| None | genColorCenterStarts (bool generate) |
| Enables or disables the generation of starting transformations at color (pharmacophore) feature centers. More... | |
| bool | genColorCenterStarts () |
| Tells whether starting transformations at color (pharmacophore) feature centers are generated. More... | |
| None | genNonColorCenterStarts (bool generate) |
| Enables or disables the generation of starting transformations at non-color (shape) element centers. More... | |
| bool | genNonColorCenterStarts () |
| Tells whether starting transformations at non-color (shape) element centers are generated. More... | |
| None | genRandomStarts (bool generate) |
| Enables or disables the generation of random starting transformations. More... | |
| bool | genRandomStarts () |
| Tells whether random starting transformations are generated. More... | |
| None | genForAlignedShapeCenters (bool generate) |
| Specifies whether element-/color-center starts shall be generated for centers of the aligned shape. More... | |
| bool | genForAlignedShapeCenters () |
| Tells whether element-/color-center starts are generated for centers of the aligned shape. More... | |
| None | genForReferenceShapeCenters (bool generate) |
| Specifies whether element-/color-center starts shall be generated for centers of the reference shape. More... | |
| bool | genForReferenceShapeCenters () |
| Tells whether element-/color-center starts are generated for centers of the reference shape. More... | |
| None | genForLargerShapeCenters (bool generate) |
| Specifies whether element-/color-center starts shall be generated for centers of the shape with more elements (instead of both shapes). More... | |
| bool | genForLargerShapeCenters () |
| Tells whether element-/color-center starts are generated for centers of the shape with more elements (instead of both shapes). More... | |
| None | setMaxRandomTranslation (float max_trans) |
| Sets the maximum random translation magnitude applied to random starts. More... | |
| float | getMaxRandomTranslation () |
| Returns the currently configured maximum random translation. More... | |
| None | setNumRandomStarts (int num_starts) |
| Sets the number of random starting transformations. More... | |
| int | getNumRandomStarts () |
| Returns the currently configured number of random starts. More... | |
| None | setRandomSeed (int seed) |
| Sets the seed used by the random number generator that produces the random starts. More... | |
| PrincipalAxesAlignmentStartGenerator | assign (PrincipalAxesAlignmentStartGenerator gen) |
Replaces the current state of self with a copy of the state of the PrincipalAxesAlignmentStartGenerator instance gen. More... | |
| Public Member Functions inherited from CDPL.Shape.GaussianShapeAlignmentStartGenerator | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| int | setupReference (GaussianShapeFunction func, Math.Matrix4D xform) |
| Prepares the reference shape function for use by the start generator. More... | |
| int | setupAligned (GaussianShapeFunction func, Math.Matrix4D xform) |
| Prepares the aligned shape function for use by the start generator. More... | |
| None | setReference (GaussianShapeFunction func, int sym_class) |
| bool | generate (GaussianShapeFunction func, int sym_class) |
| Generates the set of starting transformations for the alignment of func. More... | |
| int | getNumStartTransforms () |
| Returns the number of starting transformations produced by the last generate() call. More... | |
| int | getNumStartSubTransforms () |
| Returns the number of sub-transformations sharing the same starting transformation index space. More... | |
| Math.Vector7D | getStartTransform (int idx) |
| Returns the starting transformation at index idx. More... | |
| int | __len__ () |
| Math.Vector7D | __getitem__ (int idx) |
Static Public Attributes | |
| float | DEF_SYMMETRY_THRESHOLD = 0.15 |
| Default relative threshold for treating two principal moments as equal. | |
| int | DEF_NUM_RANDOM_STARTS = 4 |
| Default number of random starting transformations. | |
| float | DEF_MAX_RANDOM_TRANSLATION = 2.0 |
| Default maximum random translation magnitude applied to random starts. | |
Properties | |
| symmetryThreshold = property(getSymmetryThreshold, setSymmetryThreshold) | |
| maxRandomTranslation = property(getMaxRandomTranslation, setMaxRandomTranslation) | |
| numRandomStarts = property(getNumRandomStarts, setNumRandomStarts) | |
| shapeCenterStarts = property(genShapeCenterStarts, genShapeCenterStarts) | |
| colorCenterStarts = property(genColorCenterStarts, genColorCenterStarts) | |
| nonColorCenterStarts = property(genNonColorCenterStarts, genNonColorCenterStarts) | |
| randomStarts = property(getNumRandomStarts, setNumRandomStarts) | |
| genForAlignedShapeCtrs = property(genForAlignedShapeCenters, genForAlignedShapeCenters) | |
| genForReferenceShapeCrs = property(genForReferenceShapeCenters, genForReferenceShapeCenters) | |
| genForLargerShapeCtrs = property(genForLargerShapeCenters, genForLargerShapeCenters) | |
| Properties inherited from CDPL.Shape.GaussianShapeAlignmentStartGenerator | |
| objectID = property(getObjectID) | |
| numStartSubTransforms = property(getNumStartSubTransforms) | |
Generator that produces alignment starting transformations by aligning the principal axes of the aligned shape to those of the reference shape.
Starting transformations can be derived from any combination of (a) the shape centroid, (b) shape element (atom) centers, (c) color (pharmacophore) feature centers, and (d) random rotations applied to translated centers. The exact combination of starts is configured via the various gen* setter methods.
| None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.__init__ | ( | PrincipalAxesAlignmentStartGenerator | gen | ) |
Initializes a copy of the PrincipalAxesAlignmentStartGenerator instance gen.
| gen | The PrincipalAxesAlignmentStartGenerator instance to copy. |
| None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.setSymmetryThreshold | ( | float | thresh | ) |
Sets the relative threshold for treating two principal moments as equal.
| thresh | The new symmetry threshold. |
| float CDPL.Shape.PrincipalAxesAlignmentStartGenerator.getSymmetryThreshold | ( | ) |
Returns the currently configured symmetry threshold.
| None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genShapeCenterStarts | ( | bool | generate | ) |
Enables or disables the generation of a starting transformation at the shape centroid.
| generate | True to enable the shape-centroid start, and False to disable it. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genShapeCenterStarts | ( | ) |
Tells whether a starting transformation at the shape centroid is generated.
True if a shape-centroid start is generated, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genColorCenterStarts | ( | bool | generate | ) |
Enables or disables the generation of starting transformations at color (pharmacophore) feature centers.
| generate | True to enable the color-center starts, and False to disable them. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genColorCenterStarts | ( | ) |
Tells whether starting transformations at color (pharmacophore) feature centers are generated.
True if color-center starts are generated, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genNonColorCenterStarts | ( | bool | generate | ) |
Enables or disables the generation of starting transformations at non-color (shape) element centers.
| generate | True to enable the non-color-center starts, and False to disable them. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genNonColorCenterStarts | ( | ) |
Tells whether starting transformations at non-color (shape) element centers are generated.
True if non-color-center starts are generated, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genRandomStarts | ( | bool | generate | ) |
Enables or disables the generation of random starting transformations.
| generate | True to enable the random starts, and False to disable them. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genRandomStarts | ( | ) |
Tells whether random starting transformations are generated.
True if random starts are generated, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genForAlignedShapeCenters | ( | bool | generate | ) |
Specifies whether element-/color-center starts shall be generated for centers of the aligned shape.
| generate | True to consider aligned-shape centers, and False to ignore them. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genForAlignedShapeCenters | ( | ) |
Tells whether element-/color-center starts are generated for centers of the aligned shape.
True if aligned-shape centers are considered, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genForReferenceShapeCenters | ( | bool | generate | ) |
Specifies whether element-/color-center starts shall be generated for centers of the reference shape.
| generate | True to consider reference-shape centers, and False to ignore them. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genForReferenceShapeCenters | ( | ) |
Tells whether element-/color-center starts are generated for centers of the reference shape.
True if reference-shape centers are considered, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genForLargerShapeCenters | ( | bool | generate | ) |
Specifies whether element-/color-center starts shall be generated for centers of the shape with more elements (instead of both shapes).
| generate | True to use only the centers of the larger shape, and False to use the centers of all configured shapes. |
| bool CDPL.Shape.PrincipalAxesAlignmentStartGenerator.genForLargerShapeCenters | ( | ) |
Tells whether element-/color-center starts are generated for centers of the shape with more elements (instead of both shapes).
True if only the centers of the larger shape are used, and False otherwise. | None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.setMaxRandomTranslation | ( | float | max_trans | ) |
Sets the maximum random translation magnitude applied to random starts.
| max_trans | The new maximum random translation magnitude. |
| float CDPL.Shape.PrincipalAxesAlignmentStartGenerator.getMaxRandomTranslation | ( | ) |
Returns the currently configured maximum random translation.
| None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.setNumRandomStarts | ( | int | num_starts | ) |
Sets the number of random starting transformations.
| num_starts | The new number of random starts. |
| int CDPL.Shape.PrincipalAxesAlignmentStartGenerator.getNumRandomStarts | ( | ) |
Returns the currently configured number of random starts.
| None CDPL.Shape.PrincipalAxesAlignmentStartGenerator.setRandomSeed | ( | int | seed | ) |
Sets the seed used by the random number generator that produces the random starts.
| seed | The new random seed. |
| PrincipalAxesAlignmentStartGenerator CDPL.Shape.PrincipalAxesAlignmentStartGenerator.assign | ( | PrincipalAxesAlignmentStartGenerator | gen | ) |
Replaces the current state of self with a copy of the state of the PrincipalAxesAlignmentStartGenerator instance gen.
| gen | The PrincipalAxesAlignmentStartGenerator instance to copy. |
1.9.1