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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Generates Shape::GaussianShape instances from molecular graphs. More...
#include <GaussianShapeGenerator.hpp>
Public Types | |
| typedef std::shared_ptr< GaussianShapeGenerator > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated GaussianShapeGenerator instances. More... | |
Public Member Functions | |
| GaussianShapeGenerator () | |
Constructs the GaussianShapeGenerator instance. More... | |
| void | generateMoleculeShape (bool generate) |
| Specifies whether a molecular (atom-based) shape shall be generated. More... | |
| bool | generateMoleculeShape () const |
| Tells whether a molecular (atom-based) shape is generated. More... | |
| void | generatePharmacophoreShape (bool generate) |
| Specifies whether a pharmacophore (feature-based) shape shall be generated. More... | |
| bool | generatePharmacophoreShape () const |
| Tells whether a pharmacophore (feature-based) shape is generated. More... | |
| void | multiConformerMode (bool multi_conf) |
| Specifies whether to emit one shape per conformer (instead of using the first conformer only). More... | |
| bool | multiConformerMode () const |
| Tells whether the generator runs in multi-conformer mode. More... | |
| void | includeHydrogens (bool include) |
| Specifies whether hydrogens are included when generating the molecular shape. More... | |
| bool | includeHydrogens () const |
| Tells whether hydrogens are included when generating the molecular shape. More... | |
| void | setAtomRadius (double radius) |
| Sets the sphere radius used for all atoms (negative value: use atom-specific Van der Waals radii). More... | |
| double | getAtomRadius () const |
| Returns the currently configured atom sphere radius. More... | |
| void | setAtomHardness (double hardness) |
| Sets the Gaussian hardness used for all atom spheres. More... | |
| double | getAtomHardness () |
| Returns the currently configured atom Gaussian hardness. More... | |
| void | setFeatureRadius (double radius) |
| Sets the sphere radius used for all features (negative value: use feature-specific tolerances). More... | |
| double | getFeatureRadius () const |
| Returns the currently configured feature sphere radius. More... | |
| void | setFeatureHardness (double hardness) |
| Sets the Gaussian hardness used for all feature spheres. More... | |
| double | getFeatureHardness () |
| Returns the currently configured feature Gaussian hardness. More... | |
| void | setPharmacophoreGenerator (Pharm::PharmacophoreGenerator &gen) |
| Specifies the pharmacophore generator used when emitting pharmacophore shapes. More... | |
| Pharm::PharmacophoreGenerator & | getPharmacophoreGenerator () const |
| Returns the currently configured pharmacophore generator. More... | |
| const Pharm::DefaultPharmacophoreGenerator & | getDefaultPharmacophoreGenerator () const |
| Returns the built-in default pharmacophore generator. More... | |
| Pharm::DefaultPharmacophoreGenerator & | getDefaultPharmacophoreGenerator () |
| Returns the built-in default pharmacophore generator (mutable). More... | |
| const GaussianShapeSet & | generate (const Chem::MolecularGraph &molgraph) |
| Generates the set of Gaussian shapes for molgraph. More... | |
| const GaussianShapeSet & | getShapes () const |
| Returns the shapes produced by the most recent call to generate(). More... | |
Generates Shape::GaussianShape instances from molecular graphs.
The generator can emit shape representations of the molecule itself (one sphere per atom), of a pharmacophore derived from the molecule (one sphere per feature), or both. In multi-conformer mode, one Gaussian shape is generated per conformer.
| typedef std::shared_ptr<GaussianShapeGenerator> CDPL::Shape::GaussianShapeGenerator::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated GaussianShapeGenerator instances.
| CDPL::Shape::GaussianShapeGenerator::GaussianShapeGenerator | ( | ) |
Constructs the GaussianShapeGenerator instance.
| void CDPL::Shape::GaussianShapeGenerator::generateMoleculeShape | ( | bool | generate | ) |
Specifies whether a molecular (atom-based) shape shall be generated.
| generate | true to enable the generation of the molecular shape, and false to disable it. |
| bool CDPL::Shape::GaussianShapeGenerator::generateMoleculeShape | ( | ) | const |
Tells whether a molecular (atom-based) shape is generated.
true if the molecular shape is generated, and false otherwise. | void CDPL::Shape::GaussianShapeGenerator::generatePharmacophoreShape | ( | bool | generate | ) |
Specifies whether a pharmacophore (feature-based) shape shall be generated.
| generate | true to enable the generation of the pharmacophore shape, and false to disable it. |
| bool CDPL::Shape::GaussianShapeGenerator::generatePharmacophoreShape | ( | ) | const |
Tells whether a pharmacophore (feature-based) shape is generated.
true if the pharmacophore shape is generated, and false otherwise. | void CDPL::Shape::GaussianShapeGenerator::multiConformerMode | ( | bool | multi_conf | ) |
Specifies whether to emit one shape per conformer (instead of using the first conformer only).
| multi_conf | true to enable multi-conformer mode, and false to use the first conformer only. |
| bool CDPL::Shape::GaussianShapeGenerator::multiConformerMode | ( | ) | const |
Tells whether the generator runs in multi-conformer mode.
true if multi-conformer mode is enabled, and false otherwise. | void CDPL::Shape::GaussianShapeGenerator::includeHydrogens | ( | bool | include | ) |
Specifies whether hydrogens are included when generating the molecular shape.
| include | true to include hydrogens, and false to ignore them. |
| bool CDPL::Shape::GaussianShapeGenerator::includeHydrogens | ( | ) | const |
Tells whether hydrogens are included when generating the molecular shape.
true if hydrogens are included, and false otherwise. | void CDPL::Shape::GaussianShapeGenerator::setAtomRadius | ( | double | radius | ) |
Sets the sphere radius used for all atoms (negative value: use atom-specific Van der Waals radii).
| radius | The new atom sphere radius. |
| double CDPL::Shape::GaussianShapeGenerator::getAtomRadius | ( | ) | const |
Returns the currently configured atom sphere radius.
| void CDPL::Shape::GaussianShapeGenerator::setAtomHardness | ( | double | hardness | ) |
Sets the Gaussian hardness used for all atom spheres.
| hardness | The new atom Gaussian hardness. |
| double CDPL::Shape::GaussianShapeGenerator::getAtomHardness | ( | ) |
Returns the currently configured atom Gaussian hardness.
| void CDPL::Shape::GaussianShapeGenerator::setFeatureRadius | ( | double | radius | ) |
Sets the sphere radius used for all features (negative value: use feature-specific tolerances).
| radius | The new feature sphere radius. |
| double CDPL::Shape::GaussianShapeGenerator::getFeatureRadius | ( | ) | const |
Returns the currently configured feature sphere radius.
| void CDPL::Shape::GaussianShapeGenerator::setFeatureHardness | ( | double | hardness | ) |
Sets the Gaussian hardness used for all feature spheres.
| hardness | The new feature Gaussian hardness. |
| double CDPL::Shape::GaussianShapeGenerator::getFeatureHardness | ( | ) |
Returns the currently configured feature Gaussian hardness.
| void CDPL::Shape::GaussianShapeGenerator::setPharmacophoreGenerator | ( | Pharm::PharmacophoreGenerator & | gen | ) |
Specifies the pharmacophore generator used when emitting pharmacophore shapes.
| gen | The pharmacophore generator. |
| Pharm::PharmacophoreGenerator& CDPL::Shape::GaussianShapeGenerator::getPharmacophoreGenerator | ( | ) | const |
Returns the currently configured pharmacophore generator.
| const Pharm::DefaultPharmacophoreGenerator& CDPL::Shape::GaussianShapeGenerator::getDefaultPharmacophoreGenerator | ( | ) | const |
Returns the built-in default pharmacophore generator.
const reference to the default pharmacophore generator. | Pharm::DefaultPharmacophoreGenerator& CDPL::Shape::GaussianShapeGenerator::getDefaultPharmacophoreGenerator | ( | ) |
Returns the built-in default pharmacophore generator (mutable).
| const GaussianShapeSet& CDPL::Shape::GaussianShapeGenerator::generate | ( | const Chem::MolecularGraph & | molgraph | ) |
Generates the set of Gaussian shapes for molgraph.
| molgraph | The molecular graph. |
const reference to the generated Shape::GaussianShapeSet. | const GaussianShapeSet& CDPL::Shape::GaussianShapeGenerator::getShapes | ( | ) | const |
Returns the shapes produced by the most recent call to generate().
const reference to the produced Shape::GaussianShapeSet. 
1.9.1