Driver that generates an interaction pharmacophore by perceiving a core pharmacophore on a ligand, an environment pharmacophore on the surrounding pocket residues, analyzing the inter-feature interactions and emitting features representing the detected interactions (optionally with exclusion volumes).
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#include <InteractionPharmacophoreGenerator.hpp>
Driver that generates an interaction pharmacophore by perceiving a core pharmacophore on a ligand, an environment pharmacophore on the surrounding pocket residues, analyzing the inter-feature interactions and emitting features representing the detected interactions (optionally with exclusion volumes).
◆ InteractionPharmacophoreGenerator()
Constructs the InteractionPharmacophoreGenerator instance.
- Parameters
-
| core_ph4_gen_cfg | Configuration flags for the core (ligand) pharmacophore generator. |
| env_ph4_gen_cfg | Configuration flags for the environment (pocket) pharmacophore generator. |
◆ setCoreEnvironmentRadius()
| void CDPL::Pharm::InteractionPharmacophoreGenerator::setCoreEnvironmentRadius |
( |
double |
radius | ) |
|
Sets the cutoff radius around the core used to extract the environment substructure.
- Parameters
-
| radius | The new core-environment radius. |
◆ getCoreEnvironmentRadius()
| double CDPL::Pharm::InteractionPharmacophoreGenerator::getCoreEnvironmentRadius |
( |
| ) |
const |
Returns the currently configured core-environment cutoff radius.
- Returns
- The core-environment radius.
◆ addExclusionVolumes()
| void CDPL::Pharm::InteractionPharmacophoreGenerator::addExclusionVolumes |
( |
bool |
add | ) |
|
Specifies whether exclusion volume features shall be added to the output pharmacophore.
- Parameters
-
| add | true to add exclusion volumes, and false to skip them. |
◆ exclusionVolumesAdded()
| bool CDPL::Pharm::InteractionPharmacophoreGenerator::exclusionVolumesAdded |
( |
| ) |
const |
Tells whether exclusion volume features are added.
- Returns
true if exclusion volumes are added, and false otherwise.
◆ getCorePharmacophoreGenerator() [1/2]
Returns the core (ligand) pharmacophore generator.
- Returns
- A reference to the core pharmacophore generator.
◆ getCorePharmacophoreGenerator() [2/2]
| const PharmacophoreGenerator& CDPL::Pharm::InteractionPharmacophoreGenerator::getCorePharmacophoreGenerator |
( |
| ) |
const |
Returns the core (ligand) pharmacophore generator.
- Returns
- A
const reference to the core pharmacophore generator.
◆ getEnvironmentPharmacophoreGenerator() [1/2]
| PharmacophoreGenerator& CDPL::Pharm::InteractionPharmacophoreGenerator::getEnvironmentPharmacophoreGenerator |
( |
| ) |
|
Returns the environment (pocket) pharmacophore generator.
- Returns
- A reference to the environment pharmacophore generator.
◆ getEnvironmentPharmacophoreGenerator() [2/2]
| const PharmacophoreGenerator& CDPL::Pharm::InteractionPharmacophoreGenerator::getEnvironmentPharmacophoreGenerator |
( |
| ) |
const |
Returns the environment (pocket) pharmacophore generator.
- Returns
- A
const reference to the environment pharmacophore generator.
◆ getInteractionAnalyzer() [1/2]
| InteractionAnalyzer& CDPL::Pharm::InteractionPharmacophoreGenerator::getInteractionAnalyzer |
( |
| ) |
|
Returns the interaction analyzer used to perceive feature-feature interactions.
- Returns
- A reference to the interaction analyzer.
◆ getInteractionAnalyzer() [2/2]
| const InteractionAnalyzer& CDPL::Pharm::InteractionPharmacophoreGenerator::getInteractionAnalyzer |
( |
| ) |
const |
Returns the interaction analyzer used to perceive feature-feature interactions.
- Returns
- A
const reference to the interaction analyzer.
◆ getCorePharmacophore()
| const Pharmacophore& CDPL::Pharm::InteractionPharmacophoreGenerator::getCorePharmacophore |
( |
| ) |
const |
Returns the core (ligand) pharmacophore produced by the last generate() call.
- Returns
- A
const reference to the core pharmacophore.
◆ getEnvironmentPharmacophore()
| const Pharmacophore& CDPL::Pharm::InteractionPharmacophoreGenerator::getEnvironmentPharmacophore |
( |
| ) |
const |
Returns the environment (pocket) pharmacophore produced by the last generate() call.
- Returns
- A
const reference to the environment pharmacophore.
◆ getInteractionMapping()
| const FeatureMapping& CDPL::Pharm::InteractionPharmacophoreGenerator::getInteractionMapping |
( |
| ) |
const |
Returns the feature-to-feature interaction mapping produced by the last generate() call.
- Returns
- A
const reference to the interaction mapping.
◆ getCoreEnvironment()
| const Chem::Fragment& CDPL::Pharm::InteractionPharmacophoreGenerator::getCoreEnvironment |
( |
| ) |
const |
Returns the core-environment substructure extracted by the last generate() call (only valid when extract_core_env was true).
- Returns
- A
const reference to the core-environment fragment.
◆ generate()
Generates the interaction pharmacophore for the (core, tgt) molecular graph pair.
- Parameters
-
| core | The core (ligand) molecular graph. |
| tgt | The target (pocket) molecular graph. |
| ia_pharm | The output interaction pharmacophore. |
| extract_core_env | If true, the core environment is extracted from tgt before pharmacophore generation; if false, the environment pharmacophore is generated on tgt directly. |
| append | If false, ia_pharm is cleared before any features are added. |
The documentation for this class was generated from the following file:
1.9.1