CDPL.Pharm.InteractionPharmacophoreGenerator Class Reference

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). More...

Inheritance diagram for CDPL.Pharm.InteractionPharmacophoreGenerator:

Public Member Functions
None	__init__ (Configuration core_ph4_gen_cfg=CDPL.Pharm.Configuration.DEFAULT_CONFIG, Configuration env_ph4_gen_cfg=CDPL.Pharm.Configuration.DEFAULT_CONFIG)
	Constructs the InteractionPharmacophoreGenerator instance. More...
None	__init__ (InteractionPharmacophoreGenerator gen)
	Initializes a copy of the InteractionPharmacophoreGenerator instance gen. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
InteractionPharmacophoreGenerator	assign (InteractionPharmacophoreGenerator gen)
	Replaces the current state of self with a copy of the state of the InteractionPharmacophoreGenerator instance gen. More...
None	setCoreEnvironmentRadius (float radius)
	Sets the cutoff radius around the core used to extract the environment substructure. More...
float	getCoreEnvironmentRadius ()
	Returns the currently configured core-environment cutoff radius. More...
None	addExclusionVolumes (bool add)
	Specifies whether exclusion volume features shall be added to the output pharmacophore. More...
bool	exclusionVolumesAdded ()
	Tells whether exclusion volume features are added. More...
PharmacophoreGenerator	getCorePharmacophoreGenerator ()
	Returns the core (ligand) pharmacophore generator. More...
PharmacophoreGenerator	getEnvironmentPharmacophoreGenerator ()
	Returns the environment (pocket) pharmacophore generator. More...
InteractionAnalyzer	getInteractionAnalyzer ()
	Returns the interaction analyzer used to perceive feature-feature interactions. More...
Pharmacophore	getCorePharmacophore ()
	Returns the core (ligand) pharmacophore produced by the last generate() call. More...
Pharmacophore	getEnvironmentPharmacophore ()
	Returns the environment (pocket) pharmacophore produced by the last generate() call. More...
FeatureMapping	getInteractionMapping ()
	Returns the feature-to-feature interaction mapping produced by the last generate() call. More...
Chem.Fragment	getCoreEnvironment ()
	Returns the core-environment substructure extracted by the last generate() call (only valid when extract_core_env was True). More...
None	generate (Chem.MolecularGraph core, Chem.MolecularGraph tgt, Pharmacophore ia_pharm, bool extract_core_env, bool append=False)
	Generates the interaction pharmacophore for the (core, tgt) molecular graph pair. More...

Properties
	objectID = property(getObjectID)
	coreEnvironmentRadius = property(getCoreEnvironmentRadius, setCoreEnvironmentRadius)
	addXVolumes = property(exclusionVolumesAdded, addExclusionVolumes)
	corePharmacophoreGenerator = property(getCorePharmacophoreGenerator)
	envPharmacophoreGenerator = property(getEnvironmentPharmacophoreGenerator)
	interactionAnalyzer = property(getInteractionAnalyzer)
	corePharmacophore = property(getCorePharmacophore)
	envPharmacophore = property(getEnvironmentPharmacophore)
	interactionMapping = property(getInteractionMapping)
	coreEnvironment = property(getCoreEnvironment)

Detailed Description

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).

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.Pharm.InteractionPharmacophoreGenerator.__init__	(	Configuration	core_ph4_gen_cfg = CDPL.Pharm.Configuration.DEFAULT_CONFIG,
		Configuration	env_ph4_gen_cfg = CDPL.Pharm.Configuration.DEFAULT_CONFIG
	)

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.

__init__() [2/2]

None CDPL.Pharm.InteractionPharmacophoreGenerator.__init__

(

InteractionPharmacophoreGenerator

gen

)

Initializes a copy of the InteractionPharmacophoreGenerator instance gen.

Parameters

gen	The InteractionPharmacophoreGenerator instance to copy.

Member Function Documentation

getObjectID()

int CDPL.Pharm.InteractionPharmacophoreGenerator.getObjectID

(

)

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

Different Python InteractionPharmacophoreGenerator 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 InteractionPharmacophoreGenerator 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()

InteractionPharmacophoreGenerator CDPL.Pharm.InteractionPharmacophoreGenerator.assign

(

InteractionPharmacophoreGenerator

gen

)

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

Parameters

gen	The InteractionPharmacophoreGenerator instance to copy.

Returns

self

setCoreEnvironmentRadius()

None CDPL.Pharm.InteractionPharmacophoreGenerator.setCoreEnvironmentRadius

(

float

radius

)

Sets the cutoff radius around the core used to extract the environment substructure.

Parameters

radius

The new core-environment radius.

getCoreEnvironmentRadius()

float CDPL.Pharm.InteractionPharmacophoreGenerator.getCoreEnvironmentRadius

(

)

Returns the currently configured core-environment cutoff radius.

Returns

The core-environment radius.

addExclusionVolumes()

None 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

(

)

Tells whether exclusion volume features are added.

Returns

True if exclusion volumes are added, and False otherwise.

getCorePharmacophoreGenerator()

PharmacophoreGenerator CDPL.Pharm.InteractionPharmacophoreGenerator.getCorePharmacophoreGenerator

(

)

Returns the core (ligand) pharmacophore generator.

Returns

A reference to the core pharmacophore generator.

getEnvironmentPharmacophoreGenerator()

PharmacophoreGenerator CDPL.Pharm.InteractionPharmacophoreGenerator.getEnvironmentPharmacophoreGenerator

(

)

Returns the environment (pocket) pharmacophore generator.

Returns

A reference to the environment pharmacophore generator.

getInteractionAnalyzer()

InteractionAnalyzer CDPL.Pharm.InteractionPharmacophoreGenerator.getInteractionAnalyzer

(

)

Returns the interaction analyzer used to perceive feature-feature interactions.

Returns

A reference to the interaction analyzer.

getCorePharmacophore()

Pharmacophore CDPL.Pharm.InteractionPharmacophoreGenerator.getCorePharmacophore

(

)

Returns the core (ligand) pharmacophore produced by the last generate() call.

Returns

A reference to the core pharmacophore.

getEnvironmentPharmacophore()

Pharmacophore CDPL.Pharm.InteractionPharmacophoreGenerator.getEnvironmentPharmacophore

(

)

Returns the environment (pocket) pharmacophore produced by the last generate() call.

Returns

A reference to the environment pharmacophore.

getInteractionMapping()

FeatureMapping CDPL.Pharm.InteractionPharmacophoreGenerator.getInteractionMapping

(

)

Returns the feature-to-feature interaction mapping produced by the last generate() call.

Returns

A reference to the interaction mapping.

getCoreEnvironment()

Chem.Fragment CDPL.Pharm.InteractionPharmacophoreGenerator.getCoreEnvironment

(

)

Returns the core-environment substructure extracted by the last generate() call (only valid when extract_core_env was True).

Returns

A reference to the core-environment fragment.

generate()

None CDPL.Pharm.InteractionPharmacophoreGenerator.generate	(	Chem.MolecularGraph	core,
		Chem.MolecularGraph	tgt,
		Pharmacophore	ia_pharm,
		bool	extract_core_env,
		bool	append = False
	)

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.