CDPL.Pharm.ScreeningDBAccessor Class Reference

Abstract base class for accessors that read the data stored in pharmacophore screening databases. More...

Inheritance diagram for CDPL.Pharm.ScreeningDBAccessor:

Public Member Functions
None	__init__ ()
	Initializes the ScreeningDBAccessor instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	open (str name)
	Opens the screening database identified by name. More...
None	close ()
	Closes the currently open database.
str	getDatabaseName ()
	Returns the name of the currently open database. More...
int	getNumMolecules ()
	Returns the total number of molecules stored in the database. More...
int	getNumPharmacophores ()
	Returns the total number of pharmacophores stored in the database (one per molecule conformer). More...
int	getNumPharmacophores (int mol_idx)
	Returns the number of pharmacophores stored for the molecule at index mol_idx. More...
None	getMolecule (int mol_idx, Chem.Molecule mol, bool overwrite=True)
	Reads the molecule at index mol_idx into mol. More...
None	getPharmacophore (int pharm_idx, Pharmacophore pharm, bool overwrite=True)
	Reads the pharmacophore at index pharm_idx into pharm. More...
None	getPharmacophore (int mol_idx, int mol_conf_idx, Pharmacophore pharm, bool overwrite=True)
	Reads the pharmacophore corresponding to conformer mol_conf_idx of molecule mol_idx into pharm. More...
int	getMoleculeIndex (int pharm_idx)
	Returns the molecule index of the pharmacophore at index pharm_idx. More...
int	getConformationIndex (int pharm_idx)
	Returns the conformer index within the parent molecule of the pharmacophore at index pharm_idx. More...
FeatureTypeHistogram	getFeatureCounts (int pharm_idx)
	Returns the cached per Pharm.FeatureType frequency histogram of the pharmacophore at index pharm_idx. More...
FeatureTypeHistogram	getFeatureCounts (int mol_idx, int mol_conf_idx)
	Returns the cached per Pharm.FeatureType frequency histogram of conformer mol_conf_idx of molecule mol_idx. More...

Properties
	objectID = property(getObjectID)
	databaseName = property(getDatabaseName)
	numMolecules = property(getNumMolecules)
	numPharmacophores = property(getNumPharmacophores)

Detailed Description

Abstract base class for accessors that read the data stored in pharmacophore screening databases.

Member Function Documentation

getObjectID()

int CDPL.Pharm.ScreeningDBAccessor.getObjectID

(

)

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

Different Python ScreeningDBAccessor 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 ScreeningDBAccessor 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.

open()

None CDPL.Pharm.ScreeningDBAccessor.open

(

str

name

)

Opens the screening database identified by name.

Parameters

name	The database name (path, URI, etc., interpreted by the concrete subclass).

getDatabaseName()

str CDPL.Pharm.ScreeningDBAccessor.getDatabaseName

(

)

Returns the name of the currently open database.

Returns

A reference to the database name.

getNumMolecules()

int CDPL.Pharm.ScreeningDBAccessor.getNumMolecules

(

)

Returns the total number of molecules stored in the database.

Returns

The molecule count.

getNumPharmacophores() [1/2]

int CDPL.Pharm.ScreeningDBAccessor.getNumPharmacophores

(

)

Returns the total number of pharmacophores stored in the database (one per molecule conformer).

Returns

The pharmacophore count.

getNumPharmacophores() [2/2]

int CDPL.Pharm.ScreeningDBAccessor.getNumPharmacophores

(

int

mol_idx

)

Returns the number of pharmacophores stored for the molecule at index mol_idx.

Parameters

mol_idx

The zero-based molecule index.

Returns

The pharmacophore count for the molecule.

getMolecule()

None CDPL.Pharm.ScreeningDBAccessor.getMolecule	(	int	mol_idx,
		Chem.Molecule	mol,
		bool	overwrite = True
	)

Reads the molecule at index mol_idx into mol.

Parameters

mol_idx	The zero-based molecule index.
mol	The output molecule.
overwrite	If True, mol is cleared before reading. If False, the atoms/bonds are appended.

getPharmacophore() [1/2]

None CDPL.Pharm.ScreeningDBAccessor.getPharmacophore	(	int	pharm_idx,
		Pharmacophore	pharm,
		bool	overwrite = True
	)

Reads the pharmacophore at index pharm_idx into pharm.

Parameters

pharm_idx	The zero-based pharmacophore index (across all molecules).
pharm	The output pharmacophore.
overwrite	If True, pharm is cleared before reading. If False, the features are appended.

getPharmacophore() [2/2]

None CDPL.Pharm.ScreeningDBAccessor.getPharmacophore	(	int	mol_idx,
		int	mol_conf_idx,
		Pharmacophore	pharm,
		bool	overwrite = True
	)

Reads the pharmacophore corresponding to conformer mol_conf_idx of molecule mol_idx into pharm.

Parameters

mol_idx	The zero-based molecule index.
mol_conf_idx	The zero-based conformer index within the molecule.
pharm	The output pharmacophore.
overwrite	If True, pharm is cleared before reading. If False, the features are appended.

getMoleculeIndex()

int CDPL.Pharm.ScreeningDBAccessor.getMoleculeIndex

(

int

pharm_idx

)

Returns the molecule index of the pharmacophore at index pharm_idx.

Parameters

pharm_idx

The zero-based pharmacophore index.

Returns

The zero-based molecule index.

getConformationIndex()

int CDPL.Pharm.ScreeningDBAccessor.getConformationIndex

(

int

pharm_idx

)

Returns the conformer index within the parent molecule of the pharmacophore at index pharm_idx.

Parameters

pharm_idx

The zero-based pharmacophore index.

Returns

The zero-based conformer index.

getFeatureCounts() [1/2]

FeatureTypeHistogram CDPL.Pharm.ScreeningDBAccessor.getFeatureCounts

(

int

pharm_idx

)

Returns the cached per Pharm.FeatureType frequency histogram of the pharmacophore at index pharm_idx.

Parameters

pharm_idx

The zero-based pharmacophore index.

Returns

A reference to the feature-type histogram.

getFeatureCounts() [2/2]

FeatureTypeHistogram CDPL.Pharm.ScreeningDBAccessor.getFeatureCounts	(	int	mol_idx,
		int	mol_conf_idx
	)

Returns the cached per Pharm.FeatureType frequency histogram of conformer mol_conf_idx of molecule mol_idx.

Parameters

mol_idx	The zero-based molecule index.
mol_conf_idx	The zero-based conformer index within the molecule.

Returns

A reference to the feature-type histogram.