CDPL.Chem.ChEMBLStandardizer Class Reference

Implementation of the ChEMBL structure preprocessing pipeline. More...

Inheritance diagram for CDPL.Chem.ChEMBLStandardizer:

Classes
class	ChangeFlags
	Bitwise-OR-combined flags reporting which standardization steps modified the input molecule. More...

Public Member Functions
None	__init__ ()
	Constructs the ChEMBLStandardizer instance.
None	__init__ (ChEMBLStandardizer standardizer)
	Constructs a copy of the ChEMBLStandardizer instance standardizer. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
ChEMBLStandardizer	assign (ChEMBLStandardizer standardizer)
	Replaces the state of this standardizer by a copy of the state of standardizer. More...
ChangeFlags	standardize (Molecule mol, bool proc_excld=False)
	Standardizes mol in place. More...
ChangeFlags	standardize (MolecularGraph mol, Molecule std_mol, bool proc_excluded=False)
ChangeFlags	getParent (Molecule mol, bool neutralize=True, bool check_exclusion=True)
	Extracts the parent compound of mol in place (removing salt/solvent components). More...
ChangeFlags	getParent (MolecularGraph mol, Molecule parent_mol, bool neutralize=True, bool check_exclusion=True)

Properties
	objectID = property(getObjectID)

Detailed Description

Implementation of the ChEMBL structure preprocessing pipeline.

See also

[CSCP]

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.ChEMBLStandardizer.__init__

(

ChEMBLStandardizer

standardizer

)

Constructs a copy of the ChEMBLStandardizer instance standardizer.

Parameters

standardizer

The ChEMBLStandardizer to copy.

Member Function Documentation

getObjectID()

int CDPL.Chem.ChEMBLStandardizer.getObjectID

(

)

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

Different Python ChEMBLStandardizer 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 ChEMBLStandardizer 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()

ChEMBLStandardizer CDPL.Chem.ChEMBLStandardizer.assign

(

ChEMBLStandardizer

standardizer

)

Replaces the state of this standardizer by a copy of the state of standardizer.

Parameters

standardizer

The source ChEMBLStandardizer.

Returns

self

standardize() [1/2]

ChangeFlags CDPL.Chem.ChEMBLStandardizer.standardize	(	Molecule	mol,
		bool	proc_excld = False
	)

Standardizes mol in place.

Parameters

mol	The molecule to standardize (modified in place).
proc_excld	If True, ChEMBL exclusion criteria are ignored and the molecule is processed regardless.

Returns

A bitwise-OR combination of ChangeFlags reporting which standardization steps modified the molecule.

standardize() [2/2]

ChangeFlags CDPL.Chem.ChEMBLStandardizer.standardize	(	MolecularGraph	mol,
		Molecule	std_mol,
		bool	proc_excluded = False
	)

Parameters

mol
std_mol
proc_excluded

Returns

getParent() [1/2]

ChangeFlags CDPL.Chem.ChEMBLStandardizer.getParent	(	Molecule	mol,
		bool	neutralize = True,
		bool	check_exclusion = True
	)

Extracts the parent compound of mol in place (removing salt/solvent components).

Parameters

mol	The molecule from which to extract the parent (modified in place).
neutralize	If True, charges of the extracted parent are subsequently neutralized.
check_exclusion	If True, ChEMBL exclusion criteria are checked before processing.

Returns

A bitwise-OR combination of ChangeFlags reporting which steps modified the molecule.

getParent() [2/2]

ChangeFlags CDPL.Chem.ChEMBLStandardizer.getParent	(	MolecularGraph	mol,
		Molecule	parent_mol,
		bool	neutralize = True,
		bool	check_exclusion = True
	)

Parameters

mol
parent_mol
neutralize
check_exclusion

Returns