CDPL::Chem::ChEMBLStandardizer Class Reference

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

#include <ChEMBLStandardizer.hpp>

Public Types
enum	ChangeFlags {   NONE = 0x0 ,   EXCLUDED = 0x1 ,   EXPLICIT_HYDROGENS_REMOVED = 0x2 ,   UNKNOWN_STEREO_STANDARDIZED = 0x4 ,   BONDS_KEKULIZED = 0x8 ,   STRUCTURE_NORMALIZED = 0x10 ,   CHARGES_REMOVED = 0x20 ,   TARTRATE_STEREO_CLEARED = 0x40 ,   STRUCTURE_2D_CORRECTED = 0x80 ,   ISOTOPE_INFO_CLEARED = 0x100 ,   SALT_COMPONENTS_REMOVED = 0x200 ,   SOLVENT_COMPONENTS_REMOVED = 0x400 ,   DUPLICATE_COMPONENTS_REMOVED = 0x800 }
	Bitwise-OR-combined flags reporting which standardization steps modified the input molecule. More...
typedef std::shared_ptr< ChEMBLStandardizer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated ChEMBLStandardizer instances. More...

Public Member Functions
	ChEMBLStandardizer ()
	Constructs the ChEMBLStandardizer instance. More...
	ChEMBLStandardizer (const ChEMBLStandardizer &standardizer)
	Constructs a copy of the ChEMBLStandardizer instance standardizer. More...
ChangeFlags	standardize (Molecule &mol, bool proc_excld=false)
	Standardizes mol in place. More...
ChangeFlags	standardize (const MolecularGraph &molgraph, Molecule &std_mol, bool proc_excluded=false)
	Writes a standardized copy of molgraph to std_mol. More...
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 (const MolecularGraph &molgraph, Molecule &parent_mol, bool neutralize=true, bool check_exclusion=true)
	Extracts the parent compound of molgraph into parent_mol. More...
ChEMBLStandardizer &	operator= (const ChEMBLStandardizer &standardizer)
	Replaces the state of this standardizer by a copy of the state of standardizer. More...

Detailed Description

Implementation of the ChEMBL structure preprocessing pipeline.

See also

[CSCP]

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<ChEMBLStandardizer> CDPL::Chem::ChEMBLStandardizer::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated ChEMBLStandardizer instances.

Member Enumeration Documentation

ChangeFlags

enum CDPL::Chem::ChEMBLStandardizer::ChangeFlags

Bitwise-OR-combined flags reporting which standardization steps modified the input molecule.

Enumerator
NONE	No changes were applied.
EXCLUDED	The molecule matched a ChEMBL exclusion criterion and was not processed further.
EXPLICIT_HYDROGENS_REMOVED	Removable explicit hydrogen atoms were removed.
UNKNOWN_STEREO_STANDARDIZED	Atoms/bonds with unknown stereo descriptors were standardized.
BONDS_KEKULIZED	Aromatic bonds were kekulized to alternating single/double bonds.
STRUCTURE_NORMALIZED	Functional-group structure normalizations were applied.
CHARGES_REMOVED	Atom formal charges were removed where possible.
TARTRATE_STEREO_CLEARED	Defined stereo at tartrate-like substructures was cleared.
STRUCTURE_2D_CORRECTED	2D bond-angle artefacts were corrected.
ISOTOPE_INFO_CLEARED	Atom isotope information was cleared.
SALT_COMPONENTS_REMOVED	Salt components were removed (parent extraction only).
SOLVENT_COMPONENTS_REMOVED	Common solvent components were removed (parent extraction only).
DUPLICATE_COMPONENTS_REMOVED	Duplicate disconnected components were collapsed (parent extraction only).

Constructor & Destructor Documentation

ChEMBLStandardizer() [1/2]

CDPL::Chem::ChEMBLStandardizer::ChEMBLStandardizer

(

)

Constructs the ChEMBLStandardizer instance.

ChEMBLStandardizer() [2/2]

CDPL::Chem::ChEMBLStandardizer::ChEMBLStandardizer

(

const ChEMBLStandardizer &

standardizer

)

Constructs a copy of the ChEMBLStandardizer instance standardizer.

Parameters

standardizer

The ChEMBLStandardizer to copy.

Member Function Documentation

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	(	const MolecularGraph &	molgraph,
		Molecule &	std_mol,
		bool	proc_excluded = false
	)

Writes a standardized copy of molgraph to std_mol.

Parameters

molgraph	The input molecular graph.
std_mol	The output molecule receiving the standardized copy.
proc_excluded	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.

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	(	const MolecularGraph &	molgraph,
		Molecule &	parent_mol,
		bool	neutralize = true,
		bool	check_exclusion = true
	)

Extracts the parent compound of molgraph into parent_mol.

Parameters

molgraph	The input molecular graph.
parent_mol	The output molecule receiving the parent compound.
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.

operator=()

ChEMBLStandardizer& CDPL::Chem::ChEMBLStandardizer::operator=

(

const ChEMBLStandardizer &

standardizer

)

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

Parameters

standardizer

The source ChEMBLStandardizer.

Returns

A reference to itself.

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The documentation for this class was generated from the following file:

• ChEMBLStandardizer.hpp