CDPL::Chem::SymmetryClassCalculator Class Reference

Perceives topological-symmetry classes of the atoms in a molecular graph. More...

#include <SymmetryClassCalculator.hpp>

Public Member Functions
	SymmetryClassCalculator ()
	Constructs the SymmetryClassCalculator instance. More...
	SymmetryClassCalculator (const MolecularGraph &molgraph, Util::STArray &class_ids)
	Constructs the SymmetryClassCalculator instance and perceives the topological symmetry classes of the atoms in the molecular graph molgraph. More...
	SymmetryClassCalculator (const SymmetryClassCalculator &)=delete
SymmetryClassCalculator &	operator= (const SymmetryClassCalculator &)=delete
void	setAtomPropertyFlags (unsigned int flags)
	Allows to specify the set of atomic properties that has to be considered in the perception of topological symmetry classes. More...
unsigned int	getAtomPropertyFlags () const
	Returns the set of atomic properties that gets considered in the perception of topological symmetry classes. More...
void	setBondPropertyFlags (unsigned int flags)
	Allows to specify the set of bond properties that has to be considered in the perception of topological symmetry classes. More...
unsigned int	getBondPropertyFlags () const
	Returns the set of bond properties that gets considered in the perception of topological symmetry classes. More...
void	includeImplicitHydrogens (bool include)
	Allows to specify whether implicit hydrogen atoms shall be ignored or treated in the same way as explicit ones. More...
bool	implicitHydrogensIncluded () const
	Tells whether implicit hydrogen atoms are ignored or treated in the same way as explicit ones. More...
void	calculate (const MolecularGraph &molgraph, Util::STArray &class_ids)
	Perceives the topological symmetry classes of the atoms in the molecular graph molgraph. More...

Static Public Attributes
static constexpr unsigned int	DEF_ATOM_PROPERTY_FLAGS
	Specifies the default set of atomic properties considered in the perception of topological symmetry classes. More...
static constexpr unsigned int	DEF_BOND_PROPERTY_FLAGS
	Specifies the default set of bond properties considered in the perception of topological symmetry classes. More...

Detailed Description

Perceives topological-symmetry classes of the atoms in a molecular graph.

Two atoms are placed in the same class when the topology and configurable atom/bond properties (see DEF_ATOM_PROPERTY_FLAGS and DEF_BOND_PROPERTY_FLAGS) of their respective graph neighbourhoods are indistinguishable. The class identifiers are returned as a Util::STArray indexed by the atom index in the molecular graph. Treatment of implicit hydrogens can be configured via includeImplicitHydrogens().

See also

[TOPSY]

Constructor & Destructor Documentation

SymmetryClassCalculator() [1/3]

CDPL::Chem::SymmetryClassCalculator::SymmetryClassCalculator

(

)

Constructs the SymmetryClassCalculator instance.

SymmetryClassCalculator() [2/3]

CDPL::Chem::SymmetryClassCalculator::SymmetryClassCalculator	(	const MolecularGraph &	molgraph,
		Util::STArray &	class_ids
	)

Constructs the SymmetryClassCalculator instance and perceives the topological symmetry classes of the atoms in the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to perceive the symmetry classes.
class_ids	An array containing the perceived symmetry class IDs. The class IDs are stored in the same order as the atoms appear in the atom list of the molecular graph (i.e. the symmetry class of an atom is accessible via its index).

SymmetryClassCalculator() [3/3]

CDPL::Chem::SymmetryClassCalculator::SymmetryClassCalculator ( const SymmetryClassCalculator &  )

delete

Member Function Documentation

operator=()

SymmetryClassCalculator& CDPL::Chem::SymmetryClassCalculator::operator= ( const SymmetryClassCalculator &  )

delete

setAtomPropertyFlags()

void CDPL::Chem::SymmetryClassCalculator::setAtomPropertyFlags

(

unsigned int

flags

)

Allows to specify the set of atomic properties that has to be considered in the perception of topological symmetry classes.

The flags argument is an OR combination of the constants defined in namespace Chem::AtomPropertyFlag. Supported property flags are:

• Chem::AtomPropertyFlag::TYPE
• Chem::AtomPropertyFlag::ISOTOPE
• Chem::AtomPropertyFlag::FORMAL_CHARGE
• Chem::AtomPropertyFlag::AROMATICITY
• and Chem::AtomPropertyFlag::H_COUNT

Parameters

flags

The set of atomic properties to consider.

Note

The default set of atomic properties is specified by SymmetryClassCalculator::DEF_ATOM_PROPERTY_FLAGS.

getAtomPropertyFlags()

unsigned int CDPL::Chem::SymmetryClassCalculator::getAtomPropertyFlags

(

)

const

Returns the set of atomic properties that gets considered in the perception of topological symmetry classes.

Returns

The set of considered atomic properties.

See also

setAtomPropertyFlags()

setBondPropertyFlags()

void CDPL::Chem::SymmetryClassCalculator::setBondPropertyFlags

(

unsigned int

flags

)

Allows to specify the set of bond properties that has to be considered in the perception of topological symmetry classes.

The flags argument is an OR combination of the constants defined in namespace Chem::BondPropertyFlag. Supported property flags are:

• Chem::BondPropertyFlag::ORDER
• and Chem::BondPropertyFlag::AROMATICITY

Parameters

flags

The set of bond properties to consider.

Note

The default set of bond properties is specified by SymmetryClassCalculator::DEF_BOND_PROPERTY_FLAGS.

getBondPropertyFlags()

unsigned int CDPL::Chem::SymmetryClassCalculator::getBondPropertyFlags

(

)

const

Returns the set of bond properties that gets considered in the perception of topological symmetry classes.

Returns

The set of considered bond properties.

See also

setBondPropertyFlags()

includeImplicitHydrogens()

void CDPL::Chem::SymmetryClassCalculator::includeImplicitHydrogens

(

bool

include

)

Allows to specify whether implicit hydrogen atoms shall be ignored or treated in the same way as explicit ones.

Parameters

include

If true, implicit hydrogen atoms are treated as if they were explicit and are ignored otherwise.

Note

By default, implicit hydrogen atoms are treated in the same way as explicit ones.

implicitHydrogensIncluded()

bool CDPL::Chem::SymmetryClassCalculator::implicitHydrogensIncluded

(

)

const

Tells whether implicit hydrogen atoms are ignored or treated in the same way as explicit ones.

Returns

true if implicit hydrogen atoms are treated in the same way as explicit ones, and false if they are ignored.

calculate()

void CDPL::Chem::SymmetryClassCalculator::calculate	(	const MolecularGraph &	molgraph,
		Util::STArray &	class_ids
	)

Perceives the topological symmetry classes of the atoms in the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to perceive the symmetry classes.
class_ids	An array containing the perceived symmetry class IDs. The class IDs are stored in the same order as the atoms appear in the atom list of the molecular graph (i.e. the symmetry class of an atom is accessible via its index).

Member Data Documentation

DEF_ATOM_PROPERTY_FLAGS

constexpr unsigned int CDPL::Chem::SymmetryClassCalculator::DEF_ATOM_PROPERTY_FLAGS

staticconstexpr

Initial value:

=
                AtomPropertyFlag::TYPE | AtomPropertyFlag::ISOTOPE | AtomPropertyFlag::H_COUNT |
                AtomPropertyFlag::AROMATICITY | AtomPropertyFlag::FORMAL_CHARGE

Specifies the default set of atomic properties considered in the perception of topological symmetry classes.

DEF_BOND_PROPERTY_FLAGS

constexpr unsigned int CDPL::Chem::SymmetryClassCalculator::DEF_BOND_PROPERTY_FLAGS

staticconstexpr

Initial value:

=
                BondPropertyFlag::ORDER | BondPropertyFlag::AROMATICITY

Specifies the default set of bond properties considered in the perception of topological symmetry classes.

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

• SymmetryClassCalculator.hpp