A helper class by which AtomTypes can return all possible atom types for a given atom in a structure that is easily accessed by orbital type. More...

#include <GasteigerAtomTyper.hh>

Inheritance diagram for core::chemical::gasteiger::PossibleAtomTypesForAtom:

[legend]

Public Member Functions
	PossibleAtomTypesForAtom ()
	default constructor More...

void	gasteiger_atom_type_set (GasteigerAtomTypeSetCOP GASTEIGER_ATOM_TYPE_SET)

bool	CouldHaveHybridization (const GasteigerAtomTypeData::HybridOrbitalType HYBRID) const
	tell whether a particular hybrid orbital type is possible given what we know about this atom More...

core::Size	GetNumberPossibleTypes () const
	return the number of types that the atom has the potential to become More...

GasteigerAtomTypeDataCOP	GetMostStableType () const
	return the most stable type More...

void	AddAtomType (GasteigerAtomTypeDataCOP ATOM_TYPE)
	add an atom type to be considered More...

void	SetToType (GasteigerAtomTypeDataCOP ATOM_TYPE)
	set this object to only consider the given atom type More...

void	Finalize (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	set the final type based on the given atom and smallest ring size More...

core::Size	hybridization_rank (GasteigerAtomTypeData::HybridOrbitalType const hybrid)

void	RemoveHybridization (const GasteigerAtomTypeData::HybridOrbitalType HYBRID)
	remove a particular hybrid orbital type from the possible types, unless that would remove all possibilities More...

void	AddAromaticAtomType (GasteigerAtomTypeDataCOP ATOM_TYPE, const int DESIRED_CHARGE)
	add an atom type to the search using a set of rules for atom types in aromatic rings More...

void	Finalize ()
	Select the best choice for the atom type wherever possible. More...

void	FinalizeUnhybridized ()
	choose the preferred atom type (using VSEPR theory) assuming that the orbitals do not hybridize More...

void	FinalizeAromatic (const int DESIRED_CHARGE)
	only keep the most stable types for the atom that span the set of desired pi orbital electrons (0-2) More...

void	FinalizeNitrogenTwoSingle (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	choose the final atom type for Nitrogen with two single bonds More...

void	FinalizeNitrogenSingleDouble (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	choose the final atom type for a nitrogen with a single and a double bond More...

void	FinalizeNitrogenThreeSingle (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	choose the final atom type for Nitrogen with three single bonds More...

void	FinalizeOxygenTwoSingle (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	choose the final atom type for Oxygen with two single bonds More...

void	FinalizeOxygenSingleDouble (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	choose the final atom type for Oxygen with a single and a double bond More...

void	FinalizeOxygenThreeSingle (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD)
	choose the final atom type for Oxygen with three single bonds More...

bool	IsUnsaturated (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD) const
	test whether a particular atom is unsaturated, without relying on atom types having already been set More...

core::Size	CountUnsaturatedNeighbors (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD) const
	count unsaturated neighbors More...

bool	IsBondedToAHalogen (const core::chemical::RealResidueGraph &graph, const core::chemical::RealResidueVD &atomVD) const
	test whether atom is bonded to any halogens More...

Static Public Member Functions
static PossibleAtomTypesForAtom	FindPossibleAtomTypesForAtom (GasteigerAtomTypeSetCOP GASTEIGER_ATOM_TYPE_SET, const Element &ELEMENT, const core::Size NUMBER_ELECTRONS_IN_BONDS, const core::Size NUMBER_BONDS, const int SUSPECTED_CHARGE, const bool IN_AROMATIC_RING)
	constructor from the known information about the atom More...

Static Private Member Functions
static std::map< std::string, PossibleAtomTypesForAtom >	CreateAtomicEnvironmentToTypesMap (const bool IN_AROMATIC_RING, GasteigerAtomTypeSetCOP GASTEIGER_ATOM_TYPE_SET)
	Create the map from atom environment string to possible atom types. More...

Private Attributes
GasteigerAtomTypeSetCOP	gasteiger_atom_type_set_
	< Number of atom types with each hybridization More...

std::map< std::string, PossibleAtomTypesForAtom >	s_atomic_env_outside_arom_ring_to_types_map

std::map< std::string, PossibleAtomTypesForAtom >	s_element_bonds_in_arom_ring_to_types_map

utility::vector0< core::Size >	m_NumberAtomTypesWithHybridization

std::list < GasteigerAtomTypeDataCOP >	m_AtomTypesByDecreasingStability
	Most stable types first. More...

core::Size	m_NumberConjugatedTypes
	Number of conjugated types in the list. More...

void(PossibleAtomTypesForAtom::*	m_FinalizeFunction )(core::chemical::RealResidueGraph const &, core::chemical::RealResidueVD const &)

Detailed Description

A helper class by which AtomTypes can return all possible atom types for a given atom in a structure that is easily accessed by orbital type.

See also: example_chemistry_possible_atom_types_for_atom.cpp

Author: mendenjl

Date: Aug 27, 2010

Constructor & Destructor Documentation

core::chemical::gasteiger::PossibleAtomTypesForAtom::PossibleAtomTypesForAtom ( )

default constructor

Member Function Documentation

void core::chemical::gasteiger::PossibleAtomTypesForAtom::AddAromaticAtomType	(	GasteigerAtomTypeDataCOP	ATOM_TYPE,
		const int	DESIRED_CHARGE
	)

add an atom type to the search using a set of rules for atom types in aromatic rings

Parameters

ATOM_TYPE	the type of atom to consider
DESIRED_CHARGE	the charge desired The atom type will be ordered using the distance from the desired charge as the first sort key, second by the stability. Unlike AddAtomType, AddAromaticAtomType always adds the type to the considered list

References hybridization_rank(), m_AtomTypesByDecreasingStability, m_NumberAtomTypesWithHybridization, and m_NumberConjugatedTypes.

void core::chemical::gasteiger::PossibleAtomTypesForAtom::AddAtomType ( GasteigerAtomTypeDataCOP ATOM_TYPE )

add an atom type to be considered

Parameters

ATOM_TYPE the type of atom to consider

References CouldHaveHybridization(), m_AtomTypesByDecreasingStability, m_NumberAtomTypesWithHybridization, m_NumberConjugatedTypes, and core::chemical::gasteiger::GasteigerAtomTypeData::Unhybridized.

bool core::chemical::gasteiger::PossibleAtomTypesForAtom::CouldHaveHybridization ( const GasteigerAtomTypeData::HybridOrbitalType HYBRID ) const

tell whether a particular hybrid orbital type is possible given what we know about this atom

Parameters

HYBRID the type of hybrid orbital

Returns: true iff there is a possible atom type for that hybrid orbital

References m_NumberAtomTypesWithHybridization.

Referenced by AddAtomType().

core::Size core::chemical::gasteiger::PossibleAtomTypesForAtom::CountUnsaturatedNeighbors	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)		const

count unsaturated neighbors

Returns: the number of unsaturated neighbors around ATOM

Parameters

ATOM	the atom of interest

Returns: the number of unsaturated neighbors around ATOM

Virtual atoms are treated like ordinary atoms.

References IsUnsaturated().

Referenced by FinalizeNitrogenThreeSingle(), and FinalizeOxygenTwoSingle().

std::map< std::string, PossibleAtomTypesForAtom > core::chemical::gasteiger::PossibleAtomTypesForAtom::CreateAtomicEnvironmentToTypesMap	(	const bool	IN_AROMATIC_RING,
		GasteigerAtomTypeSetCOP	GASTEIGER_ATOM_TYPE_SET
	)

staticprivate

Create the map from atom environment string to possible atom types.

store the atomic environment for each atom type in a map for fast lookup when determining atom types

Parameters

IN_AROMATIC_RING whether to only include types that could be in an aromatic ring

References core::id::to_string(), core::chemical::gasteiger::TR(), and core::chemical::gasteiger::GasteigerAtomTypeData::Unhybridized.

void core::chemical::gasteiger::PossibleAtomTypesForAtom::Finalize	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

set the final type based on the given atom and smallest ring size

Parameters

ATOM	the atom of interest
SMALLEST_RING_SIZE	the size of the smallest ring this atom is part of

References m_FinalizeFunction.

void core::chemical::gasteiger::PossibleAtomTypesForAtom::Finalize ( )

Select the best choice for the atom type wherever possible.

See also: https://structbio.vanderbilt.edu:8443/display/MeilerLab/RethinkingAtomTypeDetection

the link above contains the statistics and models used to select the current set of rules

References core::chemical::element::B, core::chemical::element::C, FinalizeNitrogenSingleDouble(), FinalizeNitrogenThreeSingle(), FinalizeNitrogenTwoSingle(), FinalizeOxygenSingleDouble(), FinalizeOxygenThreeSingle(), FinalizeOxygenTwoSingle(), FinalizeUnhybridized(), GetMostStableType(), m_AtomTypesByDecreasingStability, m_FinalizeFunction, core::chemical::element::N, core::chemical::element::O, RemoveHybridization(), core::chemical::gasteiger::GasteigerAtomTypeData::SP, core::chemical::gasteiger::GasteigerAtomTypeData::SP2, core::chemical::gasteiger::GasteigerAtomTypeData::SP3, core::chemical::gasteiger::TR(), and core::chemical::gasteiger::GasteigerAtomTypeData::Unhybridized.

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeAromatic ( const int DESIRED_CHARGE )

only keep the most stable types for the atom that span the set of desired pi orbital electrons (0-2)

Parameters

DESIRED_CHARGE the preferred charge used during construction of the maps when there is no part of standardization that should edit this class

References hybridization_rank(), m_AtomTypesByDecreasingStability, m_NumberConjugatedTypes, and core::chemical::gasteiger::GasteigerAtomTypeData::ZeroOrTwo.

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeNitrogenSingleDouble	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

choose the final atom type for a nitrogen with a single and a double bond

choose the final atom type for a single and a double bond

Parameters

ATOM	the atom of interest
SMALLEST_RING_SIZE	the size of the smallest ring this atom is part of

References gasteiger_atom_type_set_, and SetToType().

Referenced by Finalize().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeNitrogenThreeSingle	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

choose the final atom type for Nitrogen with three single bonds

References core::chemical::element::C, CountUnsaturatedNeighbors(), gasteiger_atom_type_set_, IsBondedToAHalogen(), core::chemical::element::O, and SetToType().

Referenced by Finalize().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeNitrogenTwoSingle	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

choose the final atom type for Nitrogen with two single bonds

References gasteiger_atom_type_set_, core::chemical::element::N, core::chemical::element::S, and SetToType().

Referenced by Finalize().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeOxygenSingleDouble	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

choose the final atom type for Oxygen with a single and a double bond

Parameters

ATOM	the atom of interest
SMALLEST_RING_SIZE	the size of the smallest ring this atom is part of

References gasteiger_atom_type_set_, and SetToType().

Referenced by Finalize().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeOxygenThreeSingle	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

choose the final atom type for Oxygen with three single bonds

References gasteiger_atom_type_set_, and SetToType().

Referenced by Finalize().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeOxygenTwoSingle	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)

choose the final atom type for Oxygen with two single bonds

Parameters

ATOM	the atom of interest
SMALLEST_RING_SIZE	the size of the smallest ring this atom is part of

References core::chemical::element::C, CountUnsaturatedNeighbors(), gasteiger_atom_type_set_, core::chemical::element::H, core::chemical::IsAromaticBond, IsUnsaturated(), core::chemical::element::N, core::chemical::element::O, core::chemical::element::S, SetToType(), and core::chemical::element::Si.

Referenced by Finalize().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeUnhybridized ( )

choose the preferred atom type (using VSEPR theory) assuming that the orbitals do not hybridize

This is used for elements in group 1, 2, & 7, which do hybridize in the gasteiger scheme

References m_AtomTypesByDecreasingStability, RemoveHybridization(), SetToType(), core::chemical::gasteiger::GasteigerAtomTypeData::SP, core::chemical::gasteiger::GasteigerAtomTypeData::SP2, core::chemical::gasteiger::GasteigerAtomTypeData::SP3, and core::id::swap().

Referenced by Finalize().

PossibleAtomTypesForAtom core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom	(	GasteigerAtomTypeSetCOP	gasteiger_atom_type_set,
		const Element &	ELEMENT,
		const core::Size	NUMBER_ELECTRONS_IN_BONDS,
		const core::Size	NUMBER_BONDS,
		const int	SUSPECTED_CHARGE,
		const bool	IN_AROMATIC_RING
	)

static

constructor from the known information about the atom

Parameters

ELEMENT	element type,
NUMBER_ELECTRONS_IN_BONDS	number of electrons in bonds for the atom type
NUMBER_BONDS	number of bonds for the atom
SUSPECTED_CHARGE;	expected charge, ignored if no atom type matching the other criteria if found
IN_AROMATIC_RING	true iff the atom has bonds of the aromatic unspecified type
ELEMENT	element type,
NUMBER_ELECTRONS_IN_BONDS	number of electrons in bonds for the atom type; for atom in declared aromatic environment, number of exocyclic bonds
NUMBER_BONDS	number of bonds for the atom
SUSPECTED_CHARGE;	expected charge, ignored if no atom type matching the other criteria if found
IN_AROMATIC_RING	true iff the atom has bonds of the aromatic unspecified type

References core::chemical::Element::get_chemical_name(), core::chemical::Element::get_chemical_symbol(), core::id::to_string(), and core::chemical::gasteiger::TR().

Referenced by core::chemical::gasteiger::GetPossibleTypesForAtom().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::gasteiger_atom_type_set ( GasteigerAtomTypeSetCOP GASTEIGER_ATOM_TYPE_SET )

References gasteiger_atom_type_set_.

GasteigerAtomTypeDataCOP core::chemical::gasteiger::PossibleAtomTypesForAtom::GetMostStableType ( ) const

return the most stable type

Returns: the most stable type - NULL if no such type exists

References m_AtomTypesByDecreasingStability.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), and Finalize().

core::Size core::chemical::gasteiger::PossibleAtomTypesForAtom::GetNumberPossibleTypes ( ) const

return the number of types that the atom has the potential to become

Returns: the number of types that the atom has the potential to become

References m_AtomTypesByDecreasingStability.

Referenced by RemoveHybridization().

core::Size core::chemical::gasteiger::PossibleAtomTypesForAtom::hybridization_rank ( GasteigerAtomTypeData::HybridOrbitalType const hybrid )

References core::chemical::gasteiger::GasteigerAtomTypeData::SP, core::chemical::gasteiger::GasteigerAtomTypeData::SP2, core::chemical::gasteiger::GasteigerAtomTypeData::SP3, core::chemical::gasteiger::TR(), and core::chemical::gasteiger::GasteigerAtomTypeData::Unhybridized.

Referenced by AddAromaticAtomType(), and FinalizeAromatic().

bool core::chemical::gasteiger::PossibleAtomTypesForAtom::IsBondedToAHalogen	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)		const

test whether atom is bonded to any halogens

Parameters

ATOM	the atom of interest

Returns: true if the atom is bonded to any halogens

Referenced by FinalizeNitrogenThreeSingle().

bool core::chemical::gasteiger::PossibleAtomTypesForAtom::IsUnsaturated	(	const core::chemical::RealResidueGraph &	graph,
		const core::chemical::RealResidueVD &	atomVD
	)		const

test whether a particular atom is unsaturated, without relying on atom types having already been set

test whether a particular atom is unsaturated

Returns: true if atom has no A. unsaturated bonds or B. is part of an aromatic ring or C. has empty orbitals; true if atom has no A. unsaturated bonds or B. is part of an aromatic ring or C. has empty orbitals

Virtual atoms are treated like ordinary atoms.

References core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, protocols::forge::methods::order(), and core::chemical::TripleBondOrder.

Referenced by CountUnsaturatedNeighbors(), and FinalizeOxygenTwoSingle().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::RemoveHybridization ( const GasteigerAtomTypeData::HybridOrbitalType HYBRID )

remove a particular hybrid orbital type from the possible types, unless that would remove all possibilities

Parameters

HYBRID the type of hybrid orbital to remove

References GetNumberPossibleTypes(), m_AtomTypesByDecreasingStability, m_NumberAtomTypesWithHybridization, and m_NumberConjugatedTypes.

Referenced by Finalize(), and FinalizeUnhybridized().

void core::chemical::gasteiger::PossibleAtomTypesForAtom::SetToType ( GasteigerAtomTypeDataCOP ATOM_TYPE )

set this object to only consider the given atom type

Parameters

ATOM_TYPE the atom type desired

References m_AtomTypesByDecreasingStability, m_FinalizeFunction, m_NumberAtomTypesWithHybridization, m_NumberConjugatedTypes, core::chemical::gasteiger::GasteigerAtomTypeData::NumberHybridOrbitalType, and core::chemical::gasteiger::TR().

Referenced by FinalizeNitrogenSingleDouble(), FinalizeNitrogenThreeSingle(), FinalizeNitrogenTwoSingle(), FinalizeOxygenSingleDouble(), FinalizeOxygenThreeSingle(), FinalizeOxygenTwoSingle(), and FinalizeUnhybridized().

Member Data Documentation

GasteigerAtomTypeSetCOP core::chemical::gasteiger::PossibleAtomTypesForAtom::gasteiger_atom_type_set_

private

< Number of atom types with each hybridization

Referenced by FinalizeNitrogenSingleDouble(), FinalizeNitrogenThreeSingle(), FinalizeNitrogenTwoSingle(), FinalizeOxygenSingleDouble(), FinalizeOxygenThreeSingle(), FinalizeOxygenTwoSingle(), and gasteiger_atom_type_set().

std::list< GasteigerAtomTypeDataCOP > core::chemical::gasteiger::PossibleAtomTypesForAtom::m_AtomTypesByDecreasingStability

private

Most stable types first.

Referenced by AddAromaticAtomType(), AddAtomType(), Finalize(), FinalizeAromatic(), FinalizeUnhybridized(), GetMostStableType(), GetNumberPossibleTypes(), RemoveHybridization(), and SetToType().

void( PossibleAtomTypesForAtom::* core::chemical::gasteiger::PossibleAtomTypesForAtom::m_FinalizeFunction)(core::chemical::RealResidueGraph const &, core::chemical::RealResidueVD const &)

private

Function used to resolve the final atom type; only used in a few ambiguous cases such as trigonal vs. tetrahedral nitrogen with 3 bonds, otherwise NULL Parameters are

the atom
the size of the smallest ring that this atom is part of

Referenced by Finalize(), and SetToType().

utility::vector0< core::Size > core::chemical::gasteiger::PossibleAtomTypesForAtom::m_NumberAtomTypesWithHybridization

private

Referenced by AddAromaticAtomType(), AddAtomType(), CouldHaveHybridization(), RemoveHybridization(), and SetToType().

core::Size core::chemical::gasteiger::PossibleAtomTypesForAtom::m_NumberConjugatedTypes

private

Number of conjugated types in the list.

Referenced by AddAromaticAtomType(), AddAtomType(), FinalizeAromatic(), RemoveHybridization(), and SetToType().

std::map< std::string, PossibleAtomTypesForAtom> core::chemical::gasteiger::PossibleAtomTypesForAtom::s_atomic_env_outside_arom_ring_to_types_map

private

std::map< std::string, PossibleAtomTypesForAtom> core::chemical::gasteiger::PossibleAtomTypesForAtom::s_element_bonds_in_arom_ring_to_types_map

private

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

src/core/chemical/gasteiger/GasteigerAtomTyper.hh
src/core/chemical/gasteiger/GasteigerAtomTyper.cc

Public Member Functions

Static Public Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation