#include <GasteigerAtomTypeData.hh>

Inheritance diagram for core::chemical::gasteiger::GasteigerAtomTypeData:

Public Types
enum	Properties { SigmaValenceStateIonizationPotential, SigmaValenceStateElectronAffinity, SigmaOrbitalElectronegativityMulliken, SigmaOrbitalElectronegativityPauling, PiValenceStateIonizationPotential, PiValenceStateElectronAffinity, PiOrbitalElectronegativityMulliken, PiOrbitalElectronegativityPauling, LonePairIonizationPotential, LonePairElectronAffinity, LonePairElectronegativityMulliken, AdditiveAtomicPolarizability, VdWaalsRadiusCSD, CovalentRadiusSingleBond, CovalentRadiusDoubleBond, CovalentRadiusTripleBond, CovalentRadiusAromaticBond, NumberOfProperties }
	enum properties for atom types More...

enum	PiContributionType { Zero, One, Two, ZeroOrTwo }
	how the atom type can contribute to a pi system More...

enum	AtomicOrbitalTypes { S, Px, Py, Pz, Dxy, Dxz, Dyz, Dz2, Dx2y2, NumberOfAtomicOrbitalTypes }

enum	HybridOrbitalType { Unhybridized, SP, SP2, SP3, NumberHybridOrbitalType }

enum	TypeDifference { None, NumberBondingSOrbitals, NumberBondingPOrbitals, NumberLonePairOrbitals, Other, NumberTypeDifferences }
	Type difference specifies the difference between two atom types. More...

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

	~GasteigerAtomTypeData ()
	destructor More...

	GasteigerAtomTypeData (const std::string &NAME, const ElementOP &ELEMENT_TYPE, const HybridOrbitalType &HYBRIDIZATION, const core::Size &HYBRID_ORBITALS_IN_SIGMA_BONDS, const core::Size &HYBRID_ORBITALS_NONBINDING, const std::set< AtomicOrbitalTypes > &PI_ORBITALS_IN_BONDS, const std::set< AtomicOrbitalTypes > &ATOMIC_ORBITALS_NONBINDING, const core::Real &SIGMA_VALENCE_STATE_IONIZATION_POTENTIAL, const core::Real &SIGMA_VALENCE_STATE_ELECTRON_AFFINITY, const core::Real &PI_VALENCE_STATE_IONIZATION_POTENTIAL, const core::Real &PI_VALENCE_STATE_ELECTRON_AFFINITY, const core::Real &LONE_PAIR_IONIZATION_POTENTIAL, const core::Real &LONE_PAIR_ELECTRON_AFFINITY, const core::Real &ATOMIC_POLARIZABILITY)
	the usual constructor More...

	GasteigerAtomTypeData (const std::string &NAME, const std::string &ELEMENT, const HybridOrbitalType &HYBRIDIZATION, const core::Size &HYBRID_ORBITALS_IN_SIGMA_BONDS, const core::Size &HYBRID_ORBITALS_NONBINDING, const std::set< AtomicOrbitalTypes > &PI_ORBITALS_IN_BONDS, const std::set< AtomicOrbitalTypes > &ATOMIC_ORBITALS_NONBINDING, const core::Real &SIGMA_VALENCE_STATE_IONIZATION_POTENTIAL, const core::Real &SIGMA_VALENCE_STATE_ELECTRON_AFFINITY, const core::Real &PI_VALENCE_STATE_IONIZATION_POTENTIAL, const core::Real &PI_VALENCE_STATE_ELECTRON_AFFINITY, const core::Real &LONE_PAIR_IONIZATION_POTENTIAL, const core::Real &LONE_PAIR_ELECTRON_AFFINITY, const core::Real &ATOMIC_POLARIZABILITY, ElementSetCOP ele_set)
	the usual constructor, with element set. More...

	GasteigerAtomTypeData (const std::string &NAME, ElementOP ELEMENT_TYPE, const short &CHARGE)
	constructor from just an element type and charge More...

GasteigerAtomTypeDataOP	Clone () const
	Clone function. More...

std::string const &	get_name () const
	return Name More...

ElementCOP	get_element_type () const
	return ElementType More...

HybridOrbitalType	get_hybrid_orbital_type () const
	returns the hybridization of the atom type More...

core::Size	get_number_hybrid_orbitals () const
	returns the number of hybridized orbitals More...

core::Size	get_nNumber_hybrid_lone_pairs () const
	returns the number of lone pairs in hybrid orbitals More...

core::Size	get_number_hybrid_bonds () const
	return Number of bonds More...

core::Size	get_number_bonds () const

core::Size	get_number_unhybridized_sigma_orbitals () const
	return Number of Sigma orbitals that are not hybridized More...

core::Size	get_number_sigma_orbitals () const
	return Number of Sigma orbitals More...

core::Size	get_number_electrons_in_p_orbitals () const
	return Number of occupied p orbitals More...

core::Size	get_number_pi_orbitals () const
	return Number of pi-orbitals More...

short	get_formal_charge () const
	return Charge More...

core::Size	get_valence_electrons_sp () const

core::Size	get_number_electrons_in_bonds () const
	get_number_electrons_in_bonds calculates the total number of electrons in pi-orbital and sigma bonds More...

core::Size	get_number_unhybridized_lone_pairs () const
	return Number of unhybridized lone pairs More...

core::Real	get_atom_type_property (const GasteigerAtomTypeData::Properties PROPERTY) const
	atom type property as core::Real More...

core::Real	get_orbital_E_neg_pos () const

bool	is_conjugated () const
	determine if this atom type can participate in pi-bond conjugation More...

bool	is_gasteiger_atom_type () const
	is this a well characterized gasteiger atom type More...

core::Size	get_maxE_contribution_to_pi_system () const
	Get the max number of electrons available for contribution to an aromatic ring. More...

PiContributionType	get_pi_electron_contribution_type () const
	Get the type of contribution this atom type can make to a pi system. More...

core::Real	get_stability_metric () const
	Get the stability metric. Electronic stability is indicated by a larger number This is used to decide between atom types when no other means are possible. More...

std::istream &	read (std::istream &ISTREAM, ElementSetCAP ele_set)
	read from std::istream More...

std::ostream &	write (std::ostream &OSTREAM) const
	write to std::ostream More...

core::Real	calculate_stability_metric () const
	calculate the stability metric. Electronic stability is indicated by a larger number This is used to decide between atom types when no other means are possible More...

core::Real	get_average_ip_change_cation_to_neutral (const TypeDifference TYPE_DIFFERENCE) const
	get the average ionization potential ratio between cation and neutral atom type that differ by TYPE_DIFFERENCE More...

core::Real	get_average_ip_change_neutral_to_anion (const TypeDifference TYPE_DIFFERENCE) const
	get the average ionization potential ratio between neutral and cation atom type that differ by TYPE_DIFFERENCE More...

TypeDifference	difference_from (const GasteigerAtomTypeData &OTHER)
	determine the difference betweent his atom type data and another More...

core::Real	get_electronegativity (const TypeDifference TYPE_DIFFERENCE) const
	get the electronegativity type corresponding to a TypeDifference More...

core::Real	get_ionization_potential (const TypeDifference TYPE_DIFFERENCE) const
	get the ionization potential type corresponding to a TypeDifference More...

core::Real	get_electron_affinity (const TypeDifference TYPE_DIFFERENCE) const
	get the electron affinity type corresponding to a TypeDifference More...

void	set_property (const Properties DATA, const core::Real VALUE)
	set a particular data More...

Static Public Member Functions
static const std::string &	GetPropertyName (const Properties PROPERTY)
	element type property as string More...

static std::vector < std::string > const &	AtomicOrbitalTypes_strings ()

static const std::string &	get_type_difference_name (const TypeDifference TYPE_DIFFERENCE)
	type difference as string More...

static core::Real	get_average_neutral_sigma_ip_to_anion_ip_ratio ()
	GetAverageNeutralSigmaIVToEARatio helper function for AtomTypes::CalculateElectronegativityValues. More...

static core::Real	get_average_neutral_pi_ip_to_anion_ip_ratio ()
	get_average_neutral_pi_ip_to_anion_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues More...

static core::Real	get_average_cation_sigma_ip_to_neutral_ip_ratio ()
	get_average_cation_sigma_ip_to_neutral_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues More...

static core::Real	get_average_cation_pi_ip_to_neutral_ip_ratio ()
	get_average_cation_pi_ip_to_neutral_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues More...

Private Member Functions
void	initialize ()
	Initialize derived values. More...

Private Attributes
std::string	name_

ElementCOP	element_type_
	name of the atom type More...

HybridOrbitalType	hybridization_
	Unhybridized, SP, SP2, or SP3. More...

core::Size	number_hybrid_orbitals_sigma_binding_
	hybrid orbitals that are binding More...

core::Size	number_hybrid_orbitals_nonbinding_
	hybrid orbitals that are non binding with their electrons More...

core::Size	number_electrons_in_bonds_
	Number of e- bonds (calculated) More...

core::Size	number_bonds_
	Number of bonds (calculated) More...

core::Size	max_e_contribution_to_pi_system_
	Number of e- in pi system (calculated) More...

std::set< AtomicOrbitalTypes >	pi_orbitals_binding_
	pi orbitals involved in binding More...

std::set< AtomicOrbitalTypes >	atomic_orbitals_nonbinding_
	non hybridized non binding orbitals with their electrons More...

core::Real	properties_ [int(NumberOfProperties)]
	real-valued properties More...

core::Real	orbital_e_neg_pos_
	orbital electronegativity associated with the charged state More...

core::Real	stability_metric_
	estimated stability of the atom type; only used to resolve clashes in atom types More...

short	charge_
	charge of atom type = difference between electrons in bonds and non-bonds minus valence electrons More...

bool	conjugated_
	whether this atom is conjugated More...

core::Real	sigma_charge_to_en_inflection_
	Inflection point for sigma charge to inflection. More...

core::Real	pi_charge_to_en_inflection_
	Inflection point for pi charge to inflection. More...

core::Real	sigma_charge_to_lone_pair_en_inflection_
	Inflection point for sigma charge to inflection. More...

bool	is_gasteiger_type_
	Is the type a proper gasteiger type. More...

PiContributionType	pi_contribution_
	Contribution of this atom type to a pi-conjugated system. More...

Member Enumeration Documentation

enum core::chemical::gasteiger::GasteigerAtomTypeData::AtomicOrbitalTypes

Enumerator
S
Px
Py
Pz
Dxy
Dxz
Dyz
Dz2
Dx2y2
NumberOfAtomicOrbitalTypes

enum core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType

Enumerator
Unhybridized
SP
SP2
SP3
NumberHybridOrbitalType

enum core::chemical::gasteiger::GasteigerAtomTypeData::PiContributionType

how the atom type can contribute to a pi system

Enumerator
Zero	no pi electrons will be contributed; e.g. atom type with no non-singular bonds, no lone pairs, like B_TrTrTr
One	exactly one pi electron will be contributed by this atom type (atom type with a double bond)
Two	exactly two pi electrons will be contributed by this atom type (atom type with a triple bond or two 2x bonds)
ZeroOrTwo	Either zero or two pi electrons will be contributed by this atom type (atom type with lone pairs but only singular bonds)

enum core::chemical::gasteiger::GasteigerAtomTypeData::Properties

enum properties for atom types

Enumerator
SigmaValenceStateIonizationPotential	sigma ionization potential
SigmaValenceStateElectronAffinity	sigma electron affinity
SigmaOrbitalElectronegativityMulliken	sigma orbital electronegativity, Mulliken scale
SigmaOrbitalElectronegativityPauling	sigma orbital electronegativity, Pauli scale
PiValenceStateIonizationPotential	pi ionization potential
PiValenceStateElectronAffinity	pi electron affinity
PiOrbitalElectronegativityMulliken	pi orbital electronegativity, Mulliken scale
PiOrbitalElectronegativityPauling	pi orbital electronegativity, Pauli scale
LonePairIonizationPotential	lone pair ionization potential
LonePairElectronAffinity	lone pair electron affinity
LonePairElectronegativityMulliken	lone pair electronegativity
AdditiveAtomicPolarizability	additive atomic polarizability, see J. Am. Chem. Soc. 1990, 112, 8533-8542
VdWaalsRadiusCSD	Vdw radius for the atom type using data from the CSD; see notes below.
CovalentRadiusSingleBond	Covalent radius for single bond.
CovalentRadiusDoubleBond	Covalent radius for double bond.
CovalentRadiusTripleBond	Covalent radius for triple bond.
CovalentRadiusAromaticBond	Covalent radius for an aromatic bond.
NumberOfProperties	Number of properties.

enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference

Type difference specifies the difference between two atom types.

Enumerator
None	atom types are identical
NumberBondingSOrbitals	different # of electrons in bonding s-orbitals
NumberBondingPOrbitals	different # of electrons in bonding p-orbitals
NumberLonePairOrbitals	different # of electrons in lone pairs
Other	multiple differences or other differences (e.g. element type),
NumberTypeDifferences

Constructor & Destructor Documentation

core::chemical::gasteiger::GasteigerAtomTypeData::GasteigerAtomTypeData ( )

default constructor

References NumberOfProperties, and properties_.

Referenced by Clone().

core::chemical::gasteiger::GasteigerAtomTypeData::~GasteigerAtomTypeData ( )

destructor

core::chemical::gasteiger::GasteigerAtomTypeData::GasteigerAtomTypeData	(	const std::string &	NAME,
		const ElementOP &	ELEMENT_TYPE,
		const HybridOrbitalType &	HYBRIDIZATION,
		const core::Size &	HYBRID_ORBITALS_IN_SIGMA_BONDS,
		const core::Size &	HYBRID_ORBITALS_NONBINDING,
		const std::set< AtomicOrbitalTypes > &	PI_ORBITALS_IN_BONDS,
		const std::set< AtomicOrbitalTypes > &	ATOMIC_ORBITALS_NONBINDING,
		const core::Real &	SIGMA_VALENCE_STATE_IONIZATION_POTENTIAL,
		const core::Real &	SIGMA_VALENCE_STATE_ELECTRON_AFFINITY,
		const core::Real &	PI_VALENCE_STATE_IONIZATION_POTENTIAL,
		const core::Real &	PI_VALENCE_STATE_ELECTRON_AFFINITY,
		const core::Real &	LONE_PAIR_IONIZATION_POTENTIAL,
		const core::Real &	LONE_PAIR_ELECTRON_AFFINITY,
		const core::Real &	ATOMIC_POLARIZABILITY
	)

the usual constructor

core::chemical::gasteiger::GasteigerAtomTypeData::GasteigerAtomTypeData	(	const std::string &	NAME,
		const std::string &	ELEMENT,
		const HybridOrbitalType &	HYBRIDIZATION,
		const core::Size &	HYBRID_ORBITALS_IN_SIGMA_BONDS,
		const core::Size &	HYBRID_ORBITALS_NONBINDING,
		const std::set< AtomicOrbitalTypes > &	PI_ORBITALS_IN_BONDS,
		const std::set< AtomicOrbitalTypes > &	ATOMIC_ORBITALS_NONBINDING,
		const core::Real &	SIGMA_VALENCE_STATE_IONIZATION_POTENTIAL,
		const core::Real &	SIGMA_VALENCE_STATE_ELECTRON_AFFINITY,
		const core::Real &	PI_VALENCE_STATE_IONIZATION_POTENTIAL,
		const core::Real &	PI_VALENCE_STATE_ELECTRON_AFFINITY,
		const core::Real &	LONE_PAIR_IONIZATION_POTENTIAL,
		const core::Real &	LONE_PAIR_ELECTRON_AFFINITY,
		const core::Real &	ATOMIC_POLARIZABILITY,
		ElementSetCOP	ele_set
	)

the usual constructor, with element set.

the usual constructor

core::chemical::gasteiger::GasteigerAtomTypeData::GasteigerAtomTypeData	(	const std::string &	NAME,
		ElementOP	ELEMENT_TYPE,
		const short &	CHARGE
	)

constructor from just an element type and charge

Member Function Documentation

std::vector< std::string > const & core::chemical::gasteiger::GasteigerAtomTypeData::AtomicOrbitalTypes_strings ( )

static

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::calculate_stability_metric ( ) const

calculate the stability metric. Electronic stability is indicated by a larger number This is used to decide between atom types when no other means are possible

References PiValenceStateElectronAffinity, PiValenceStateIonizationPotential, properties_, SigmaValenceStateElectronAffinity, and SigmaValenceStateIonizationPotential.

Referenced by initialize().

GasteigerAtomTypeDataOP core::chemical::gasteiger::GasteigerAtomTypeData::Clone ( ) const

Clone function.

Returns: pointer to new AtomTypeData; pointer to new GasteigerAtomTypeData

References GasteigerAtomTypeData().

GasteigerAtomTypeData::TypeDifference core::chemical::gasteiger::GasteigerAtomTypeData::difference_from ( const GasteigerAtomTypeData & OTHER )

determine the difference betweent his atom type data and another

Parameters

OTHER the atom type data to compare this atom type data to

Returns: the corresponding TypeDifference

References charge_, element_type_, get_nNumber_hybrid_lone_pairs(), get_number_bonds(), get_number_hybrid_orbitals(), get_number_sigma_orbitals(), get_number_unhybridized_lone_pairs(), hybridization_, None, number_electrons_in_bonds_, NumberBondingPOrbitals, NumberBondingSOrbitals, NumberLonePairOrbitals, and Other.

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_atom_type_property ( const GasteigerAtomTypeData::Properties PROPERTY ) const

atom type property as core::Real

Parameters

PROPERTY the property desired

Returns: the property as core::Real

References properties_.

Referenced by core::chemical::create_bond_length().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_average_cation_pi_ip_to_neutral_ip_ratio ( )

static

get_average_cation_pi_ip_to_neutral_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues

Returns: reference to a core::Real, which returns the ratio of Average(PiValenceStateIonizationPotential) for cations vs. neutral atoms

Referenced by get_average_ip_change_cation_to_neutral().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_average_cation_sigma_ip_to_neutral_ip_ratio ( )

static

get_average_cation_sigma_ip_to_neutral_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues

Returns: reference to a core::Real, which returns the ratio of Average(SigmaValenceStateIonizationPotential) for cations vs. neutral atoms

Referenced by get_average_ip_change_cation_to_neutral().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_average_ip_change_cation_to_neutral ( const TypeDifference TYPE_DIFFERENCE ) const

get the average ionization potential ratio between cation and neutral atom type that differ by TYPE_DIFFERENCE

Parameters

TYPE_DIFFERENCE the type difference to get the corresponding ratio for

Returns: the ratio

References get_average_cation_pi_ip_to_neutral_ip_ratio(), get_average_cation_sigma_ip_to_neutral_ip_ratio(), NumberBondingPOrbitals, NumberBondingSOrbitals, and NumberLonePairOrbitals.

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_average_ip_change_neutral_to_anion ( const TypeDifference TYPE_DIFFERENCE ) const

get the average ionization potential ratio between neutral and cation atom type that differ by TYPE_DIFFERENCE

Parameters

TYPE_DIFFERENCE the type difference to get the corresponding ratio for

Returns: the ratio

References get_average_neutral_pi_ip_to_anion_ip_ratio(), get_average_neutral_sigma_ip_to_anion_ip_ratio(), NumberBondingPOrbitals, NumberBondingSOrbitals, and NumberLonePairOrbitals.

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_average_neutral_pi_ip_to_anion_ip_ratio ( )

static

get_average_neutral_pi_ip_to_anion_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues

Returns: reference to a core::Real, which returns the ratio of Average(PiValenceStateIonizationPotential) for neutral atoms vs. anions

Referenced by get_average_ip_change_neutral_to_anion().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_average_neutral_sigma_ip_to_anion_ip_ratio ( )

static

GetAverageNeutralSigmaIVToEARatio helper function for AtomTypes::CalculateElectronegativityValues.

Returns: reference to a core::Real, which returns the ratio of Average(SigmaValenceStateIonizationPotential) for neutral atoms vs. anions

Referenced by get_average_ip_change_neutral_to_anion().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_electron_affinity ( const TypeDifference TYPE_DIFFERENCE ) const

get the electron affinity type corresponding to a TypeDifference

get the electron affinity type corresponding to TypeDifference

Parameters

TYPE_DIFFERENCE the type difference to get the corresponding electron affinity for

Returns: the electron affinity type corresponding to TypeDifference

References LonePairElectronAffinity, NumberBondingPOrbitals, NumberBondingSOrbitals, NumberLonePairOrbitals, PiValenceStateElectronAffinity, properties_, and SigmaValenceStateElectronAffinity.

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_electronegativity ( const TypeDifference TYPE_DIFFERENCE ) const

get the electronegativity type corresponding to a TypeDifference

get the electronegativity type corresponding to TypeDifference

Parameters

TYPE_DIFFERENCE the type difference to get the corresponding electronegativity for

Returns: the electronegativity type corresponding to TypeDifference

References LonePairElectronegativityMulliken, NumberBondingPOrbitals, NumberBondingSOrbitals, NumberLonePairOrbitals, PiOrbitalElectronegativityMulliken, properties_, and SigmaOrbitalElectronegativityMulliken.

ElementCOP core::chemical::gasteiger::GasteigerAtomTypeData::get_element_type ( ) const

return ElementType

References element_type_.

short core::chemical::gasteiger::GasteigerAtomTypeData::get_formal_charge ( ) const

return Charge

Returns: Charge

References charge_.

Referenced by get_valence_electrons_sp().

GasteigerAtomTypeData::HybridOrbitalType core::chemical::gasteiger::GasteigerAtomTypeData::get_hybrid_orbital_type ( ) const

returns the hybridization of the atom type

Returns: the type of hybrid orbital

References hybridization_.

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_ionization_potential ( const TypeDifference TYPE_DIFFERENCE ) const

get the ionization potential type corresponding to a TypeDifference

get the ionization potential type corresponding to TypeDifference

Parameters

TYPE_DIFFERENCE the type difference to get the corresponding ionization potential for

Returns: the ionization potential type corresponding to TypeDifference

References LonePairIonizationPotential, NumberBondingPOrbitals, NumberBondingSOrbitals, NumberLonePairOrbitals, PiValenceStateIonizationPotential, properties_, and SigmaValenceStateIonizationPotential.

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_maxE_contribution_to_pi_system ( ) const

Get the max number of electrons available for contribution to an aromatic ring.

Returns: the max electrons contributed by this atom type to a pi system

References max_e_contribution_to_pi_system_.

std::string const & core::chemical::gasteiger::GasteigerAtomTypeData::get_name ( ) const

return Name

References name_.

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_nNumber_hybrid_lone_pairs ( ) const

returns the number of lone pairs in hybrid orbitals

Returns: the number of lone pairs in hybrid orbitals

References number_hybrid_orbitals_nonbinding_.

Referenced by difference_from(), and initialize().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_bonds ( ) const

Returns: Number of bonds

References number_bonds_.

Referenced by difference_from().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_electrons_in_bonds ( ) const

get_number_electrons_in_bonds calculates the total number of electrons in pi-orbital and sigma bonds

References number_electrons_in_bonds_.

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_electrons_in_p_orbitals ( ) const

return Number of occupied p orbitals

Returns: Number of electrons in p orbitals (whether hybridized or not)

References get_number_unhybridized_sigma_orbitals(), and number_electrons_in_bonds_.

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_hybrid_bonds ( ) const

return Number of bonds

Returns: Number of hybridized bonds

References number_hybrid_orbitals_sigma_binding_, and pi_orbitals_binding_.

Referenced by initialize().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_hybrid_orbitals ( ) const

returns the number of hybridized orbitals

Returns: the number of hybridized orbitals

References number_hybrid_orbitals_nonbinding_, and number_hybrid_orbitals_sigma_binding_.

Referenced by difference_from().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_pi_orbitals ( ) const

return Number of pi-orbitals

Returns: Number of pi-orbitals

References pi_orbitals_binding_.

Referenced by initialize().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_sigma_orbitals ( ) const

return Number of Sigma orbitals

Returns: Number of Sigma orbitals

References get_number_unhybridized_sigma_orbitals(), and number_hybrid_orbitals_sigma_binding_.

Referenced by difference_from().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_unhybridized_lone_pairs ( ) const

return Number of unhybridized lone pairs

References atomic_orbitals_nonbinding_.

Referenced by difference_from(), and initialize().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_number_unhybridized_sigma_orbitals ( ) const

return Number of Sigma orbitals that are not hybridized

Returns: Number of Sigma orbitals that are not hybridized

References pi_orbitals_binding_, and S.

Referenced by get_number_electrons_in_p_orbitals(), get_number_sigma_orbitals(), and initialize().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_orbital_E_neg_pos ( ) const

Returns: the orbital electronegativity associated with the charged state

References orbital_e_neg_pos_.

GasteigerAtomTypeData::PiContributionType core::chemical::gasteiger::GasteigerAtomTypeData::get_pi_electron_contribution_type ( ) const

Get the type of contribution this atom type can make to a pi system.

Returns: the type of contribution this atom type can make to a pi system

References pi_contribution_.

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::get_stability_metric ( ) const

Get the stability metric. Electronic stability is indicated by a larger number This is used to decide between atom types when no other means are possible.

References stability_metric_.

const std::string & core::chemical::gasteiger::GasteigerAtomTypeData::get_type_difference_name ( const TypeDifference TYPE_DIFFERENCE )

static

type difference as string

Parameters

TYPE_DIFFERENCE the type difference for which a string is desired

Returns: the type difference as a string

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::get_valence_electrons_sp ( ) const

Returns: valence electrons in sp orbitals

References element_type_, and get_formal_charge().

const std::string & core::chemical::gasteiger::GasteigerAtomTypeData::GetPropertyName ( const Properties PROPERTY )

static

element type property as string

Note: VdWaalsRadiusCSD is only valid for atoms without hydrogens, and can only be used to; detect bad geometries if both atoms have no H (otherwise H bonding may lead to close contacts, also; could imply missing bonds), and which do not have opposite charges; VdWaalsRadiusCSD was calculated using data from the cambridge structural database; Vdw radii may be violated in certain bridged ring systems

Parameters

PROPERTY the property desired

Returns: the property as string

Parameters

PROPERTY the property desired

Returns: the property as string

void core::chemical::gasteiger::GasteigerAtomTypeData::initialize ( )

private

Initialize derived values.

References atomic_orbitals_nonbinding_, calculate_stability_metric(), charge_, conjugated_, element_type_, get_nNumber_hybrid_lone_pairs(), get_number_hybrid_bonds(), get_number_pi_orbitals(), get_number_unhybridized_lone_pairs(), get_number_unhybridized_sigma_orbitals(), hybridization_, is_gasteiger_type_, LonePairElectronAffinity, LonePairElectronegativityMulliken, LonePairIonizationPotential, max_e_contribution_to_pi_system_, number_bonds_, number_electrons_in_bonds_, number_hybrid_orbitals_nonbinding_, number_hybrid_orbitals_sigma_binding_, NumberOfProperties, orbital_e_neg_pos_, pi_charge_to_en_inflection_, pi_contribution_, pi_orbitals_binding_, PiOrbitalElectronegativityMulliken, PiOrbitalElectronegativityPauling, PiValenceStateElectronAffinity, PiValenceStateIonizationPotential, properties_, sigma_charge_to_en_inflection_, sigma_charge_to_lone_pair_en_inflection_, SigmaOrbitalElectronegativityMulliken, SigmaOrbitalElectronegativityPauling, SigmaValenceStateElectronAffinity, SigmaValenceStateIonizationPotential, SP2, stability_metric_, VdWaalsRadiusCSD, and ZeroOrTwo.

Referenced by read().

bool core::chemical::gasteiger::GasteigerAtomTypeData::is_conjugated ( ) const

determine if this atom type can participate in pi-bond conjugation

Returns: true iff this atom type has any non-single bonds or lone pairs; true iff this atom type has any e- in p-orbitals or lone pairs

References conjugated_.

bool core::chemical::gasteiger::GasteigerAtomTypeData::is_gasteiger_atom_type ( ) const

is this a well characterized gasteiger atom type

Returns: true iff this atom type is this a well characterized gasteiger atom type

References is_gasteiger_type_.

std::istream & core::chemical::gasteiger::GasteigerAtomTypeData::read	(	std::istream &	ISTREAM,
		ElementSetCAP	ele_set_ap
	)

read from std::istream

Parameters

ISTREAM input stream

Returns: istream which was read from

References AdditiveAtomicPolarizability, atomic_orbitals_nonbinding_, element_type_, hybridization_, initialize(), LonePairElectronAffinity, LonePairIonizationPotential, name_, number_hybrid_orbitals_nonbinding_, number_hybrid_orbitals_sigma_binding_, pi_orbitals_binding_, PiValenceStateElectronAffinity, PiValenceStateIonizationPotential, properties_, core::chemical::gasteiger::safe_read(), SigmaValenceStateElectronAffinity, and SigmaValenceStateIonizationPotential.

void core::chemical::gasteiger::GasteigerAtomTypeData::set_property	(	const Properties	DATA,
		const core::Real	VALUE
	)

set a particular data

Parameters

DATA	the property to set
VALUE	the value to set the property to

References properties_.

std::ostream & core::chemical::gasteiger::GasteigerAtomTypeData::write ( std::ostream & OSTREAM ) const

write to std::ostream

Parameters

OSTREAM	output stream to write to
INDENT	number of indentations

Returns: output stream which was written to

References AdditiveAtomicPolarizability, atomic_orbitals_nonbinding_, core::chemical::gasteiger::compact_enum_set(), element_type_, hybridization_, LonePairElectronAffinity, LonePairIonizationPotential, name_, number_hybrid_orbitals_nonbinding_, number_hybrid_orbitals_sigma_binding_, pi_orbitals_binding_, PiValenceStateElectronAffinity, PiValenceStateIonizationPotential, properties_, core::chemical::gasteiger::safe_write(), SigmaValenceStateElectronAffinity, and SigmaValenceStateIonizationPotential.

Referenced by core::chemical::gasteiger::operator<<().

Member Data Documentation

std::set< AtomicOrbitalTypes > core::chemical::gasteiger::GasteigerAtomTypeData::atomic_orbitals_nonbinding_

private

non hybridized non binding orbitals with their electrons

Referenced by get_number_unhybridized_lone_pairs(), initialize(), read(), and write().

short core::chemical::gasteiger::GasteigerAtomTypeData::charge_

private

charge of atom type = difference between electrons in bonds and non-bonds minus valence electrons

Referenced by difference_from(), get_formal_charge(), and initialize().

bool core::chemical::gasteiger::GasteigerAtomTypeData::conjugated_

private

whether this atom is conjugated

Referenced by initialize(), and is_conjugated().

ElementCOP core::chemical::gasteiger::GasteigerAtomTypeData::element_type_

private

name of the atom type

element type

Referenced by difference_from(), get_element_type(), get_valence_electrons_sp(), initialize(), read(), and write().

HybridOrbitalType core::chemical::gasteiger::GasteigerAtomTypeData::hybridization_

private

Unhybridized, SP, SP2, or SP3.

Referenced by difference_from(), get_hybrid_orbital_type(), initialize(), read(), and write().

bool core::chemical::gasteiger::GasteigerAtomTypeData::is_gasteiger_type_

private

Is the type a proper gasteiger type.

Referenced by initialize(), and is_gasteiger_atom_type().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::max_e_contribution_to_pi_system_

private

Number of e- in pi system (calculated)

Referenced by get_maxE_contribution_to_pi_system(), and initialize().

std::string core::chemical::gasteiger::GasteigerAtomTypeData::name_

private

Referenced by get_name(), read(), and write().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::number_bonds_

private

Number of bonds (calculated)

Referenced by get_number_bonds(), and initialize().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::number_electrons_in_bonds_

private

Number of e- bonds (calculated)

Referenced by difference_from(), get_number_electrons_in_bonds(), get_number_electrons_in_p_orbitals(), and initialize().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::number_hybrid_orbitals_nonbinding_

private

hybrid orbitals that are non binding with their electrons

Referenced by get_nNumber_hybrid_lone_pairs(), get_number_hybrid_orbitals(), initialize(), read(), and write().

core::Size core::chemical::gasteiger::GasteigerAtomTypeData::number_hybrid_orbitals_sigma_binding_

private

hybrid orbitals that are binding

Referenced by get_number_hybrid_bonds(), get_number_hybrid_orbitals(), get_number_sigma_orbitals(), initialize(), read(), and write().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::orbital_e_neg_pos_

private

orbital electronegativity associated with the charged state

Referenced by get_orbital_E_neg_pos(), and initialize().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::pi_charge_to_en_inflection_

private

Inflection point for pi charge to inflection.

Referenced by initialize().

PiContributionType core::chemical::gasteiger::GasteigerAtomTypeData::pi_contribution_

private

Contribution of this atom type to a pi-conjugated system.

Referenced by get_pi_electron_contribution_type(), and initialize().

std::set< AtomicOrbitalTypes > core::chemical::gasteiger::GasteigerAtomTypeData::pi_orbitals_binding_

private

pi orbitals involved in binding

Referenced by get_number_hybrid_bonds(), get_number_pi_orbitals(), get_number_unhybridized_sigma_orbitals(), initialize(), read(), and write().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::properties_[int(NumberOfProperties)]

private

real-valued properties

Referenced by calculate_stability_metric(), GasteigerAtomTypeData(), get_atom_type_property(), get_electron_affinity(), get_electronegativity(), get_ionization_potential(), initialize(), read(), set_property(), and write().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::sigma_charge_to_en_inflection_

private

Inflection point for sigma charge to inflection.

Referenced by initialize().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::sigma_charge_to_lone_pair_en_inflection_

private

Inflection point for sigma charge to inflection.

Referenced by initialize().

core::Real core::chemical::gasteiger::GasteigerAtomTypeData::stability_metric_

private

estimated stability of the atom type; only used to resolve clashes in atom types

Referenced by get_stability_metric(), and initialize().

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

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

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

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Constructor & Destructor Documentation

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