core::chemical::Bond Class Reference

basic chemical Bond More...

#include <Bond.hh>

Public Member Functions
	Bond ()
	Bond (Real d, BondName name, bool cut_bond=false)
	Bond (Real d, BondOrder order, BondConjugability conj, BondAromaticity aroma, BondRingness ring=UnknownRingness, BondIsometry isom=UnknownIsometry, bool cut_bond=false)
void	bond_name (BondName bond_name)
void	cut_bond (bool cut_bond)
void	order (BondOrder order)
void	conjugability (BondConjugability conjug)
void	aromaticity (BondAromaticity aroma)
void	ringness (BondRingness ring)
void	isometry (BondIsometry isom)
BondName	bond_name () const
bool	cut_bond () const
BondOrder	order () const
BondConjugability	conjugability () const
BondAromaticity	aromaticity () const
BondRingness	ringness () const
BondIsometry	isometry () const
void	print (std::ostream &out) const
void	SetSDFType (const core::Size SDF_ID)
	Reset the internal data such that it matches the appropriate value for the SDF datatype. More...
core::Size	GetNumberOfElectrons () const
core::Size	GetMinimumElectrons () const
core::Size	GetMaximumElectrons () const
bool	IsBondOrderKnown () const
bool	IsBondInRing () const
core::Size	GetSDFileID () const
core::Size	GetSDAltFileID () const
bool	is_fake () const
	Return true if this bond represents a non-physical bond. More...

Private Attributes
bool	cut_bond_
	Is the bond allowed to be in the atom tree? More...
BondName	bond_name_
BondOrder	order_
	The bond order (single double triple ..) More...
BondConjugability	conjug_
	Can the bond participate in a conjugated system. More...
BondAromaticity	aroma_
	Is the bond in an aromatic ring? (Distinct from being conjugatable and in a ring.) More...
BondRingness	ring_
	Is the bond in a ring? More...
BondIsometry	isometry_
	For double bonds, what's the E/Z isometry? More...

Friends
std::ostream &	operator<< (std::ostream &out, Bond const &bond)

Detailed Description

basic chemical Bond

name, element, certain properties and parameters from .params file

Constructor & Destructor Documentation

Bond() [1/3]

core::chemical::Bond::Bond

(

)

Bond() [2/3]

core::chemical::Bond::Bond	(	Real	d,
		BondName	name,
		bool	cut_bond = false
	)

References bond_name().

Bond() [3/3]

core::chemical::Bond::Bond	(	Real	d,
		BondOrder	order,
		BondConjugability	conj,
		BondAromaticity	aroma,
		BondRingness	ring = UnknownRingness,
		BondIsometry	isom = UnknownIsometry,
		bool	cut_bond = false
	)

References core::chemical::AromaticBond, bond_name_, core::chemical::BondInRing, core::chemical::DoubleBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, isometry_, core::chemical::NoBondIsometry, core::chemical::OrbitalBond, core::chemical::OrbitalBondOrder, order(), core::chemical::PseudoBond, core::chemical::PseudoBondOrder, ring_, core::chemical::SingleBond, core::chemical::SingleBondOrder, core::chemical::TripleBond, core::chemical::TripleBondOrder, core::chemical::UnknownBond, core::chemical::UnknownIsometry, and core::chemical::UnknownRingness.

Member Function Documentation

aromaticity() [1/2]

BondAromaticity core::chemical::Bond::aromaticity ( ) const

inline

References aroma_.

aromaticity() [2/2]

void core::chemical::Bond::aromaticity

(

BondAromaticity

aroma

)

References aroma_, core::chemical::AromaticBond, bond_name_, core::chemical::IsAromaticBond, core::chemical::NonaromaticBond, core::chemical::UnknownAromaticity, and core::chemical::UnknownBond.

Referenced by core::chemical::modifications::Reprotonate::is_conjugatable(), and core::chemical::GraphvizPropertyWriter::operator()().

bond_name() [1/2]

BondName core::chemical::Bond::bond_name ( ) const

inline

References bond_name_.

Referenced by Bond().

bond_name() [2/2]

void core::chemical::Bond::bond_name

(

BondName

bond_name

)

References aroma_, core::chemical::AromaticBond, bond_name_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, isometry_, core::chemical::NoBondIsometry, core::chemical::OrbitalBond, core::chemical::OrbitalBondOrder, order_, core::chemical::PseudoBond, core::chemical::PseudoBondOrder, core::chemical::SingleBond, core::chemical::SingleBondOrder, core::chemical::TripleBond, and core::chemical::TripleBondOrder.

Referenced by core::chemical::sdf::MolWriter::compose_bonds(), core::chemical::ResidueType::copy_atom_info(), core::chemical::find_chi_bonds(), core::chemical::is_sp2_proton_chi(), and core::chemical::rdkit::RestypeToRDMol::Mol().

conjugability() [1/2]

BondConjugability core::chemical::Bond::conjugability ( ) const

inline

References conjug_.

conjugability() [2/2]

void core::chemical::Bond::conjugability ( BondConjugability  conjug )

inline

References conjug_.

cut_bond() [1/2]

bool core::chemical::Bond::cut_bond ( ) const

inline

References cut_bond_.

Referenced by cut_bond().

cut_bond() [2/2]

void core::chemical::Bond::cut_bond ( bool  cut_bond )

inline

References cut_bond(), and cut_bond_.

Referenced by core::chemical::annotate_backbone(), core::chemical::ResidueType::copy_atom_info(), core::chemical::MutableResidueType::copy_atom_info(), and core::chemical::RerootEdgeSorter::operator()().

GetMaximumElectrons()

core::Size core::chemical::Bond::GetMaximumElectrons

(

)

const

References aroma_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, core::chemical::OrbitalBondOrder, order_, core::chemical::PseudoBondOrder, core::chemical::SingleBondOrder, core::chemical::TR(), core::chemical::TripleBondOrder, and core::chemical::UnknownBondOrder.

GetMinimumElectrons()

core::Size core::chemical::Bond::GetMinimumElectrons

(

)

const

References aroma_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, core::chemical::OrbitalBondOrder, order_, core::chemical::PseudoBondOrder, core::chemical::SingleBondOrder, core::chemical::TR(), core::chemical::TripleBondOrder, and core::chemical::UnknownBondOrder.

GetNumberOfElectrons()

core::Size core::chemical::Bond::GetNumberOfElectrons

(

)

const

References aroma_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, core::chemical::OrbitalBondOrder, order_, core::chemical::PseudoBondOrder, core::chemical::SingleBondOrder, core::chemical::TR(), core::chemical::TripleBondOrder, and core::chemical::UnknownBondOrder.

GetSDAltFileID()

core::Size core::chemical::Bond::GetSDAltFileID

(

)

const

References aroma_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, order_, core::chemical::SingleBondOrder, core::chemical::TR(), and core::chemical::TripleBondOrder.

GetSDFileID()

core::Size core::chemical::Bond::GetSDFileID

(

)

const

References aroma_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, core::chemical::OrbitalBondOrder, order_, core::chemical::PseudoBondOrder, core::chemical::SingleBondOrder, core::chemical::TR(), core::chemical::TripleBondOrder, and core::chemical::UnknownBondOrder.

is_fake()

bool core::chemical::Bond::is_fake ( ) const

inline

Return true if this bond represents a non-physical bond.

References core::chemical::OrbitalBondOrder, order_, and core::chemical::PseudoBondOrder.

Referenced by core::chemical::RerootEdgeSorter::operator()().

IsBondInRing()

bool core::chemical::Bond::IsBondInRing ( ) const

inline

References core::chemical::BondInRing, and ring_.

IsBondOrderKnown()

bool core::chemical::Bond::IsBondOrderKnown ( ) const

inline

References order_, and core::chemical::UnknownBondOrder.

isometry() [1/2]

BondIsometry core::chemical::Bond::isometry ( ) const

inline

References isometry_.

isometry() [2/2]

void core::chemical::Bond::isometry ( BondIsometry  isom )

inline

References isometry_.

order() [1/2]

BondOrder core::chemical::Bond::order ( ) const

inline

References order_.

Referenced by Bond(), and order().

order() [2/2]

void core::chemical::Bond::order

(

BondOrder

order

)

References aroma_, bond_name_, core::chemical::DoubleBond, core::chemical::DoubleBondOrder, core::chemical::NonaromaticBond, core::chemical::OrbitalBond, core::chemical::OrbitalBondOrder, order(), order_, core::chemical::PseudoBond, core::chemical::PseudoBondOrder, core::chemical::SingleBond, core::chemical::SingleBondOrder, core::chemical::TripleBond, and core::chemical::TripleBondOrder.

Referenced by core::chemical::modifications::Reprotonate::apply(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::find_chi_bonds(), core::chemical::modifications::Reprotonate::find_electron_sink(), core::chemical::modifications::Reprotonate::is_conjugatable(), core::chemical::rdkit::RestypeToRDMol::Mol(), and core::chemical::GraphvizPropertyWriter::operator()().

print()

void core::chemical::Bond::print

(

std::ostream &

out

)

const

References bond_name_, and core::conformation::membrane::out.

ringness() [1/2]

BondRingness core::chemical::Bond::ringness ( ) const

inline

References ring_.

ringness() [2/2]

void core::chemical::Bond::ringness ( BondRingness  ring )

inline

References ring_.

Referenced by core::chemical::complex_ring_detection(), core::chemical::ResidueType::copy_atom_info(), core::chemical::MutableResidueType::copy_atom_info(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::find_bonds_in_rings(), core::chemical::find_chi_bonds(), core::chemical::quick_ring_detection(), and core::chemical::read_topology_file().

SetSDFType()

void core::chemical::Bond::SetSDFType

(

const core::Size

SDF_ID

)

Reset the internal data such that it matches the appropriate value for the SDF datatype.

Substitution (taken from) for BCL's FindBondTypeFromSDFInfo( const std::size_t &SDF_ID)

References aroma_, core::chemical::AromaticBond, bond_name_, conjug_, core::chemical::ConjugableBond, core::chemical::DoubleBond, core::chemical::DoubleBondOrder, core::chemical::IsAromaticBond, isometry_, core::chemical::NoBondIsometry, core::chemical::NotConjugableBond, order_, ring_, core::chemical::SingleBond, core::chemical::SingleBondOrder, core::chemical::TR(), core::chemical::TripleBond, core::chemical::TripleBondOrder, core::chemical::UnknownAromaticity, core::chemical::UnknownBond, core::chemical::UnknownBondOrder, core::chemical::UnknownConjugability, core::chemical::UnknownIsometry, and core::chemical::UnknownRingness.

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  out, Bond const &  bond  )

friend

Member Data Documentation

aroma_

BondAromaticity core::chemical::Bond::aroma_

private

Is the bond in an aromatic ring? (Distinct from being conjugatable and in a ring.)

Referenced by aromaticity(), bond_name(), GetMaximumElectrons(), GetMinimumElectrons(), GetNumberOfElectrons(), GetSDAltFileID(), GetSDFileID(), order(), and SetSDFType().

bond_name_

BondName core::chemical::Bond::bond_name_

private

Referenced by aromaticity(), Bond(), bond_name(), order(), print(), and SetSDFType().

conjug_

BondConjugability core::chemical::Bond::conjug_

private

Can the bond participate in a conjugated system.

Referenced by bond_name(), conjugability(), GetMaximumElectrons(), GetMinimumElectrons(), GetNumberOfElectrons(), GetSDAltFileID(), GetSDFileID(), and SetSDFType().

cut_bond_

bool core::chemical::Bond::cut_bond_

private

Is the bond allowed to be in the atom tree?

Referenced by cut_bond().

isometry_

BondIsometry core::chemical::Bond::isometry_

private

For double bonds, what's the E/Z isometry?

Referenced by Bond(), bond_name(), isometry(), and SetSDFType().

order_

BondOrder core::chemical::Bond::order_

private

The bond order (single double triple ..)

Referenced by bond_name(), GetMaximumElectrons(), GetMinimumElectrons(), GetNumberOfElectrons(), GetSDAltFileID(), GetSDFileID(), is_fake(), IsBondOrderKnown(), order(), and SetSDFType().

ring_

BondRingness core::chemical::Bond::ring_

private

Is the bond in a ring?

Referenced by Bond(), IsBondInRing(), ringness(), and SetSDFType().

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

• src/core/chemical/Bond.hh
• src/core/chemical/Bond.cc