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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...


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

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

References bond_name().

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

Member Function Documentation

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

References aroma_.

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

References bond_name_.

Referenced by Bond().

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

References conjug_.

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

References conjug_.

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

References cut_bond_.

Referenced by cut_bond().

core::Size core::chemical::Bond::GetMaximumElectrons ( ) const
core::Size core::chemical::Bond::GetMinimumElectrons ( ) const
core::Size core::chemical::Bond::GetNumberOfElectrons ( ) const
core::Size core::chemical::Bond::GetSDAltFileID ( ) const
core::Size core::chemical::Bond::GetSDFileID ( ) const
bool core::chemical::Bond::is_fake ( ) const

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()().

bool core::chemical::Bond::IsBondInRing ( ) const
bool core::chemical::Bond::IsBondOrderKnown ( ) const
void core::chemical::Bond::isometry ( BondIsometry  isom)

References isometry_.

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

References isometry_.

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

References order_.

Referenced by order().

void core::chemical::Bond::print ( std::ostream &  out) const

References bond_name_.

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

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

References ring_.

void core::chemical::Bond::SetSDFType ( const core::Size  SDF_ID)

Friends And Related Function Documentation

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

Member Data Documentation

BondAromaticity core::chemical::Bond::aroma_

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().

BondName core::chemical::Bond::bond_name_
BondConjugability core::chemical::Bond::conjug_
bool core::chemical::Bond::cut_bond_

Is the bond allowed to be in the atom tree?

Referenced by cut_bond().

BondIsometry core::chemical::Bond::isometry_

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

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

BondOrder core::chemical::Bond::order_
BondRingness core::chemical::Bond::ring_

Is the bond in a ring?

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

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