stormm::structure::MdlMolBond Class Reference

A bond, as presented in the MDL molecule file format. This unguarded struct will be returned to the developer from a private array inside of the MdlMolObj object, so further protection would be a hindrance. More...

#include <mdlmol_bond.h>

Public Member Functions
int	getFirstAtom () const
	Get the first atom in the bond. Having separate functions for each atom is a more intuitive way to offer the getter functions, whereas in a BoundedRestraint object the atom index getter takes an argument for the first, second, third, or fourth atom.
int	getSecondAtom () const
	Get the second atom in the bond.
MdlMolBondOrder	getOrder () const
	Get the order of the bond.
MdlMolBondStereo	getStereochemistry () const
	Get the order of the bond.
MolObjRingState	getRingStatus () const
	Get the ring status–is the bond known to be part of a ring?
MolObjReactionCenter	getReactivity () const
	Get the reactive potential of the bond.
void	setFirstAtom (int index_in)
	Set the index of the first atom in the bond.
void	setSecondAtom (int index_in)
	Set the index of the second atom in the bond.
void	setOrder (MdlMolBondOrder order_in)
	Set the order of the bond, perhaps after computations with an associated ChemicalFeatures object.
void	setStereochemistry (MdlMolBondStereo stereo_in)
	Set the stereochemical details of the bond.
void	setRingStatus (MolObjRingState status_in)
	Mark the status of the bond with respect to any ring features.
void	setReactivity (MolObjReactionCenter potential_in)
	Mark the reactive potential of the bond.
	MdlMolBond ()
	The constructor can take all member variables, or just the atoms so that more information can be filled in later.
	MdlMolBond (int i_atom_in, int j_atom_in)
	MdlMolBond (int i_atom_in, int j_atom_in, MdlMolBondOrder order_in, MdlMolBondStereo stereo_in, MolObjRingState ring_state_in, MolObjReactionCenter reactivity_in)
	MdlMolBond (const TextFile &tf, int line_number, const std::string &title=std::string(""))
	MdlMolBond (const MdlMolBond &original)=default
	The default copy and move constructors as well as assignment operators are adequate.
	MdlMolBond (MdlMolBond &&original)=default
MdlMolBond &	operator= (const MdlMolBond &other)=default
MdlMolBond &	operator= (MdlMolBond &&other)=default

Detailed Description

A bond, as presented in the MDL molecule file format. This unguarded struct will be returned to the developer from a private array inside of the MdlMolObj object, so further protection would be a hindrance.

Constructor & Destructor Documentation

MdlMolBond()

stormm::structure::MdlMolBond::MdlMolBond

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The constructor can take all member variables, or just the atoms so that more information can be filled in later.

Overloaded:

• Construct a blank object with -1 atom indices to indicate its invalid nature
• Construct an object with just the atom indices
• Construct a complete object with all details pre-loaded
• Construct the object based on text input of trusted bounds

Parameters

tf	Text of the original .sdf or .mol file, read into RAM
line_number	Number of the line on which to read the data
title	The title of the structure, if known, for error tracing purposes

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

• src/MoleculeFormat/mdlmol_bond.h
• src/MoleculeFormat/mdlmol_bond.cpp