PAPRECA::PredefinedBondForm Class Reference

child class of PAPRECA::PredefinedReaction associated with bond formation events. This is a Predefined template for PAPRECA::BondForm events. More...

#include <event_list.h>

Inheritance diagram for PAPRECA::PredefinedBondForm:

Collaboration diagram for PAPRECA::PredefinedBondForm:

Public Member Functions
	PredefinedBondForm (const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in, const double &bond_dist_sqr_in, const int &delete_atoms_in, const int &lone_candidates_in, const bool &same_mol_in)
	PredefinedBondForm (const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in, const double &bond_dist_sqr_in, const int &delete_atoms_in, const int &lone_candidates_in, const bool &same_mol_in, const std::vector< int > &catalyzing_types_in)
	~PredefinedBondForm ()
const double &	getBondDistSqr () const
const bool &	isSameMol () const
const int &	isDeleteAtoms () const
const int &	isLone () const
Public Member Functions inherited from PAPRECA::PredefinedReaction
	PredefinedReaction (const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in)
	PredefinedReaction (const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in, const std::vector< int > &catalyzing_types_in)
	~PredefinedReaction ()
const int &	getAtom1Type () const
const int &	getAtom2Type () const
const int &	getBondType () const
const double &	getRate () const
const std::vector< int > &	getCatalyzingTypes () const
const bool &	isForm () const

Protected Attributes
double	bond_dist_sqr = 0.0
	if the distance between atom1 and atom2 is less than or equal to bond_dist then the formation event is valid. More...
bool	same_mol = false
	if true, then bond formation can occur even if the molecule IDs of atom1 and atom2 are the same. More...
int	delete_atoms = 0
	if delete_atoms=1, then atom1 and atom2 are deleted after the formation event. This variable is "technically boolean" but defined as an int to facilitate the communication of data among MPI processes (MPI_INT is supported by the MPI protocol). More...
int	lone_candidates = 0
	Lones are atoms without any bonds. If line_candidates=true, then both atom1 and atom2 have to be "lone". Otherwise, the formation event is invalid. More...
Protected Attributes inherited from PAPRECA::PredefinedReaction
int	atom1_type = -1
int	atom2_type = -2
int	bond_type = -3
double	rate = 0.0
std::vector< int >	catalyzing_types
	these types of atoms have to be present in the neighborhood of atom1 or atom2. Otherwise, the reaction event is invalid. If the catalyzing_types vector is empty, the neighborhood of atom1 and atom2 is not scanned for catalyzing types. More...
bool	is_form = false
	this variable allows us to differentiate between the parent class PAPRECA::PredefinedReaction and the child class PAPRECA::PredefinedBondForm More...

Detailed Description

child class of PAPRECA::PredefinedReaction associated with bond formation events. This is a Predefined template for PAPRECA::BondForm events.

Constructor & Destructor Documentation

PredefinedBondForm() [1/2]

PAPRECA::PredefinedBondForm::PredefinedBondForm	(	const int &	atom1_type_in,
		const int &	atom2_type_in,
		const int &	bond_type_in,
		const double &	rate_in,
		const double &	bond_dist_sqr_in,
		const int &	delete_atoms_in,
		const int &	lone_candidates_in,
		const bool &	same_mol_in
	)

PredefinedBondForm() [2/2]

PAPRECA::PredefinedBondForm::PredefinedBondForm	(	const int &	atom1_type_in,
		const int &	atom2_type_in,
		const int &	bond_type_in,
		const double &	rate_in,
		const double &	bond_dist_sqr_in,
		const int &	delete_atoms_in,
		const int &	lone_candidates_in,
		const bool &	same_mol_in,
		const std::vector< int > &	catalyzing_types_in
	)

~PredefinedBondForm()

PAPRECA::PredefinedBondForm::~PredefinedBondForm

(

)

Member Function Documentation

getBondDistSqr()

const double & PAPRECA::PredefinedBondForm::getBondDistSqr

(

)

const

isDeleteAtoms()

const int & PAPRECA::PredefinedBondForm::isDeleteAtoms

(

)

const

isLone()

const int & PAPRECA::PredefinedBondForm::isLone

(

)

const

isSameMol()

const bool & PAPRECA::PredefinedBondForm::isSameMol

(

)

const

Member Data Documentation

bond_dist_sqr

double PAPRECA::PredefinedBondForm::bond_dist_sqr = 0.0

protected

if the distance between atom1 and atom2 is less than or equal to bond_dist then the formation event is valid.

delete_atoms

int PAPRECA::PredefinedBondForm::delete_atoms = 0

protected

if delete_atoms=1, then atom1 and atom2 are deleted after the formation event. This variable is "technically boolean" but defined as an int to facilitate the communication of data among MPI processes (MPI_INT is supported by the MPI protocol).

lone_candidates

int PAPRECA::PredefinedBondForm::lone_candidates = 0

protected

Lones are atoms without any bonds. If line_candidates=true, then both atom1 and atom2 have to be "lone". Otherwise, the formation event is invalid.

same_mol

bool PAPRECA::PredefinedBondForm::same_mol = false

protected

if true, then bond formation can occur even if the molecule IDs of atom1 and atom2 are the same.

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

• event_list.h
• event_list.cpp