PNAB::Base Class Reference

Class to fully define bases (i.e. Adenine, Cytosine) More...

#include <Containers.h>

Public Member Functions
	Base ()
	Empty constructor. More...
	Base (std::string name, std::string code, std::string file_path, std::array< std::size_t, 2 > linker, std::string pair_name="")
	Create Base from basic set of parameters. More...
OpenBabel::OBAtom *	getLinker ()
	Gives the atom of the base that connects directly to the backbone, Base::linker[0]. More...
OpenBabel::OBAtom *	getVector ()
	Gives the (most likely hydrogen) atom of the base connected to the atom from getLinker() which defines how the base connects, Base::linker[1]. More...
OpenBabel::OBMol	getMolecule ()
	Returns a copy of the base molecule, Base::base. More...
std::string	getCode ()
	Gives the three-letter code of the base, Base::code. More...
std::string	getName ()
	Gives the full name of the base, Base::name. More...
void	deleteVectorAtom ()
	Deletes the atom from getVector() safely. If the atom is already deleted, nothing happens. More...
std::string	getBasePairName ()
	Get the name of the pair base, Base::pair_name. More...

Public Attributes
std::string	name
	Full name of base (i.e. "Adenine" or just "A") More...
std::string	code
	Three character code to define base ("Adenine": "ADE") More...
std::string	pair_name
	Name of the pair base. More...
std::string	file_path
	Path to a file containing the base. More...
OpenBabel::OBMol	base
	The OBMol defining the base. More...
std::array< std::size_t, 2 >	linker
	Holds indices for atoms forming a vector to connect to backbone {linker, hydrogen}. More...

Private Member Functions
void	validate ()
	Does some basic sanity checks (such as whether or not the indices of the atom are within the range of the molecule). More...

Private Attributes
bool	vector_atom_deleted
	Whether or not the getVector() atom was deleted. More...

Detailed Description

Class to fully define bases (i.e. Adenine, Cytosine)

This class holds information on the molecular structure of one nucleobase and the bond that it should form with the backbone. This class also has functions to manipulate the nucleobase and gets information about it.

See also

Bases

BaseUnit

Constructor & Destructor Documentation

Base() [1/2]

PNAB::Base::Base ( )

inline

Empty constructor.

This empty constructor can be used. After that, values for the member variables should be specified.

Base() [2/2]

Base::Base	(	std::string	name,
		std::string	code,
		std::string	file_path,
		std::array< std::size_t, 2 >	linker,
		std::string	pair_name = ""
	)

Create Base from basic set of parameters.

Parameters

name	name of the base
code	three-letter code
file_path	path to the backbone file
linker	indices for atoms forming the vector connecting to the backbone
pair_name	Name of the pairing base

Member Function Documentation

deleteVectorAtom()

void PNAB::Base::deleteVectorAtom ( )

inline

Deletes the atom from getVector() safely. If the atom is already deleted, nothing happens.

getBasePairName()

std::string PNAB::Base::getBasePairName ( )

inline

Get the name of the pair base, Base::pair_name.

Returns

Pair name

getCode()

std::string PNAB::Base::getCode ( )

inline

Gives the three-letter code of the base, Base::code.

Returns

The code of the base

getLinker()

OpenBabel::OBAtom* PNAB::Base::getLinker ( )

inline

Gives the atom of the base that connects directly to the backbone, Base::linker[0].

Returns

A pointer to the atom that connects to the backbone

getMolecule()

OpenBabel::OBMol PNAB::Base::getMolecule ( )

inline

Returns a copy of the base molecule, Base::base.

Returns

A copy of the base molecule

getName()

std::string PNAB::Base::getName ( )

inline

Gives the full name of the base, Base::name.

Returns

The full name of the base

getVector()

OpenBabel::OBAtom* PNAB::Base::getVector ( )

inline

Gives the (most likely hydrogen) atom of the base connected to the atom from getLinker() which defines how the base connects, Base::linker[1].

Returns

A pointer to the atom forming the vector connecting to the backbone

validate()

void Base::validate ( )

private

Does some basic sanity checks (such as whether or not the indices of the atom are within the range of the molecule).

Member Data Documentation

base

OpenBabel::OBMol PNAB::Base::base

The OBMol defining the base.

code

std::string PNAB::Base::code

Three character code to define base ("Adenine": "ADE")

file_path

std::string PNAB::Base::file_path

Path to a file containing the base.

linker

std::array<std::size_t, 2 > PNAB::Base::linker

Holds indices for atoms forming a vector to connect to backbone {linker, hydrogen}.

name

std::string PNAB::Base::name

Full name of base (i.e. "Adenine" or just "A")

pair_name

std::string PNAB::Base::pair_name

Name of the pair base.

vector_atom_deleted

bool PNAB::Base::vector_atom_deleted

private

Whether or not the getVector() atom was deleted.

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

• Containers.h
• Containers.cpp