PNAB::Backbone Class Reference

Class for holding backbone information. More...

#include <Containers.h>

Public Member Functions
	Backbone ()
	Empty constructor. More...
	Backbone (std::string file_path, std::array< unsigned, 2 > interconnects, std::array< unsigned, 2 > linker, std::vector< std::vector< unsigned >> fixed_bonds={})
	Constructor for the backbone unit. More...
OpenBabel::OBAtom *	getHead ()
	Gives the pointer to an atom that is the head from Backbone::interconnects{head, tail}. More...
OpenBabel::OBAtom *	getTail ()
	Gives the pointer to an atom that is the tail from Backbone::interconnects{head, tail}. More...
OpenBabel::OBAtom *	getLinker ()
	Get the first Backbone::linker atom pointer. More...
OpenBabel::OBAtom *	getVector ()
	Get the second Backbone::linker atom pointer (which is probably a hydrogen) More...
void	center ()
	Centers the molecule. Basically just an alias of the Center() function from OpenBabel. More...
void	rotate (double *rot)
	Rotates the molecule by a matrix. Basically just an alias of the Rotate() function from OpenBabel. More...
void	translate (OpenBabel::vector3 vec)
	Translates the molecule by a vector. Basically just an alias of the Translate() function from OpenBabel. More...
OpenBabel::OBMol	getMolecule ()
	Gives a copy of the molecule in the backbone, Backbone::backbone. More...
void	deleteVectorAtom ()
	Deletes the atom from getVector() safely. If the atom is already deleted, nothing happens. More...

Public Attributes
std::array< unsigned, 2 >	interconnects
	The atom indices that define the periodic conditions between backbones { head, tail }. More...
std::array< unsigned, 2 >	linker
	The atom indices used to align and connect backbone to base in the nucleotide. More...
std::vector< std::vector< unsigned > >	fixed_bonds
	A vector containing pairs of indices defining fixed rotatable bonds during dihedral search. More...
OpenBabel::OBMol	backbone
	The molecule for the backbone. More...
std::string	file_path
	The path to the file containing the molecule. 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 atom from getVector() has been deleted. More...

Detailed Description

Class for holding backbone information.

The backbone here refers to the backbone in a single nucleotide. This class holds information on the molecular structure of the backbone and the bonds that the backbone form with the nucleobases and the adjacent backbones. This class also has functions to manipulate the backbone.

See also

BaseUnit

ConformationSearch

Constructor & Destructor Documentation

Backbone() [1/2]

PNAB::Backbone::Backbone ( )

inline

Empty constructor.

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

Backbone() [2/2]

Backbone::Backbone	(	std::string	file_path,
		std::array< unsigned, 2 >	interconnects,
		std::array< unsigned, 2 >	linker,
		std::vector< std::vector< unsigned >>	fixed_bonds = {}
	)

Constructor for the backbone unit.

Parameters

file_path	The path to the file containing the molecule.
interconnects	The atom indices that define the periodic conditions between backbones { head, tail }.
linker	The atom indices used to align and connect backbone to base in the nucleotide.
fixed_bonds	A vector containing pairs of indices defining fixed rotatable bonds during dihedral search.

Member Function Documentation

center()

void PNAB::Backbone::center ( )

inline

Centers the molecule. Basically just an alias of the Center() function from OpenBabel.

deleteVectorAtom()

void Backbone::deleteVectorAtom

(

)

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

getHead()

OpenBabel::OBAtom* PNAB::Backbone::getHead ( )

inline

Gives the pointer to an atom that is the head from Backbone::interconnects{head, tail}.

Returns

The atom pointer from the backbone OBMol object

getLinker()

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

inline

Get the first Backbone::linker atom pointer.

Returns

Pointer to the atom that is the one linking to the Base

getMolecule()

OpenBabel::OBMol PNAB::Backbone::getMolecule ( )

inline

Gives a copy of the molecule in the backbone, Backbone::backbone.

Returns

A copy of the backbone molecule

getTail()

OpenBabel::OBAtom* PNAB::Backbone::getTail ( )

inline

Gives the pointer to an atom that is the tail from Backbone::interconnects{head, tail}.

Returns

Pointer to the atom for the tail

getVector()

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

inline

Get the second Backbone::linker atom pointer (which is probably a hydrogen)

Returns

Pointer to the atom that defines the vector from the backbone to the base

rotate()

void PNAB::Backbone::rotate ( double *  rot )

inline

Rotates the molecule by a matrix. Basically just an alias of the Rotate() function from OpenBabel.

Parameters

rot	The matrix by which to rotate the molecule

translate()

void PNAB::Backbone::translate ( OpenBabel::vector3  vec )

inline

Translates the molecule by a vector. Basically just an alias of the Translate() function from OpenBabel.

Parameters

vec	The vector by which to translate the molecule

validate()

void Backbone::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

backbone

OpenBabel::OBMol PNAB::Backbone::backbone

The molecule for the backbone.

file_path

std::string PNAB::Backbone::file_path

The path to the file containing the molecule.

fixed_bonds

std::vector<std::vector<unsigned> > PNAB::Backbone::fixed_bonds

A vector containing pairs of indices defining fixed rotatable bonds during dihedral search.

interconnects

std::array<unsigned , 2> PNAB::Backbone::interconnects

The atom indices that define the periodic conditions between backbones { head, tail }.

linker

std::array<unsigned , 2> PNAB::Backbone::linker

The atom indices used to align and connect backbone to base in the nucleotide.

vector_atom_deleted

bool PNAB::Backbone::vector_atom_deleted

private

Whether or not the atom from getVector() has been deleted.

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

• Containers.h
• Containers.cpp