PNAB::BaseUnit Class Reference

Class to hold bases with backbones attached (nucleotides), along with associated necessary information. More...

#include <Containers.h>

Public Member Functions
	BaseUnit (Base b, Backbone backbone, double glycosidic_bond_distance=0.0)
	BaseUnit ()
	Empty constructor. More...
const OpenBabel::OBMol	getMol ()
	Returns the nucleotide molecule, BaseUnit::unit. More...
const std::array< std::size_t, 2 >	getBaseIndexRange ()
	Returns the indices for the begining and end of the nucleobase atom indices, BaseUnit::base_index_range. More...
const std::array< std::size_t, 2 >	getBackboneIndexRange ()
	Returns the indices for the begining and end of the backbone atom indices, BaseUnit::backbone_index_range. More...
const std::array< std::size_t, 2 >	getBackboneLinkers ()
	Returns the indices for atoms where the backbone connects, BaseUnit::backbone_interconnects. More...
std::size_t	getBaseConnectIndex ()
	Returns the index of the atom where the nucleobase connects to the backbone, BaseUnit::base_connect_index. More...
std::vector< std::vector< unsigned > >	getFixedBonds ()
	Returns a vector of the pair of indices for fixed rotatable dihedrals in the backbone, BaseUnit::fixed_bonds. More...

Private Attributes
OpenBabel::OBMol	unit
	Holds molecule containing base with backbone attached. More...
std::array< std::size_t, 2 >	base_index_range
	Range of indices of the unit that are a part of the base, [start, stop]. More...
std::array< std::size_t, 2 >	backbone_index_range
	Range of indices of the unit that are a part of the backbone, [start, stop]. More...
std::size_t	base_connect_index
	Atom index where backbone connects to base (the base atom) More...
std::array< std::size_t, 2 >	backbone_interconnects
	Atom indices defining where backbone connects. More...
std::vector< std::vector< unsigned > >	fixed_bonds
	Indices of fixed bonds in dihedral search. More...

Detailed Description

Class to hold bases with backbones attached (nucleotides), along with associated necessary information.

See also

Base

Backbone

Chain::setupChain

ConformationSearch

Constructor & Destructor Documentation

BaseUnit() [1/2]

BaseUnit::BaseUnit	(	Base	b,
		Backbone	backbone,
		double	glycosidic_bond_distance = 0.0
	)

Constructor for the base unit

Parameters

b	Base instance
backbone	Backbone instance
glycosidic_bond_distance	The glycosidic bond distance. If zero (default), set it by using the van der Waals radii

BaseUnit() [2/2]

PNAB::BaseUnit::BaseUnit ( )

inline

Empty constructor.

Member Function Documentation

getBackboneIndexRange()

const std::array< std::size_t, 2 > PNAB::BaseUnit::getBackboneIndexRange ( )

inline

Returns the indices for the begining and end of the backbone atom indices, BaseUnit::backbone_index_range.

Returns

The indices for the limits of the backbone

getBackboneLinkers()

const std::array< std::size_t, 2 > PNAB::BaseUnit::getBackboneLinkers ( )

inline

Returns the indices for atoms where the backbone connects, BaseUnit::backbone_interconnects.

Returns

The indices for atoms where the backbone connects

getBaseConnectIndex()

std::size_t PNAB::BaseUnit::getBaseConnectIndex ( )

inline

Returns the index of the atom where the nucleobase connects to the backbone, BaseUnit::base_connect_index.

Returns

The nucleobase index connecting to the backbone

getBaseIndexRange()

const std::array< std::size_t, 2 > PNAB::BaseUnit::getBaseIndexRange ( )

inline

Returns the indices for the begining and end of the nucleobase atom indices, BaseUnit::base_index_range.

Returns

The indices for the limits of the nucleobases

getFixedBonds()

std::vector<std::vector<unsigned> > PNAB::BaseUnit::getFixedBonds ( )

inline

Returns a vector of the pair of indices for fixed rotatable dihedrals in the backbone, BaseUnit::fixed_bonds.

Returns

The indices of the fixed rotatable dihedrals

getMol()

const OpenBabel::OBMol PNAB::BaseUnit::getMol ( )

inline

Returns the nucleotide molecule, BaseUnit::unit.

Returns

The nucleotide molecule

Member Data Documentation

backbone_index_range

std::array< std::size_t, 2 > PNAB::BaseUnit::backbone_index_range

private

Range of indices of the unit that are a part of the backbone, [start, stop].

backbone_interconnects

std::array< std::size_t, 2 > PNAB::BaseUnit::backbone_interconnects

private

Atom indices defining where backbone connects.

base_connect_index

std::size_t PNAB::BaseUnit::base_connect_index

private

Atom index where backbone connects to base (the base atom)

base_index_range

std::array< std::size_t, 2 > PNAB::BaseUnit::base_index_range

private

Range of indices of the unit that are a part of the base, [start, stop].

fixed_bonds

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

private

Indices of fixed bonds in dihedral search.

unit

OpenBabel::OBMol PNAB::BaseUnit::unit

private

Holds molecule containing base with backbone attached.

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

• Containers.h
• Containers.cpp