#include <residue.h>

Public Member Functions
	Residue (ResidueType const &rtype, String const &name, int const &num, String const &chain_id, String const &i_code)

	Residue (Residue const &r)

	Residue (String const &s, ResidueTypeSet const &rts)

	~Residue ()

void	setup_atoms (AtomOPs &)

AtomOP const &	get_atom (String const &name) const

int	connected_to (Residue const &res, float cutoff=3.0) const

void	new_uuid ()

Beads	get_beads () const

String	to_str () const

String	to_pdb_str (int &acount)

String	to_pdb_str (int &, int, String const &) const

void	to_pdb (String const)

bool	operator== (const Residue &r) const

void	num (int nnum)

void	chain_id (String const &nchain_id)

void	uuid (Uuid const &uuid)

String const &	name () const

String const &	chain_id () const

String const &	i_code () const

int const &	num () const

String const &	short_name () const

AtomOPs const &	atoms () const

Uuid const &	uuid () const

Detailed Description

Store residue information from pdb file, stores all Atom objects that belong to residue. Implementation is designed to be extremely lightweight.

To get an example instance of Residue please include:
#include "instances/structure_instances.hpp"

Example of Common Usage:

//grabbing example instance
#include "instances/structure_instances.hpp"
auto r = instances::residue();
//simply getting name of residue, etc: A,G,C or U
std::cout << r->name() << std::endl; //OUTPUT: "G"
//getting a specific atom from residue
auto a = r->get_atom("C1'");
std::cout << a->coords() << std::endl; //OUTPUT: "-23.806 -50.289  86.732"
auto beads = r->get_beads();
std::cout << beads[0]->btype() << " " << beads[0]->center() << std::endl;
//OUTPUT: "1 24.027 -48.5001111111 86.368"
//get PDB formatted String (can also write to file with r->to_pdb("test.pdb") )
std::cout << r->to_pdb_str() << std::endl; //OUTPUT -->
ATOM      1 O5'  G   A 103     -26.469 -47.756  84.669  1.00  0.00
ATOM      2 C5'  G   A 103     -25.050 -47.579  84.775  1.00  0.00
ATOM      3 C4'  G   A 103     -24.521 -48.156  86.068  1.00  0.00
ATOM      4 O4'  G   A 103     -24.861 -49.568  86.118  1.00  0.00
ATOM      5 C3'  G   A 103     -23.009 -48.119  86.281  1.00  0.00
ATOM      6 O3'  G   A 103     -22.548 -46.872  86.808  1.00  0.00
.
.
.

Constructor & Destructor Documentation

Residue::Residue	(	ResidueType const &	rtype,
		String const &	name,
		int const &	num,
		String const &	chain_id,
		String const &	i_code
	)

inline

Standard constructor for Bead object.

Parameters

rtype	residue type, dictates residue topology and information
name	name of residue i.e. "GUA", "CYT", etc
num	residue num
chain_id	the id of the chain i.e. "A", "B", only one character
i_code	residue insertion code, usually nothing ("")

Residue::Residue ( Residue const & r )

inline

Copy constructor

Parameters

r	Residue object copying from

Residue::Residue	(	String const &	s,
		ResidueTypeSet const &	rts
	)

inline

Construction from String, used in reading data from files

Parameters

s	string generated from to_str()

See also: to_str()

Residue::~Residue ( )

inline

Empty deconstructor

Member Function Documentation

AtomOPs const& Residue::atoms ( ) const

inline

getter for the internal atom vector

void Residue::chain_id ( String const & nchain_id )

inline

setter for nchain id

Parameters

chain_id new chain id

String const& Residue::chain_id ( ) const

inline

getter the chain_id

int Residue::connected_to	(	Residue const &	res,
		float	cutoff = `3.0`
	)		const

inline

Determine if another residue is connected to this residue, returns 0 if res is not connected to self, returns 1 if connection is going from 5' to 3' and returns -1 if connection is going from 3' to 5'

Parameters

res	another residue
cutoff	distance to be considered connected, default: 3 Angstroms

AtomOP const& Residue::get_atom ( String const & name ) const

inline

get atom object by its name

Parameters

name	name of atom

examples:

auto a = r->get_atom("C1'");
std::cout << a->coords() << std::endl;
//OUTPUT -23.806 -50.289  86.732

Beads Residue::get_beads ( ) const

Generates steric beads required for checking for steric clashes between motifs. Each residues has three beads modeled after the typical three bead models used in coarse grain modeling. The three beads are:

#include "instances/structure_instances.hpp"
auto r = instances::residue();
auto beads = r->get_beads();
//Test instance is the first residue in a chain with no phosphate so it has 
//only two beads
std::cout << beads.size() << std::endl;
//OUTPUT 2
std::cout << beads[0].btype() == BeadType::SUGAR << std::endl;
//OUTPUT 1

String const& Residue::i_code ( ) const

inline

getter for the residue insertion code

String const& Residue::name ( ) const

inline

getter for the name of the residue, i.e. "A", "G" etc

void Residue::new_uuid ( )

inline

give residue a new unique indentifier code. There is probably no reason why you should call this unless writing a new, motif structure.

void Residue::num ( int nnum )

inline

setter for residue num

Parameters

nnum	new residue num

int const& Residue::num ( ) const

inline

getter for the residue num

bool Residue::operator== ( const Residue & r ) const

inline

equal operator checks whether the unique indentifier is the same

Parameters

r	another residue to check if its the same

void Residue::setup_atoms ( AtomOPs & atoms )

put atoms in correct positon in internal atom list, also corrects some named atom names to their correct name

Parameters

atoms list of atom objects that are to be part of this residue

String const& Residue::short_name ( ) const

inline

getter for the one letter residue type

void Residue::to_pdb ( String const fname )

writes a PDB string formmated verision of this Residue object to file

Parameters

filename of output PDB file

String Residue::to_pdb_str ( int & acount )

inline

wrapper for to_pdb_str(int &, int, String const &) when one does not care about renumbering atoms and residue

String Residue::to_pdb_str	(	int &	acount,
		int	rnum,
		String const &	chain_id
	)		const

returns pdb formatted string of residue's coordinate information

Parameters

acount	current atom index, default: 1
rnum	starting residue number
chain_id	the chain id of the chain, i.e. "A", "B" etc #include "instances/structure_instances.hpp" auto r = instances::residue(); //get PDB formatted String (can also write to file with r->to_pdb("test.pdb") ) std::cout << r->to_pdb_str() << std::endl; //OUTPUT --> ATOM 1 O5' G A 103 -26.469 -47.756 84.669 1.00 0.00 ATOM 2 C5' G A 103 -25.050 -47.579 84.775 1.00 0.00 ATOM 3 C4' G A 103 -24.521 -48.156 86.068 1.00 0.00 ATOM 4 O4' G A 103 -24.861 -49.568 86.118 1.00 0.00 ATOM 5 C3' G A 103 -23.009 -48.119 86.281 1.00 0.00 ATOM 6 O3' G A 103 -22.548 -46.872 86.808 1.00 0.00 . . .

String Residue::to_str ( ) const

stringifes residue object

#include "instances/structure_instances.hpp"
auto r = instances::residue();
std::cout << r->to_str() << std::endl;
//OUTPUT 
GUA,G,103,A,,N,N,N,O5' -26.469 -47.756 84.669,C5' -25.05 -47.579 84.775,C4' -24.521 -48.156 
86.068,O4' -24.861 -49.568 86.118,C3' -23.009 -48.119 86.281,O3' -22.548 -46.872 86.808,C1'
-23.806 -50.289 86.732,C2' -22.812 -49.259 87.269,O2' -23.167 -48.903 88.592,N1 -19.538 -52.485 
85.025,C2 -19.717 -51.643 86.097,N2 -18.624 -51.354 86.809,N3 -20.884 -51.124 86.445,C4 -21.881
-51.521 85.623,C5 -21.811 -52.356 84.527,C6 -20.546 -52.91 84.164,O6 -20.273 -53.677 83.228,N7 
-23.063 -52.513 83.947,C8 -23.858 -51.786 84.686,N9 -23.21 -51.159 85.722,

void Residue::uuid ( Uuid const & uuid )

inline

setter for the residue unique indentifier, do not do this without really knowing what you are doing

Parameters

uuid	new residue unique indentifier

Uuid const& Residue::uuid ( ) const

inline

getter for residue unique indentifier

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

src/structure/residue.h
src/structure/residue.cc

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation