T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure > Class Template Reference

Builds a covalent structure from a given structure. More...

#include <Molecular_covalent_structure_builder_for_proteins.hpp>

Public Types
typedef T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >	Self
typedef CovalentStructure::Particle_info	Particle_info
typedef T_Particle_info_traits< Particle_info >	Particle_info_traits
typedef Particle_info_traits::Aliases	Particle_info_aliases
typedef Particle_info_traits::Builder	Particle_info_builder
typedef CovalentStructure::Particle_rep	Particle_rep

Public Member Functions
	T_Molecular_covalent_structure_builder_for_proteins (unsigned coarse_level=0, double max_bond_distance=3)
template<class Structure >
bool	operator() (Structure &structure, CovalentStructure &S) const
template<class Residue >
Particle_rep	add_water (Residue &residue, CovalentStructure &S) const
template<class Residue >
std::pair< bool, typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep >	make_atom (Residue &residue, CovalentStructure &S, const char *atom_names[], int k, int ter) const
template<class Residue >
std::pair< bool, typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep >	make_atom (Residue &residue, CovalentStructure &S, const std::string &atom_name, int ter) const
template<class Residue >
std::pair< std::size_t, std::pair< typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep, typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep > >	make_backbone (Residue &residue, CovalentStructure &S, Particle_rep &c_alpha, int ter) const
template<class Residue >
std::pair< typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep, typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep >	make_martini (Residue &residue, CovalentStructure &S, bool &b) const
template<class Residue >
std::pair< typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep, typename T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep >	make_residue (Residue &residue, CovalentStructure &S, bool &b) const

Detailed Description

template<class CovalentStructure>
class SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >

Builds a covalent structure from a given structure.

Builds a covalent structure from a given structure. It can handle different level of coarse graining, where vertices may represent any atom, heavy atom or residues. The input is a map from chain identifiers to list of pairs (res_id, res_name) representing the residues.

Template Parameters

CovalentStructure

Representation of a covalent structure of a conformation.

Member Typedef Documentation

Particle_info

typedef CovalentStructure::Particle_info Particle_info

Particle_info_aliases

typedef Particle_info_traits::Aliases Particle_info_aliases

Particle_info_builder

typedef Particle_info_traits::Builder Particle_info_builder

Particle_info_traits

typedef T_Particle_info_traits<Particle_info> Particle_info_traits

Particle_rep

typedef CovalentStructure::Particle_rep Particle_rep

Self

typedef T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure> Self

Constructor & Destructor Documentation

T_Molecular_covalent_structure_builder_for_proteins()

T_Molecular_covalent_structure_builder_for_proteins ( unsigned  coarse_level = 0, double  max_bond_distance = 3  )

inline

Member Function Documentation

add_water()

T_Molecular_covalent_structure_builder_for_proteins< CovalentStructure >::Particle_rep add_water ( Residue &  residue, CovalentStructure &  S  ) const

inline

Adds a water molecule to the covalent structure and returns the oxygen / HOH particle.

make_atom() [1/2]

std::pair<bool, typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep> make_atom	(	Residue &	residue,
		CovalentStructure &	S,
		const char *	atom_names[],
		int	k,
		int	ter
	)		const

make_atom() [2/2]

std::pair<bool, typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep> make_atom	(	Residue &	residue,
		CovalentStructure &	S,
		const std::string &	atom_name,
		int	ter
	)		const

make_backbone()

std::pair<std::size_t, std::pair<typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep, typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep> > make_backbone	(	Residue &	residue,
		CovalentStructure &	S,
		Particle_rep &	c_alpha,
		int	ter
	)		const

make_martini()

std::pair<typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep, typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep> make_martini	(	Residue &	residue,
		CovalentStructure &	S,
		bool &	b
	)		const

make_residue()

std::pair<typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep, typename T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure>::Particle_rep> make_residue	(	Residue &	residue,
		CovalentStructure &	S,
		bool &	b
	)		const

operator()()

bool operator() ( Structure &  structure, CovalentStructure &  S  ) const

inline

Builds the covalent structure from a structure, that is a map from chain ids to a collection of residues, them selves represented by pairs of id / name.