Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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_infoParticle_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_repmake_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_repmake_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_repmake_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_repmake_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
CovalentStructureRepresentation 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

◆ Particle_rep

typedef CovalentStructure::Particle_rep Particle_rep

◆ 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.