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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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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 |
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.
CovalentStructure | Representation of a covalent structure of a conformation. |
typedef CovalentStructure::Particle_info Particle_info |
typedef Particle_info_traits::Aliases Particle_info_aliases |
typedef Particle_info_traits::Builder Particle_info_builder |
typedef CovalentStructure::Particle_rep Particle_rep |
typedef T_Molecular_covalent_structure_builder_for_proteins<CovalentStructure> Self |
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inline |
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inline |
Adds a water molecule to the covalent structure and returns the oxygen / HOH particle.
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 |
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 |
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 |
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 |
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 |
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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.