Optimized representation of the covalent structure of a molecular conformation.
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std::vector< Particle_info > & | get_particles () |
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unsigned | get_non_bonded_parameters_index (Particle_rep p) const |
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void | set_non_bonded_parameters_index (Particle_rep p, unsigned i) |
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std::vector< Bond_rep > & | get_bonds () |
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std::vector< std::list< Bond_rep > > & | get_incident_bonds () |
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std::vector< Bond_angle_rep > & | get_bond_angles () |
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std::vector< Torsion_angle_rep > & | get_proper_angles () |
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std::vector< Torsion_angle_rep > & | get_improper_angles () |
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std::unordered_map< std::size_t, Bond_rep > & | get_particles_to_bond_map () |
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std::unordered_map< std::size_t, Bond_angle_rep > & | get_bonds_to_bond_angle_map () |
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std::unordered_map< std::size_t, Torsion_angle_rep > & | get_bonds_to_proper_angle_map () |
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std::unordered_map< std::size_t, Torsion_angle_rep > & | get_bonds_to_improper_angle_map () |
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ParticleInfo_to_particleRep_map_type & | get_info_map () |
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std::vector< unsigned > & | get_molecules_vec (void) |
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template<class OutputIterator > |
| OutputIterator | get_molecules (OutputIterator out) |
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std::vector< unsigned > & | get_molecule_vec (void) |
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template<class OutputIterator > |
| OutputIterator | get_particles_in_molecule (std::size_t p, OutputIterator out) |
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std::vector< bool > & | get_are_12 () |
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std::vector< bool > & | get_are_13 () |
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std::vector< bool > & | get_are_14 () |
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bool | are_1_4 (const Particle_rep &p, const Particle_rep &q) const |
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bool | are_1_3 (const Particle_rep &p, const Particle_rep &q) const |
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bool | are_1_2 (const Particle_rep &p, const Particle_rep &q) const |
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unsigned | get_number_of_particles (void) const |
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unsigned | get_number_of_modeled_particles (void) const |
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unsigned | get_number_of_embedded_particles (void) const |
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bool | is_fully_embedded (void) const |
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unsigned | get_number_of_bonds (void) const |
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unsigned | get_number_of_modeled_bonds (void) const |
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unsigned | get_number_of_embedded_bonds (void) const |
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Particle_info | get_particle_info (Particle_rep p) const |
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std::pair< Particle_rep, Particle_rep > | get_particles (Bond_rep b) const |
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Bond_rep | get_bond (Bond_angle_rep b, unsigned i) const |
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Bond_rep | get_bond (Torsion_angle_rep b, unsigned i) const |
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Particle_rep | get_particle_rep (Bond_rep b, unsigned i) const |
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Particle_rep | get_particle_rep (Bond_angle_rep b, unsigned i) const |
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Particle_rep | get_particle_rep (Torsion_angle_rep b, unsigned i) const |
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std::pair< bool, Bond_rep > | get_bond_rep (Particle_rep p, Particle_rep q) const |
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Bond_rep | get_mirror_bond_rep (Bond_rep u) const |
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std::pair< bool, Bond_angle_rep > | get_bond_angle_rep (Bond_rep b_1, Bond_rep b_2) const |
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std::pair< bool, Torsion_angle_rep > | get_torsion_angle_rep (Bond_rep b_1, Bond_rep b_2, Bond_rep b_3) const |
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std::pair< bool, Particle_rep > | find_particle (const Particle_info &info) const |
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int | get_particle_linearPosition (Particle_rep p) const |
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template<class Conformation > |
| SBL::CSB::T_Conformation_traits< Conformation >::FT | get_x (const Conformation &C, Particle_rep p) const |
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template<class Conformation > |
| SBL::CSB::T_Conformation_traits< Conformation >::FT | get_y (const Conformation &C, Particle_rep p) const |
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template<class Conformation > |
| SBL::CSB::T_Conformation_traits< Conformation >::FT | get_z (const Conformation &C, Particle_rep p) const |
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Particles_iterator | particles_begin (bool is_embedded=true) const |
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Particles_iterator | particles_end (bool is_embedded=true) const |
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Bonds_iterator | bonds_begin (bool is_embedded=true) const |
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Bonds_iterator | bonds_end (bool is_embedded=true) const |
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Incident_bonds_iterator | incident_bonds_begin (Particle_rep p, bool is_embedded=true) const |
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Incident_bonds_iterator | incident_bonds_end (Particle_rep p, bool is_embedded=true) const |
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| Bond_angles_iterator | bond_angles_begin (bool is_embedded=true) const |
| | Iterate over the bond angles (u, v, w) so that u and v are the largest indices lower than w such that (u, v) and (v, w) are bonds. More...
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| Bond_angles_iterator | bond_angles_end (bool is_embedded=true) const |
| | Iterate over the bond angles (u, v, w) so that u and v are the largest indices lower than w such that (u, v) and (v, w) are bonds. More...
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| Dihedral_angles_iterator | dihedral_angles_begin (bool is_embedded=true) const |
| | Iterate over the torsion angles (u, v, w, t) so that u, v and w are the largest indices lower than t such that (u, v), (v, w) and (w, t) are bonds. More...
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| Dihedral_angles_iterator | dihedral_angles_end (bool is_embedded=true) const |
| | Iterate over the torsion angles (u, v, w, t) so that u, v and w are the largest indices lower than t such that (u, v), (v, w) and (w, t) are bonds. More...
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| Improper_angles_iterator | improper_angles_begin (bool is_embedded=true) const |
| | Iterate over the torsion angles (u, v, w, t) so that (u, v), (u, w) and (u, t) are bonds. More...
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| Improper_angles_iterator | improper_angles_end (bool is_embedded=true) const |
| | Iterate over the torsion angles (u, v, w, t) so that (u, v), (u, w) and (u, t) are bonds. More...
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template<class ParticleInfo = std::string>
class SBL::CSB::T_Molecular_covalent_structure_optimal< ParticleInfo >
Optimized representation of the covalent structure of a molecular conformation.
ASK Augustin
- Template Parameters
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| ParticleInfo | Information to attached to the particle (default is a simple string). It should be comparable (less operator) and streamable. |
1.9.1