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enum | Bond_type { SIMPLE_BOND = 1
, DOUBLE_BOND = 2
, TRIPLE_BOND = 3
} |
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typedef T_Molecular_covalent_structure< ParticleInfo > | Self |
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typedef T_Particle_info_traits< ParticleInfo > | Particle_info_traits |
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typedef Particle_info_traits::Particle_info | Particle_info |
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typedef boost::subgraph< boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Particle_info, boost::property< boost::edge_index_t, int, Bond_type > > > | Covalent_structure_graph |
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typedef boost::graph_traits< Covalent_structure_graph > | Covalent_structure_graph_traits |
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typedef Covalent_structure_graph_traits::vertex_descriptor | Particle_rep |
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typedef Covalent_structure_graph_traits::edge_descriptor | Bond_rep |
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typedef boost::tuple< Bond_rep, Bond_rep > | Bond_angle_rep |
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typedef boost::tuple< Bond_rep, Bond_rep, Bond_rep > | Torsion_angle_rep |
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typedef Covalent_structure_graph_traits::vertex_iterator | Particles_iterator_base |
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typedef boost::filter_iterator< Is_embedded, Particles_iterator_base > | Particles_iterator |
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typedef Covalent_structure_graph_traits::edge_iterator | Bonds_iterator_base |
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typedef boost::filter_iterator< Is_embedded, Bonds_iterator_base > | Bonds_iterator_filtered |
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typedef boost::transform_iterator< Make_valid, Bonds_iterator_filtered > | Bonds_iterator |
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typedef Covalent_structure_graph_traits::out_edge_iterator | Incident_bonds_iterator_base |
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typedef boost::filter_iterator< Is_embedded, Incident_bonds_iterator_base > | Incident_bonds_iterator |
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typedef boost::filter_iterator< Is_valid, Bond_angles_iterator_base > | Bond_angles_iterator |
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typedef boost::filter_iterator< Is_valid, Dihedral_angles_iterator_base > | Dihedral_angles_iterator |
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typedef std::vector< Torsion_angle_rep >::const_iterator | Improper_angles_iterator_base |
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typedef boost::filter_iterator< Is_valid, Improper_angles_iterator_base > | Improper_angles_iterator |
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const Covalent_structure_graph & | get_graph (void) const |
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Covalent_structure_graph & | get_graph (void) |
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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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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 |
| Get the (i+1)-th bond from a bond angle, with i = 0 or 1. More...
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Bond_rep | get_bond (Torsion_angle_rep b, unsigned i) const |
| Get the (i+1)-th bond from a torsion angle, with i = 0,1 or 2. More...
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Particle_rep | get_particle_rep (Bond_rep b, unsigned i) const |
| Get the (i+1)-th particle from a bond, with i = 0 or 1. More...
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Particle_rep | get_particle_rep (Bond_angle_rep b, unsigned i) const |
| Get the (i+1)-th particle from a bond angle, with i = 0,1 or 2. More...
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Particle_rep | get_particle_rep (Torsion_angle_rep b, unsigned i) const |
| Get the (i+1)-th particle from a torsion angle, with i = 0, 1, 2 or 3. More...
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std::pair< bool, Bond_rep > | get_bond_rep (Particle_rep p, Particle_rep q) const |
| Get the bond represented by the two input particles, if any. More...
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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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Bond_rep | get_canonical_rep (Bond_rep b) const |
| Return the bond such that the smallest vertex index is first. More...
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Bond_angle_rep | get_canonical_rep (Bond_angle_rep a) const |
| Return the bond angle such that the smallest vertex index is first – out of the first and third vertices. More...
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Torsion_angle_rep | get_canonical_rep (Torsion_angle_rep a) const |
| If a proper angle: second and third vertices sorted; if improper angle: central atom first, remaining three sorted. More...
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std::pair< bool, Particle_rep > | find_particle (const Particle_info &info) const |
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bool | has_model (Particle_rep p) const |
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bool | is_embedded (Particle_rep p) const |
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int | get_particle_linearPosition (Particle_rep p) const |
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template<class Conformation > |
const SBL::Models::T_Conformation_traits< Conformation >::FT & | get_x (const Conformation &C, Particle_rep p) const |
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template<class Conformation > |
SBL::Models::T_Conformation_traits< Conformation >::FT & | get_x (Conformation &C, Particle_rep p) const |
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template<class Conformation > |
const SBL::Models::T_Conformation_traits< Conformation >::FT & | get_y (const Conformation &C, Particle_rep p) const |
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template<class Conformation > |
SBL::Models::T_Conformation_traits< Conformation >::FT & | get_y (Conformation &C, Particle_rep p) const |
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template<class Conformation > |
const SBL::Models::T_Conformation_traits< Conformation >::FT & | get_z (const Conformation &C, Particle_rep p) const |
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template<class Conformation > |
SBL::Models::T_Conformation_traits< Conformation >::FT & | get_z (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 OutputIterator > |
OutputIterator | get_molecules (OutputIterator out) const |
| Computes the connected components of this graph and returns one vertex for each connected component. More...
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template<class OutputIterator > |
OutputIterator | get_particles_in_molecule (Particle_rep p, OutputIterator out) const |
| Returns the ensemble of particles in the same molecule (i.e connected component) as p. More...
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template<class InputIterator > |
Self & | get_sub_structure (InputIterator begin, InputIterator end, Self &S) |
| Builds a new covalent structure containing only the particles in the input range; note that no new copy of the information is created, and modifying the underlying graph of one covalent structure affects the other one. More...
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Self & | get_molecule (Particle_rep p, Self &S) |
| Builds a new covalent structure containing only the particles of the molecule containing p;. More...
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template<class ParticleInfo = std::string>
class SBL::CSB::T_Molecular_covalent_structure< ParticleInfo >
Representation of the covalent structure of a molecular conformation.
It uses a boost graph for encoding that covalent structure and offers the possibility to access internal and cartesian coordinates of the structure.
- 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. |