atom Struct Reference

#include <atom.h>

Inheritance diagram for atom:

Collaboration diagram for atom:

Public Types
enum	t { EL, AD, XS, SY }

Public Member Functions
	atom ()
sz	get (t atom_typing_used) const
bool	is_hydrogen () const
bool	is_heteroatom () const
bool	acceptable_type () const
void	assign_el ()
bool	same_element (const atom_type &a) const
fl	covalent_radius () const
fl	optimal_covalent_bond_length (const atom_type &x) const

Public Attributes
vec	coords
std::vector< bond >	bonds
fl	charge
sz	el
sz	ad
sz	xs
sz	sy

Private Member Functions
template<class Archive >
void	serialize (Archive &ar, const unsigned version)

Friends
class	boost::serialization::access

Member Enumeration Documentation

enum atom_type::t

inherited

Enumerator:

EL
AD
XS
SY

Constructor & Destructor Documentation

atom::atom ( )

inline

Member Function Documentation

template<class Archive >

void atom::serialize ( Archive &  ar, const unsigned  version  )

inlineprivate

References bonds, and coords.

sz atom_type::get ( t  atom_typing_used ) const

inlineinherited

References atom_type::AD, atom_type::ad, atom_type::EL, atom_type::el, max_sz, atom_type::SY, atom_type::sy, atom_type::XS, and atom_type::xs.

Referenced by model::append(), naive_non_cache::eval(), non_cache::eval(), cache::eval(), usable::eval(), non_cache::eval_deriv(), cache::eval_deriv(), model::eval_intramolecular(), terms::evale_robust(), model::get_movable_atom_types(), get_type_pair_index(), cache::populate(), and szv_grid::szv_grid().

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bool atom_type::is_hydrogen ( ) const

inlineinherited

References atom_type::ad, and ad_is_hydrogen().

Referenced by conf_independent_inputs::atom_rotors(), conf_independent_inputs::num_bonded_heavy_atoms(), and model::rmsd_lower_bound_asymmetric().

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bool atom_type::is_heteroatom ( ) const

inlineinherited

References atom_type::ad, ad_is_heteroatom(), atom_type::xs, and XS_TYPE_Met_D.

Referenced by model::bonded_to_heteroatom().

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bool atom_type::acceptable_type ( ) const

inlineinherited

References atom_type::ad, AD_TYPE_SIZE, atom_type::xs, and XS_TYPE_Met_D.

Referenced by parse_pdbqt_atom_string().

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void atom_type::assign_el ( )

inlineinherited

References atom_type::ad, AD_TYPE_SIZE, ad_type_to_el_type(), atom_type::el, EL_TYPE_Met, atom_type::xs, and XS_TYPE_Met_D.

Referenced by model::assign_types().

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bool atom_type::same_element ( const atom_type &  a ) const

inlineinherited

References atom_type::el.

Referenced by model::rmsd_lower_bound_asymmetric().

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fl atom_type::covalent_radius ( ) const

inlineinherited

References atom_type::ad, ad_type_property(), AD_TYPE_SIZE, atom_kind::covalent_radius, metal_covalent_radius, VINA_CHECK, atom_type::xs, and XS_TYPE_Met_D.

Referenced by atom_type::optimal_covalent_bond_length().

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fl atom_type::optimal_covalent_bond_length ( const atom_type &  x ) const

inlineinherited

References atom_type::covalent_radius().

Referenced by model::assign_bonds().

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Friends And Related Function Documentation

friend class boost::serialization::access

friend

Member Data Documentation

vec atom::coords

Referenced by naive_non_cache::eval(), non_cache::eval(), non_cache::eval_deriv(), model::eval_intramolecular(), terms::evale(), terms::evale_robust(), pdbqt_initializer::initialize_from_nrp(), parsing_struct::node_t< T >::insert(), parsed_atom::parsed_atom(), cache::populate(), postprocess_branch(), postprocess_residue(), model::print_stuff(), serialize(), and szv_grid::szv_grid().

std::vector<bond> atom::bonds

Referenced by model::assign_bonds(), conf_independent_inputs::atom_rotors(), model::bonded_to_HD(), model::bonded_to_heteroatom(), conf_independent_inputs::num_bonded_heavy_atoms(), model::print_stuff(), serialize(), appender::update(), and model::verify_bond_lengths().

fl atom_base::charge

inherited

Referenced by electrostatic< i >::eval(), ad4_solvation::eval(), parsed_atom::parsed_atom(), model::print_stuff(), and atom_base::serialize().

sz atom_type::el

inherited

Referenced by atom_type::assign_el(), model::assign_types(), conf_independent_inputs::conf_independent_inputs(), atom_type::get(), model::print_stuff(), model::rmsd_ligands_upper_bound(), model::rmsd_lower_bound_asymmetric(), model::rmsd_upper_bound(), atom_type::same_element(), and atom_type::serialize().

sz atom_type::ad

inherited

Referenced by atom_type::acceptable_type(), model::assign_bonds(), atom_type::assign_el(), model::assign_types(), model::bonded_to_HD(), atom_type::covalent_radius(), ad4_solvation::eval(), atom_type::get(), atom_type::is_heteroatom(), atom_type::is_hydrogen(), parsed_atom::parsed_atom(), model::print_stuff(), model::rmsd_ligands_upper_bound(), model::rmsd_upper_bound(), atom_type::serialize(), solvation_parameter(), and volume().

sz atom_type::xs

inherited

Referenced by atom_type::acceptable_type(), atom_type::assign_el(), model::assign_types(), conf_independent_inputs::conf_independent_inputs(), atom_type::covalent_radius(), atom_type::get(), atom_type::is_heteroatom(), parse_pdbqt_atom_string(), model::print_stuff(), model::rmsd_ligands_upper_bound(), model::rmsd_upper_bound(), atom_type::serialize(), solvation_parameter(), and volume().

sz atom_type::sy

inherited

Referenced by atom_type::get(), model::print_stuff(), and atom_type::serialize().

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The documentation for this struct was generated from the following file:

• atom.h