VinaLC: Parallel Molecular Docking Program

Biochemical and Biophysical Systems Group
VinaLC version: 1.1.2

atom_base Struct Reference

#include <atom_base.h>

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Public Types

enum  t { EL, AD, XS, SY }
 

Public Member Functions

 atom_base ()
 
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

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_base::atom_base ( )
inline

Member Function Documentation

template<class Archive >
void atom_base::serialize ( Archive &  ar,
const unsigned  version 
)
inlineprivate

References charge.

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

sz atom_type::sy
inherited

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