rosetta.core.chemical._core_chemical

This class contains the "chemical" information for atoms. This does not contain the actual xyz coordinates of the atom, (which are found in core/conformation/Atom.hh). The atom_type properties are assigned by the class AtomSet, which is initiated from the ChemicalManager. AtomType properties are currently read in from the file chemical/atom_type_sets/fa_standard/atom_properties.txt. These properties contain the the properties of LJ_RADIUS, LJ_WDEPTH, LK_DGRFREE, LK_LAMBDA, and LK_VOLUME and are used in the scoring methods fa_atr, fa_rep, and fa_sol, which are located in the Etable (core/scoring/etable/Etable.hh). Additional parameters are acceptor/donor, hybridization, and orbital paramaters. This class should not have information associated with the Conformation or ResidueType; it represents an atom divorced from a particular conformation or residue but not from things that affect it chemically. It is distinct from an Element, in that it can have a particular hybridization state, charge, etc. It is distinct from conformation::Atom in that it does not have coordinates. Everything stored here should be concerning the atom. Conformation information goes in core::conformation, while data for ResidueType is cached there. chemical::Atoms are stored in chemical::ResidueType (within its ResidueGraph); conformation::Atoms are stored in conformation::Residue

init(...)
(Constructor)


__init__( (object)arg1) -> None :

    C++ signature :
        void __init__(_object*)

__init__( (object)arg1, (str)name_in, (str)mm_name, (int)mm_atom_type_index, (Element)element, (float)charge, (xyzVector_Real)ideal_xyz) -> None :
    Construct a new atom with the name, mm type, element, charge and position.
    

    C++ signature :
        void __init__(_object*,std::string,std::string,unsigned long,boost::shared_ptr<core::chemical::Element const>,double,numeric::xyzVector<double>)

__init__( (object)arg1, (Atom)src) -> None :
    core/chemical/Atom.hh:79

    C++ signature :
        void __init__(_object*,core::chemical::Atom)

Overrides: object.__init__

str(...)
(Informal representation operator)


__str__( (Atom)arg1) -> object :

    C++ signature :
        _object* __str__(core::chemical::Atom {lvalue})

Overrides: object.__str__

assign(...)


assign( (Atom)arg1, (Atom)atom) -> Atom :
    core/chemical/Atom.hh:107

    C++ signature :
        core::chemical::Atom {lvalue} assign(core::chemical::Atom {lvalue},core::chemical::Atom)

atom_type_index(...)


atom_type_index( (Atom)arg1) -> int :
    core/chemical/Atom.hh:113

    C++ signature :
        unsigned long atom_type_index(core::chemical::Atom {lvalue})

atom_type_index( (Atom)arg1, (int)atom_type_index) -> None :
    You probably don't want to use this directly.
    Use ResidueType::set_atom_type() which correctly updates the internal state of the residuetype/atom
    

    C++ signature :
        void atom_type_index(core::chemical::Atom {lvalue},unsigned long)

bonded_orbitals(...)


bonded_orbitals( (Atom)arg1) -> vector1_Size :
    core/chemical/Atom.hh:120

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > bonded_orbitals(core::chemical::Atom {lvalue})

bonded_orbitals( (Atom)arg1) -> vector1_Size :
    core/chemical/Atom.hh:121

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue} bonded_orbitals(core::chemical::Atom {lvalue})

charge(...)


charge( (Atom)arg1) -> float :
    core/chemical/Atom.hh:118

    C++ signature :
        double charge(core::chemical::Atom {lvalue})

charge( (Atom)arg1, (float)charge) -> None :
    core/chemical/Atom.hh:143

    C++ signature :
        void charge(core::chemical::Atom {lvalue},double)

element_type(...)


element_type( (Atom)arg1) -> Element :
    core/chemical/Atom.hh:115

    C++ signature :
        boost::shared_ptr<core::chemical::Element const> element_type(core::chemical::Atom {lvalue})

element_type( (Atom)arg1, (Element)element) -> None :
    core/chemical/Atom.hh:140

    C++ signature :
        void element_type(core::chemical::Atom {lvalue},boost::shared_ptr<core::chemical::Element const>)

formal_charge(...)


formal_charge( (Atom)arg1) -> int :
    core/chemical/Atom.hh:117

    C++ signature :
        int formal_charge(core::chemical::Atom {lvalue})

formal_charge( (Atom)arg1, (int)charge) -> None :
    core/chemical/Atom.hh:142

    C++ signature :
        void formal_charge(core::chemical::Atom {lvalue},int)

gasteiger_atom_type(...)


gasteiger_atom_type( (Atom)arg1) -> object :
    core/chemical/Atom.hh:116

    C++ signature :
        boost::shared_ptr<core::chemical::gasteiger::GasteigerAtomTypeData const> gasteiger_atom_type(core::chemical::Atom {lvalue})

gasteiger_atom_type( (Atom)arg1, (object)gasteiger_atom_type) -> None :
    core/chemical/Atom.hh:141

    C++ signature :
        void gasteiger_atom_type(core::chemical::Atom {lvalue},boost::shared_ptr<core::chemical::gasteiger::GasteigerAtomTypeData const>)

has_orbitals(...)


has_orbitals( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:128

    C++ signature :
        bool has_orbitals(core::chemical::Atom {lvalue})

has_orbitals( (Atom)arg1, (bool)orbitals) -> None :
    core/chemical/Atom.hh:151

    C++ signature :
        void has_orbitals(core::chemical::Atom {lvalue},bool)

heavyatom_has_polar_hydrogens(...)


heavyatom_has_polar_hydrogens( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:122

    C++ signature :
        bool heavyatom_has_polar_hydrogens(core::chemical::Atom {lvalue})

heavyatom_has_polar_hydrogens( (Atom)arg1, (bool)heavyatom_has_polar_hydrogens) -> None :
    core/chemical/Atom.hh:145

    C++ signature :
        void heavyatom_has_polar_hydrogens(core::chemical::Atom {lvalue},bool)

ideal_xyz(...)


ideal_xyz( (Atom)arg1) -> xyzVector_Real :
    core/chemical/Atom.hh:119

    C++ signature :
        numeric::xyzVector<double> ideal_xyz(core::chemical::Atom {lvalue})

ideal_xyz( (Atom)arg1, (xyzVector_Real)ideal_xyz) -> None :
    core/chemical/Atom.hh:144

    C++ signature :
        void ideal_xyz(core::chemical::Atom {lvalue},numeric::xyzVector<double>)

is_acceptor(...)


is_acceptor( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:123

    C++ signature :
        bool is_acceptor(core::chemical::Atom {lvalue})

is_acceptor( (Atom)arg1, (bool)acceptor) -> None :
    core/chemical/Atom.hh:149

    C++ signature :
        void is_acceptor(core::chemical::Atom {lvalue},bool)

is_fake(...)


is_fake( (Atom)arg1) -> bool :
    Return true if this represents a fake/mock atom.
    

    C++ signature :
        bool is_fake(core::chemical::Atom {lvalue})

is_haro(...)


is_haro( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:126

    C++ signature :
        bool is_haro(core::chemical::Atom {lvalue})

is_haro( (Atom)arg1, (bool)haro) -> None :
    core/chemical/Atom.hh:148

    C++ signature :
        void is_haro(core::chemical::Atom {lvalue},bool)

is_hydrogen(...)


is_hydrogen( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:125

    C++ signature :
        bool is_hydrogen(core::chemical::Atom {lvalue})

is_hydrogen( (Atom)arg1, (bool)hydrogen) -> None :
    core/chemical/Atom.hh:147

    C++ signature :
        void is_hydrogen(core::chemical::Atom {lvalue},bool)

is_polar_hydrogen(...)


is_polar_hydrogen( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:124

    C++ signature :
        bool is_polar_hydrogen(core::chemical::Atom {lvalue})

is_polar_hydrogen( (Atom)arg1, (bool)polar) -> None :
    core/chemical/Atom.hh:146

    C++ signature :
        void is_polar_hydrogen(core::chemical::Atom {lvalue},bool)

is_virtual(...)


is_virtual( (Atom)arg1) -> bool :
    core/chemical/Atom.hh:127

    C++ signature :
        bool is_virtual(core::chemical::Atom {lvalue})

is_virtual( (Atom)arg1, (bool)is_virtual) -> None :
    core/chemical/Atom.hh:150

    C++ signature :
        void is_virtual(core::chemical::Atom {lvalue},bool)

mm_atom_type_index(...)


mm_atom_type_index( (Atom)arg1) -> int :
    core/chemical/Atom.hh:114

    C++ signature :
        unsigned long mm_atom_type_index(core::chemical::Atom {lvalue})

mm_atom_type_index( (Atom)arg1, (int)mm_atom_type_index) -> None :
    core/chemical/Atom.hh:139

    C++ signature :
        void mm_atom_type_index(core::chemical::Atom {lvalue},unsigned long)

mm_name(...)


mm_name( (Atom)arg1) -> str :
    core/chemical/Atom.hh:112

    C++ signature :
        std::string mm_name(core::chemical::Atom {lvalue})

mm_name( (Atom)arg1, (str)name) -> None :
    core/chemical/Atom.hh:133

    C++ signature :
        void mm_name(core::chemical::Atom {lvalue},std::string)

name(...)


name( (Atom)arg1) -> str :
    core/chemical/Atom.hh:110

    C++ signature :
        std::string name(core::chemical::Atom {lvalue})

name( (Atom)arg1, (str)name) -> None :
    core/chemical/Atom.hh:132

    C++ signature :
        void name(core::chemical::Atom {lvalue},std::string)

show(...)


show( (Atom)arg1, (OStream)out) -> None :
    Generate string representation of chemical::Atom for debugging purposes.
    

    C++ signature :
        void show(core::chemical::Atom {lvalue},std::ostream {lvalue})

Class Atom

init(...)
(Constructor)

reduce(...)

str(...)
(Informal representation operator)

assign(...)

atom_type_index(...)

bonded_orbitals(...)

charge(...)

element_type(...)

formal_charge(...)

gasteiger_atom_type(...)

has_orbitals(...)

heavyatom_has_polar_hydrogens(...)

ideal_xyz(...)

is_acceptor(...)

is_fake(...)

is_haro(...)

is_hydrogen(...)

is_polar_hydrogen(...)

is_virtual(...)

mm_atom_type_index(...)

mm_name(...)

name(...)

show(...)

Class Atom

__init__(...) (Constructor)

__reduce__(...)

__str__(...) (Informal representation operator)

assign(...)

atom_type_index(...)

bonded_orbitals(...)

charge(...)

element_type(...)

formal_charge(...)

gasteiger_atom_type(...)

has_orbitals(...)

heavyatom_has_polar_hydrogens(...)

ideal_xyz(...)

is_acceptor(...)

is_fake(...)

is_haro(...)

is_hydrogen(...)

is_polar_hydrogen(...)

is_virtual(...)

mm_atom_type_index(...)

mm_name(...)

name(...)

show(...)

init(...)
(Constructor)

reduce(...)

str(...)
(Informal representation operator)