Module _core_chemical_

aa_from_name( (str)name) -> AA :
    ///////////////////////////////////////////////////////
     Give an AA string name, return its enum type.
    ///////////////////////////////////////////////////////
    

    C++ signature :
        core::chemical::AA aa_from_name(std::string)

aa_from_oneletter_code( (str)onelettercode) -> AA :
    ////////////////////////////////////////////////////////
     give a 1 letter code and return the string name
    ////////////////////////////////////////////////////////
    

    C++ signature :
        core::chemical::AA aa_from_oneletter_code(char)

add_atom_type_set_parameters_from_command_line( (str)atom_type_set_tag, (AtomTypeSet)atom_type_set) -> None :
    Add additional parameter files not present in <atom-set-name>/extras.txt.
    

    C++ signature :
        void add_atom_type_set_parameters_from_command_line(std::string,core::chemical::AtomTypeSet {lvalue})

apply_adducts_to_residue( (ResidueType)rsd, (vector1_bool)add_mask) -> ResidueType :
    Apply adducts to residue using a boolean mask
    

    C++ signature :
        boost::shared_ptr<core::chemical::ResidueType> apply_adducts_to_residue(core::chemical::ResidueType,utility::vector1<bool, std::allocator<bool> > {lvalue})

calculate_rigid_matrix( (ResidueType)res, (vec1_vec1_Real)distances) -> None :
    Calculate the rigid matrix for neighbor atom finding
    Assume that distances has been initialized to some really large value, and is square
    

    C++ signature :
        void calculate_rigid_matrix(core::chemical::ResidueType,utility::vector1<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > {lvalue})

convert_residuetype_to_light_graph( (ResidueType)res) -> object :
    core/chemical/residue_support.hh:35

    C++ signature :
        boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_name_t, void*, boost::no_property>, boost::property<boost::edge_name_t, boost::detail::edge_desc_impl<boost::undirected_tag, void*>, boost::no_property>, boost::no_property, boost::listS> convert_residuetype_to_light_graph(core::chemical::ResidueType)

convert_to_BondName( (str)id) -> BondName :
    core/chemical/Bond.hh:33

    C++ signature :
        core::chemical::BondName convert_to_BondName(std::string)

create_bond_length( (object)atom1, (object)atom2, (BondName)bond_type) -> float :
    core/chemical/bond_support.hh:34

    C++ signature :
        double create_bond_length(core::chemical::gasteiger::GasteigerAtomTypeData,core::chemical::gasteiger::GasteigerAtomTypeData,core::chemical::BondName)

define_mainchain_atoms( (ResidueType)rsd) -> vector1_Size :
    If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER.
    

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > define_mainchain_atoms(boost::shared_ptr<core::chemical::ResidueType>)

enlarge_h_lj_wdepth( (AtomTypeSet)atom_type_set) -> None :
    core/chemical/util.hh:73

    C++ signature :
        void enlarge_h_lj_wdepth(core::chemical::AtomTypeSet {lvalue})

enlarge_h_lj_wdepth( (vector1_Real)lj_wdepth, (AtomTypeSet)atom_type_set) -> None :
    core/chemical/util.hh:70

    C++ signature :
        void enlarge_h_lj_wdepth(utility::vector1<double, std::allocator<double> > {lvalue},core::chemical::AtomTypeSet)

error_check_requested_adducts( (map_string_int)add_map, (object)rsd_types) -> None :
    Make sure requested adducts exist in some residue
    

    C++ signature :
        void error_check_requested_adducts(std::map<std::string, int, std::less<std::string>, std::allocator<std::pair<std::string const, int> > >,utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > >)

fill_ideal_xyz_from_icoor( (ResidueType)restype, (object)graph) -> None :
    core/chemical/icoor_support.hh:44

    C++ signature :
        void fill_ideal_xyz_from_icoor(core::chemical::ResidueType {lvalue},boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>)

find_bonds_in_rings( (ResidueType)res) -> None :
    Determine which bonds are in rings, and set the BondRingness property of each
    

    C++ signature :
        void find_bonds_in_rings(core::chemical::ResidueType {lvalue})

find_chi_bonds( (ResidueType)restype) -> object :
    Find which bonds are rotatatable (chi) bonds
    Returns a list of four vds representing the chi
    

    C++ signature :
        utility::vector1<utility::vector1<void*, std::allocator<void*> >, std::allocator<utility::vector1<void*, std::allocator<void*> > > > find_chi_bonds(core::chemical::ResidueType)

find_nbr_dist( (ResidueType)res, (object)nbr_atom) -> float :
    Find the neighbor distance to the given neighbor atom.
    If nbr_atom is null_vertex, give the smallest neighbor distance,
    and set nbr_atom to the atom for that distance.
    The neighbor distance here is adjusted for rotatable bonds -
    It should be at least as large as the maximum neighbor distance
    in any torsional rotamer
    If the neighbor atom is not provided, the atom chosen will be a
    multiply-bonded heavy atom.
    Assumes:
      * All atoms and bond are present
      * All ideal_xyz coordinates have been set
      * All elements have been set
        * All ring bonds have been annotated
    

    C++ signature :
        double find_nbr_dist(core::chemical::ResidueType,void* {lvalue})

fixup_patches( (str)string_in) -> str :
    Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":".
    

    C++ signature :
        std::string fixup_patches(std::string)

formatted_icoord_tree( (ResidueType)restype) -> str :
    Return a string representing the internal coordinates tree of this ResidueType.
    

    C++ signature :
        std::string formatted_icoord_tree(core::chemical::ResidueType)

get_D_equivalent( (AA)aa) -> AA :
    ///////////////////////////////////////////////////////
     Given an enum type for a L-amino acid with a
     canonical side-chain, return the enum type for the
     corresponding D-amino acid (or aa_unk if the
     corresponding D-amino acid cannot be determined).
    ///////////////////////////////////////////////////////
    

    C++ signature :
        core::chemical::AA get_D_equivalent(core::chemical::AA)

get_L_equivalent( (AA)aa) -> AA :
    ///////////////////////////////////////////////////////
     Given an enum type for a D-amino acid with a
     canonical side-chain, return the enum type for the
     corresponding L-amino acid (or aa_unk if the
     corresponding L-amino acid cannot be determined).
    ///////////////////////////////////////////////////////
    

    C++ signature :
        core::chemical::AA get_L_equivalent(core::chemical::AA)

get_bond( (ResidueType)res, (object)source, (object)target) -> object :
    core/chemical/bond_support.hh:30

    C++ signature :
        boost::detail::edge_desc_impl<boost::undirected_tag, void*> get_bond(core::chemical::ResidueType,void*,void*)

get_connecting_atoms( (object)res, (object)edge) -> object :
    core/chemical/bond_support.hh:29

    C++ signature :
        utility::vector1<void*, std::allocator<void*> > get_connecting_atoms(boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,boost::detail::edge_desc_impl<boost::undirected_tag, void*>)

get_connecting_atoms( (ResidueType)res, (object)edge) -> object :
    core/chemical/bond_support.hh:28

    C++ signature :
        utility::vector1<void*, std::allocator<void*> > get_connecting_atoms(core::chemical::ResidueType,boost::detail::edge_desc_impl<boost::undirected_tag, void*>)

get_residue_path_distances( (ResidueType)res) -> object :
    relies on class Graph to find all pairs shortest path information
    

    C++ signature :
        ObjexxFCL::FArray2D<int> get_residue_path_distances(core::chemical::ResidueType)

get_rpp_charge( (str)type) -> float :
    Get charge for atom type based on Rosetta++ aaproperties_pack.cc values
    

    C++ signature :
        double get_rpp_charge(std::string)

has( (object)graph, (object)ed) -> bool :
    Does a ResidueGraph have a given edge descriptor?
    

    C++ signature :
        bool has(boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,boost::detail::edge_desc_impl<boost::undirected_tag, void*>)

has( (object)graph, (object)vd) -> bool :
    /////////////////////////////////////////////
    //////// Convenience Functions //////////////
     Does a ResidueGraph have a given vertex descriptor?
    

    C++ signature :
        bool has(boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,void*)

is_canonical_D_aa( (AA)aa) -> bool :
    ///////////////////////////////////////////////////////
     Give an enum type, return true if and only if
     it is a D-amino acid that is the mirror image of a
     canonical alpha-L-amino acid.
     Vikram K. Mulligan (vmullig@uw.edu)
    ///////////////////////////////////////////////////////
    

    C++ signature :
        bool is_canonical_D_aa(core::chemical::AA)

is_sp2_proton_chi( (int)chi, (ResidueType)restype) -> bool :
    Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom?
    The use case is to see if the proton chi should flat or staggered with rotamers
    

    C++ signature :
        bool is_sp2_proton_chi(unsigned long,core::chemical::ResidueType)

modify_atom_properties_from_command_line( (str)atom_type_set_tag, (AtomTypeSet)atom_type_set) -> None :
    Modify atom_type properties from the command line.
    

    C++ signature :
        void modify_atom_properties_from_command_line(std::string,core::chemical::AtomTypeSet {lvalue})

name_from_aa( (AA)aa) -> str :
    ////////////////////////////////////////////////////
     give a enum type and return the string name
    ////////////////////////////////////////////////////
    

    C++ signature :
        std::string name_from_aa(core::chemical::AA)

nonadduct_variants_match( (ResidueType)res1, (ResidueType)res2) -> bool :
    Similar to variants_match(), but allows different adduct-modified states.
    

    C++ signature :
        bool nonadduct_variants_match(core::chemical::ResidueType,core::chemical::ResidueType)

oneletter_code_from_aa( (AA)aa) -> str :
    ////////////////////////////////////////////////////
     give a enum type and return the string name
    ////////////////////////////////////////////////////
    

    C++ signature :
        char oneletter_code_from_aa(core::chemical::AA)

oneletter_code_specifies_aa( (str)onelettercode) -> bool :
    core/chemical/AA.hh:194

    C++ signature :
        bool oneletter_code_specifies_aa(char)

parse_adduct_string( (object)add_vec) -> map_string_int :
    Convert input string to map of adducts->max usage
    

    C++ signature :
        std::map<std::string, int, std::less<std::string>, std::allocator<std::pair<std::string const, int> > > parse_adduct_string(utility::options::StringVectorOption {lvalue})

patch_operation_from_patch_file_line( (str)line) -> PatchOperation :
    Virtual constructor, returns 0 if no match
    

    C++ signature :
        boost::shared_ptr<core::chemical::PatchOperation> patch_operation_from_patch_file_line(std::string)

pretty_print_atomicoor( (OStream)out, (AtomICoor)start, (ResidueType)rsd_type [, (int)indent=0]) -> None :
    core/chemical/AtomICoor.hh:385

    C++ signature :
        void pretty_print_atomicoor(std::ostream {lvalue},core::chemical::AtomICoor,core::chemical::ResidueType [,unsigned long=0])

print_chis( (OStream)out, (ResidueType)res) -> None :
    Utility to examine chi output.
    

    C++ signature :
        void print_chis(std::ostream {lvalue},core::chemical::ResidueType)

read_conformers_from_database_file_for_ring_size( (str)filename, (int)ring_size) -> object :
    Return a list of ring conformers, read from a database file.
    

    C++ signature :
        utility::vector1<core::chemical::RingConformer, std::allocator<core::chemical::RingConformer> > read_conformers_from_database_file_for_ring_size(std::string,unsigned long)

read_topology_file( (object)istream, (AtomTypeSetCAP)atom_types, (ElementSetCAP)elements, (MMAtomTypeSetCAP)mm_atom_types, (OrbitalTypeSetCAP)orbital_atom_types, (ResidueTypeSetCAP)rsd_type_set) -> ResidueType :
    core/chemical/residue_io.hh:57

    C++ signature :
        boost::shared_ptr<core::chemical::ResidueType> read_topology_file(utility::io::izstream {lvalue},boost::weak_ptr<core::chemical::AtomTypeSet const>,boost::weak_ptr<core::chemical::ElementSet const>,boost::weak_ptr<core::chemical::MMAtomTypeSet const>,boost::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>,boost::weak_ptr<core::chemical::ResidueTypeSet const>)

read_topology_file( (str)filename, (AtomTypeSetCAP)atom_types, (ElementSetCAP)elements, (MMAtomTypeSetCAP)mm_atom_types, (OrbitalTypeSetCAP)orbital_atom_types, (ResidueTypeSetCAP)rsd_type_set) -> ResidueType :
    virtual constructor for ResidueType objects
    

    C++ signature :
        boost::shared_ptr<core::chemical::ResidueType> read_topology_file(std::string,boost::weak_ptr<core::chemical::AtomTypeSet const>,boost::weak_ptr<core::chemical::ElementSet const>,boost::weak_ptr<core::chemical::MMAtomTypeSet const>,boost::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>,boost::weak_ptr<core::chemical::ResidueTypeSet const>)

rename_atoms( (ResidueType)res [, (bool)preserve=True]) -> None :
    Rename atoms in the residue type such that their names are unique.
    If preserve is true, only rename those which have no names or who have
    name conflicts. (Both of the conflicting atoms will be renamed.)
    

    C++ signature :
        void rename_atoms(core::chemical::ResidueType {lvalue} [,bool=True])

reroot_restype( (ResidueType)restype, (object)graph, (object)root) -> None :
    core/chemical/icoor_support.hh:39

    C++ signature :
        void reroot_restype(core::chemical::ResidueType {lvalue},boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,void*)

residue_selector_single_from_line( (str)line) -> ResidueSelectorSingle :
    /////////////////////////////////////////////////////////////////////////////////////
     create a singe ResidueSelector from an input line.
    

    C++ signature :
        boost::shared_ptr<core::chemical::ResidueSelectorSingle> residue_selector_single_from_line(std::string)

residue_type_all_patches_name( (ResidueType)rsd_type) -> str :
    helper function, returns the name of all added patches
    

    C++ signature :
        std::string residue_type_all_patches_name(core::chemical::ResidueType)

residue_type_base_name( (ResidueType)rsd_type) -> str :
    helper function, returns the base residue name prior to any patching
    

    C++ signature :
        std::string residue_type_base_name(core::chemical::ResidueType)

retype_is_aromatic( (object)atom, (object)graph) -> bool :
    core/chemical/atomtype_support.hh:24

    C++ signature :
        bool retype_is_aromatic(void*,boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>)

rosetta_recharge_fullatom( (ResidueType)res) -> None :
    Apply molfile_to_params style partial charges to the ResidueType.
    These partial charges are based off of the Rosetta atom type,
    adjusted such that the net partial charge is equal to the net formal charge.
    These charges are almost certainly dodgy. If you have any other source of
    partial charges that are at all reasonable, you probably want to consider those instead.
    Assumes:
      * All atoms and bond are present.
      * All atom types have been set.
      * Formal charges (if any) have been set.
    

    C++ signature :
        void rosetta_recharge_fullatom(core::chemical::ResidueType {lvalue})

rosetta_retype_fullatom( (ResidueType)restype [, (bool)preserve=False]) -> None :
    Reassign Rosetta atom types based on the current fullatom heuristics.
    If preserve is true, only retype those atoms which have an atom_type_index of zero.
    

    C++ signature :
        void rosetta_retype_fullatom(core::chemical::ResidueType {lvalue} [,bool=False])

    Return a constant access pointer to the ResidueTypeSet specified by the command-line options.
    

    C++ signature :
        boost::weak_ptr<core::chemical::ResidueTypeSet const> rsd_set_from_cmd_line()

Returns: ResidueTypeSetCAP :

setup_atom_type_reassignments_from_commandline( (str)rsd_type_name, (str)rsd_type_set_name, (map_string_string)atom_type_reassignments) -> None :
    core/chemical/residue_io.hh:71

    C++ signature :
        void setup_atom_type_reassignments_from_commandline(std::string,std::string,std::map<std::string, std::string, std::less<std::string>, std::allocator<std::pair<std::string const, std::string> > > {lvalue})

setup_icoor_reassignments_from_commandline( (str)rsd_type_name, (str)rsd_type_set_name, (object)icoor_reassignments) -> None :
    core/chemical/residue_io.hh:79

    C++ signature :
        void setup_icoor_reassignments_from_commandline(std::string,std::string,std::map<std::string, utility::vector1<std::string, std::allocator<std::string> >, std::less<std::string>, std::allocator<std::pair<std::string const, utility::vector1<std::string, std::allocator<std::string> > > > > {lvalue})

turn_off_hbonds_to_ester_oxygens( (AtomTypeSet)atom_type_set) -> None :
    core/chemical/util.hh:77

    C++ signature :
        void turn_off_hbonds_to_ester_oxygens(core::chemical::AtomTypeSet {lvalue})

variants_match( (ResidueType)res1, (ResidueType)res2) -> bool :
    Are these two residues patched in exactly the same way?
    

    C++ signature :
        bool variants_match(core::chemical::ResidueType,core::chemical::ResidueType)

variants_match_with_exceptions( (ResidueType)res1, (ResidueType)res2, (object)list_of_variants_to_ignore) -> bool :
    Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions?
    

    C++ signature :
        bool variants_match_with_exceptions(core::chemical::ResidueType,core::chemical::ResidueType,utility::vector1<core::chemical::VariantType, std::allocator<core::chemical::VariantType> >)

write_topology_file( (ResidueType)rsd [, (str)filename='']) -> None :
    writes a .params file from a given ResidueType object
    

    C++ signature :
        void write_topology_file(core::chemical::ResidueType [,std::string=''])

ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ACETYLAMINO_SUGA R

ACETYLATED_NTERMINUS

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ACETYLATED_NTERM INUS

ACETYLATED_NTERMINUS_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.ACETYLATED_NTERMINUS _VARIANT

ACETYLATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.ACETYLATION

ACETYL_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ACETYL_SUGAR

ADDUCT

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ADDUCT

ADDUCT_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.ADDUCT_VARIANT

ALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ALDONIC_ACID

ALDONIC_ACID_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.ALDONIC_ACID_VARIANT

ALDOSE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ALDOSE

ALPHA_AA

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ALPHA_AA

ALPHA_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.ALPHA_SUGAR

ALTERNATIVE_PROTONATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.ALTERNATIVE_PROTONAT ION

AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.AMINO_SUGAR

AROMATIC

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.AROMATIC

AromaticBond

Value:

rosetta.core.chemical._core_chemical_.BondName.AromaticBond

BETA_AA

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.BETA_AA

BETA_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.BETA_SUGAR

BRANCH_LOWER_TERMINUS

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.BRANCH_LOWER_TER MINUS

BRANCH_LOWER_TERMINUS_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.BRANCH_LOWER_TERMINU S_VARIANT

BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.BRANCH_POINT

BondInRing

Value:

rosetta.core.chemical._core_chemical_.BondRingness.BondInRing

BondNotInRing

Value:

rosetta.core.chemical._core_chemical_.BondRingness.BondNotInRing

C1_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C1_ACETYLAMINO_SUGAR

C1_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C1_AMINO_SUGAR

C1_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C1_BRANCH_POINT

C1_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C1_DEOXY_SUGAR

C1_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C1_MODIFIED

C1_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C1_PHOSPHATE

C2_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C2_ACETYLAMINO_SUGAR

C2_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C2_AMINO_SUGAR

C2_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C2_BRANCH_POINT

C2_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C2_DEOXY_SUGAR

C2_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C2_KETOALDONIC_ACID

C2_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C2_MODIFIED

C2_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C2_PHOSPHATE

C3_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C3_ACETYLAMINO_SUGAR

C3_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C3_AMINO_SUGAR

C3_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C3_BRANCH_POINT

C3_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C3_DEOXY_SUGAR

C3_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C3_KETOALDONIC_ACID

C3_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C3_MODIFIED

C3_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C3_PHOSPHATE

C4_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C4_ACETYLAMINO_SUGAR

C4_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C4_AMINO_SUGAR

C4_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C4_BRANCH_POINT

C4_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C4_DEOXY_SUGAR

C4_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C4_KETOALDONIC_ACID

C4_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C4_MODIFIED

C4_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C4_PHOSPHATE

C5_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C5_ACETYLAMINO_SUGAR

C5_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C5_AMINO_SUGAR

C5_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C5_BRANCH_POINT

C5_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C5_DEOXY_SUGAR

C5_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C5_KETOALDONIC_ACID

C5_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C5_MODIFIED

C5_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C5_PHOSPHATE

C6_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C6_ACETYLAMINO_SUGAR

C6_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C6_AMINO_SUGAR

C6_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C6_BRANCH_POINT

C6_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C6_DEOXY_SUGAR

C6_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C6_KETOALDONIC_ACID

C6_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C6_MODIFIED

C6_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C6_PHOSPHATE

C7_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C7_ACETYLAMINO_SUGAR

C7_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C7_AMINO_SUGAR

C7_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C7_BRANCH_POINT

C7_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C7_DEOXY_SUGAR

C7_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C7_KETOALDONIC_ACID

C7_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C7_MODIFIED

C7_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C7_PHOSPHATE

C8_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C8_ACETYLAMINO_SUGAR

C8_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C8_AMINO_SUGAR

C8_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C8_BRANCH_POINT

C8_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C8_DEOXY_SUGAR

C8_KETOALDONIC_ACID

Value:

rosetta.core.chemical._core_chemical_.VariantType.C8_KETOALDONIC_ACID

C8_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C8_MODIFIED

C8_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C8_PHOSPHATE

C9_ACETYLAMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C9_ACETYLAMINO_SUGAR

C9_AMINO_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C9_AMINO_SUGAR

C9_BRANCH_POINT

Value:

rosetta.core.chemical._core_chemical_.VariantType.C9_BRANCH_POINT

C9_DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.VariantType.C9_DEOXY_SUGAR

C9_MODIFIED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.C9_MODIFIED

C9_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.C9_PHOSPHATE

CARBOHYDRATE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.CARBOHYDRATE

CARBOXYLATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.CARBOXYLATION

CENTROID_HA

Value:

rosetta.core.chemical._core_chemical_.VariantType.CENTROID_HA

CHARGED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.CHARGED

COARSE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.COARSE

CTERM_CONNECT

Value:

rosetta.core.chemical._core_chemical_.VariantType.CTERM_CONNECT

CUTPOINT_LOWER

Value:

rosetta.core.chemical._core_chemical_.VariantType.CUTPOINT_LOWER

CUTPOINT_UPPER

Value:

rosetta.core.chemical._core_chemical_.VariantType.CUTPOINT_UPPER

CYCLIC

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.CYCLIC

C_METHYLAMIDATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.C_METHYLAMIDATION

ConjugableBond

Value:

rosetta.core.chemical._core_chemical_.BondConjugability.ConjugableBond

DEOXY_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.DEOXY_SUGAR

DEPROTONATED

Value:

rosetta.core.chemical._core_chemical_.VariantType.DEPROTONATED

DIIODINATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.DIIODINATION

DIMETHYLATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.DIMETHYLATION

DISULFIDE

Value:

rosetta.core.chemical._core_chemical_.VariantType.DISULFIDE

DISULFIDE_BONDED

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.DISULFIDE_BONDED

D_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.D_SUGAR

DoubleBond

Value:

rosetta.core.chemical._core_chemical_.BondName.DoubleBond

DoubleBondOrder

Value:

rosetta.core.chemical._core_chemical_.BondOrder.DoubleBondOrder

EIsometry

Value:

rosetta.core.chemical._core_chemical_.BondIsometry.EIsometry

FIRST_PROPERTY

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.FIRST_PROPERTY

FIRST_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.FIRST_VARIANT

FIVE_PRIME_END_OH

Value:

rosetta.core.chemical._core_chemical_.VariantType.FIVE_PRIME_END_OH

FIVE_PRIME_END_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.FIVE_PRIME_END_PHOSP HATE

FIVE_PRIME_PACKABLE_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.FIVE_PRIME_PACKABLE_ PHOSPHATE

FIVE_PRIME_PHOSPHATE

Value:

rosetta.core.chemical._core_chemical_.VariantType.FIVE_PRIME_PHOSPHATE

FORMS_DISULFIDE_BOND

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.FORMS_DISULFIDE_ BOND

FURANOSE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.FURANOSE

GAMMA_AA

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.GAMMA_AA

GLYCOSIDE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.GLYCOSIDE

HBS_POST

Value:

rosetta.core.chemical._core_chemical_.VariantType.HBS_POST

HBS_PRE

Value:

rosetta.core.chemical._core_chemical_.VariantType.HBS_PRE

HYBRID_MAX

Value:

rosetta.core.chemical._core_chemical_.Hybridization.HYBRID_MAX

HYDROXYLATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.HYDROXYLATION

HYDROXYLATION1

Value:

rosetta.core.chemical._core_chemical_.VariantType.HYDROXYLATION1

HYDROXYLATION2

Value:

rosetta.core.chemical._core_chemical_.VariantType.HYDROXYLATION2

IsAromaticBond

Value:

rosetta.core.chemical._core_chemical_.BondAromaticity.IsAromaticBond

KETOSE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.KETOSE

LIGAND

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.LIGAND

LIPID

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.LIPID

LOWERTERM_TRUNC

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.LOWERTERM_TRUNC

LOWERTERM_TRUNC_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.LOWERTERM_TRUNC_VARI ANT

LOWER_TERMINUS

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.LOWER_TERMINUS

LOWER_TERMINUS_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.LOWER_TERMINUS_VARIA NT

L_SUGAR

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.L_SUGAR

MEMBRANE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.MEMBRANE

METAL

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.METAL

METALBINDING

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.METALBINDING

METHYLATED_CTERMINUS

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.METHYLATED_CTERM INUS

METHYLATED_CTERMINUS_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.METHYLATED_CTERMINUS _VARIANT

METHYLATED_NTERM_VARIANT

Value:

rosetta.core.chemical._core_chemical_.VariantType.METHYLATED_NTERM_VAR IANT

METHYLATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.METHYLATION

METHYL_GLYCOSIDE

Value:

rosetta.core.chemical._core_chemical_.VariantType.METHYL_GLYCOSIDE

NE2_CONNECT

Value:

rosetta.core.chemical._core_chemical_.VariantType.NE2_CONNECT

NTERM_CONNECT

Value:

rosetta.core.chemical._core_chemical_.VariantType.NTERM_CONNECT

N_ACETYLATION

Value:

rosetta.core.chemical._core_chemical_.VariantType.N_ACETYLATION

N_PROPERTIES

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.N_PROPERTIES

N_VARIANTS

Value:

rosetta.core.chemical._core_chemical_.VariantType.N_VARIANTS

NoBondIsometry

Value:

rosetta.core.chemical._core_chemical_.BondIsometry.NoBondIsometry

NonaromaticBond

Value:

rosetta.core.chemical._core_chemical_.BondAromaticity.NonaromaticBond

NotConjugableBond

Value:

rosetta.core.chemical._core_chemical_.BondConjugability.NotConjugableB ond

OOP_POST

Value:

rosetta.core.chemical._core_chemical_.VariantType.OOP_POST

OOP_PRE

Value:

rosetta.core.chemical._core_chemical_.VariantType.OOP_PRE

OXETOSE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.OXETOSE

OXIROSE

Value:

rosetta.core.chemical._core_chemical_.ResidueProperty.OXIROSE

OrbitalBond

Value:

rosetta.core.chemical._core_chemical_.BondName.OrbitalBond

OrbitalBondOrder

Value:

rosetta.core.chemical._core_chemical_.BondOrder.OrbitalBondOrder

PEPTOID