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core::chemical::ResidueType Class Reference

silly demo class – what would the most familiar residue look like? More...

#include <ResidueType.hh>

Inheritance diagram for core::chemical::ResidueType:
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Collaboration diagram for core::chemical::ResidueType:
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Public Member Functions

virtual ~ResidueType ()
 destructor More...
 
 ResidueType (AtomTypeSetCAP atom_types, ElementSetCAP element_types, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types)
 constructor More...
 
ResidueTypeOP clone () const
 make a copy More...
 
AtomTypeSet const & atom_type_set () const
 access by reference the atomset for which this residue is constructed More...
 
ElementSet const & element_set () const
 access by reference the atomset for which this residue is constructed More...
 
AtomTypeSetCAP atom_type_set_ptr () const
 access by const pointer the atomset for which this residue is constructed More...
 
Atomatom (Size const atom_index)
 
Atom const & atom (Size const atom_index) const
 
Atomatom (std::string const &atom_name)
 
Atom const & atom (std::string const &atom_name) const
 
Orbital const & orbital (Size const orbital_index) const
 
Orbital const & orbital (std::string const &orbital_name) const
 
AtomType const & atom_type (Size const atomno) const
 Get the chemical atom_type for this atom by it index number in this residue. More...
 
Size natoms () const
 Get the chemical atom_type index number for this atom by its index number in this residue. More...
 
Size nheavyatoms () const
 number of heavy atoms More...
 
Size n_hbond_acceptors () const
 number of hbond_acceptors More...
 
Size n_hbond_donors () const
 number of hbond_donors More...
 
Size lower_connect_atom () const
 index number of the atom which connects to the lower connection More...
 
int path_distance (Size at1, Size at2) const
 path distance (number of bonds separated) between a pair of atoms More...
 
utility::vector1< int > const & path_distance (Size atom) const
 shortest path distance for an atom to all other residue atoms More...
 
utility::vector1
< utility::vector1< int >
> const & 
path_distances () const
 accessor of path_distance_ data for this residue, which is a 2D array More...
 
Size attached_H_begin (Size const atom) const
 index number of the first attached Hydrogen on an atom More...
 
Size attached_H_end (Size const atom) const
 index number of the last attached Hydrogen on an atom More...
 
AtomIndices const & attached_H_begin () const
 for all heavy atoms, index numbers of their first attached Hydrogen More...
 
AtomIndices const & attached_H_end () const
 for all heavy atoms, index numbers of their last attached Hydrogen More...
 
Size number_bonded_hydrogens (Size const atomno) const
 indicates how many proton bonded neighbors an atom has More...
 
Size number_bonded_heavyatoms (Size const atomno) const
 indicates how many heavyatom bonded neighbors an atom has More...
 
AtomIndices const & bonded_neighbor (Size const atomno) const
 indices of the bonded neighbors for an atom More...
 
utility::vector1< BondName >
const & 
bonded_neighbor_types (Size const atomno) const
 
AtomIndices const & cut_bond_neighbor (Size const atomno) const
 indices of the bonded neighbors for an atom More...
 
AtomIndices const & nbrs (Size const atomno) const
 indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno) More...
 
AtomIndices const & chi_atoms (Size const chino) const
 indices of the atoms which are used to define a given chi angle (chino) More...
 
utility::vector1< AtomIndices >
const & 
chi_atoms () const
 indices of the atoms which are used to define all the chi angles More...
 
AtomIndices const & all_bb_atoms () const
 Indices of all backbone atoms, hydrogens and heavyatoms. More...
 
AtomIndices const & all_sc_atoms () const
 Indices of all sidechain atoms, hydrogens and heavyatoms. More...
 
AtomIndices const & Haro_index () const
 return indices of aromatic Hydrogens More...
 
AtomIndices const & Hpol_index () const
 return indices of polar Hydrogens More...
 
AtomIndices const & Hpos_polar () const
 indices of polar hydrogens as Hbond donors More...
 
AtomIndices const & Hpos_apolar () const
 indices of non-polar hydrogens as potential carbon Hbond donors More...
 
AtomIndices const & Hpos_polar_sc () const
 
AtomIndices const & accpt_pos () const
 indices of atoms as Hbond acceptors More...
 
AtomIndices const & accpt_pos_sc () const
 indices of atoms as Hbond acceptors More...
 
bool heavyatom_has_polar_hydrogens (Size ind) const
 
bool heavyatom_is_an_acceptor (Size ind) const
 
bool atom_is_polar_hydrogen (Size ind) const
 
AtomIndices const & mainchain_atoms () const
 indices of all mainchain atoms More...
 
Size mainchain_atom (Size const atm) const
 index of mainchain atom More...
 
void set_mainchain_atoms (AtomIndices const &mainchain)
 set indices of all mainchain atoms More...
 
bool has (std::string const &atom_name) const
 is this atom present in this residue? More...
 
Size atom_base (Size const atomno) const
 get index of an atom's base atom More...
 
Size abase2 (Size const atomno) const
 get index of an atom's second base atom More...
 
std::string const & atom_name (Size const index) const
 get atom name by index More...
 
bool has_atom_name (std::string const &name) const
 Check if residue type has an atom by a given atomname. More...
 
Size atom_index (std::string const &name) const
 get atom index by name More...
 
void show_all_atom_names (std::ostream &out) const
 
Size last_backbone_atom () const
 index of the last backbone heavy atom More...
 
Size first_sidechain_atom () const
 index of the first sidechain atom (heavy or hydrogen) More...
 
Size first_sidechain_hydrogen () const
 index of the first sidehchain hydrogen More...
 
bool atom_is_backbone (Size const atomno) const
 is a backbone atom (heavy or hydorgen)? More...
 
bool atom_is_hydrogen (Size const atomno) const
 quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last. More...
 
utility::vector1< Size > const & last_controlling_chi () const
 Read access to the last_controlling_chi_ array. More...
 
Size last_controlling_chi (Size atomno) const
 The last_controlling_chi for an atom. 0 if an atom is controlled by no chi. More...
 
utility::vector1< AtomIndices >
const & 
atoms_last_controlled_by_chi () const
 Read access to the atoms_last_controlled_by_chi_ array. More...
 
AtomIndices const & atoms_last_controlled_by_chi (Size chi) const
 Read access to the Atoms last controlled by a particular chi. More...
 
AtomIndices const & actcoord_atoms () const
 get indices for atoms used to define actcoord More...
 
MMAtomType const & mm_atom_type (Size const atomno) const
 Get the MM atom_type for this atom by its index number in this residue. More...
 
chemical::orbitals::OrbitalType
const & 
orbital_type (int const orbital_index) const
 Get the MM atom_type index number for this atom by its index number in this residue. More...
 
Size n_orbitals () const
 number of orbitals More...
 
utility::vector1< core::Size >
const & 
bonded_orbitals (Size const atomno) const
 indices of the orbitals bonded to an atom More...
 
bool has_orbital (std::string const &orbital_name) const
 is this orbital present in this residue? More...
 
AtomIndices const & atoms_with_orb_index () const
 
core::Size orbital_index (std::string const &name) const
 orbital name by index More...
 
ResidueTypeSet const & residue_type_set () const
 
void residue_type_set (ResidueTypeSetCAP set_in)
 set the residue type set of origin. More...
 
Size nchi () const
 number of chi angles More...
 
Size n_proton_chi () const
 number of proton chis More...
 
bool is_proton_chi (Size const chino) const
 number of proton chis More...
 
Size proton_chi_2_chi (Size proton_chi_id) const
 translate proton_chi to global chi More...
 
Size chi_2_proton_chi (Size chi_index) const
 
utility::vector1< Real > const & proton_chi_samples (Size proton_chi) const
 
utility::vector1< Real > const & proton_chi_extra_samples (Size proton_chi) const
 
void set_lower_connect_atom (std::string const &atm_name)
 set the atom which connects to the lower connection More...
 
ResidueConnection const & upper_connect () const
 
ResidueConnection const & lower_connect () const
 
Size upper_connect_id () const
 
Size lower_connect_id () const
 
Size upper_connect_atom () const
 index number of the atom which connects to the upper connection More...
 
void set_upper_connect_atom (std::string const &atm_name)
 set the atom which connects to the upper connection More...
 
utility::vector1< std::pair
< Real, Real > > const & 
chi_rotamers (Size const chino) const
 all rotamers bins (mean, std) for a given chi angle More...
 
Size n_residue_connections () const
 number of ResidueConnections, counting polymeric residue connections More...
 
Size n_polymeric_residue_connections () const
 
Size n_non_polymeric_residue_connections () const
 
ResidueConnection const & residue_connection (Size const i) const
 get a ResidueConection More...
 
ResidueConnectionresidue_connection (Size const i)
 
bool atom_forms_residue_connection (Size const atomid)
 Does an atom form any inter-residue chemical bonds? More...
 
Size n_residue_connections_for_atom (Size const atomid) const
 How many inter-residue chemical bonds does a particular atom form? More...
 
Size residue_connection_id_for_atom (Size const atomid) const
 Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom. More...
 
utility::vector1< Size > const & residue_connections_for_atom (Size const atomid) const
 
bool residue_connection_is_polymeric (Size const resconn_id) const
 
Size residue_connect_atom_index (Size const resconn_id) const
 
bool requires_actcoord () const
 require actcoord? More...
 
void update_actcoord (conformation::Residue &rot) const
 update actcoord More...
 
void add_atom (std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge)
 add an atom into this residue More...
 
void delete_atom (std::string const &name)
 flag an atom for deletion by adding its index to the delete_atom_ list More...
 
void set_atom_type (std::string const &atom_name, std::string const &atom_type_name)
 set atom type More...
 
void set_mm_atom_type (std::string const &atom_name, std::string const &mm_atom_type_name)
 set mm atom type More...
 
void add_bond (std::string const &atom_name1, std::string const &atom_name2)
 add a bond between atom1 and atom2, if bond type is not specified, default to SingleBond More...
 
void add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel)
 
void add_cut_bond (std::string const &atom_name1, std::string const &atom_name2)
 add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond More...
 
void nbr_atom (std::string const &atom_name)
 set nbr_atom used to define residue-level neighbors More...
 
Size nbr_atom () const
 get nbr_atom used to define residue-level neighbors More...
 
void nbr_radius (Real const radius)
 set nbr_radius_ used to define residue-level neighbors More...
 
Real nbr_radius () const
 get nbr_radius_ used to define residue-level neighbors More...
 
core::Real const & molecular_mass () const
 get the molecular weight of this residue More...
 
core::Real const & molar_mass () const
 get the molecular weight of this residue More...
 
void set_atom_base (std::string const &atom_name1, std::string const &atom_name2)
 sets atom_base[ atom1 ] = atom2 More...
 
void set_backbone_heavyatom (std::string const &name)
 set an atom as backbone heavy atom More...
 
void debug_dump_icoor ()
 Dump out atomnames and icoor values. More...
 
AtomICoor const & icoor (Size const atm) const
 AtomICoord of an atom. More...
 
void set_icoor (std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false)
 set AtomICoor for an atom More...
 
void set_icoor (Size const &index, std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false)
 set AtomICoor for an atom More...
 
void assign_neighbor_atom ()
 
void assign_internal_coordinates ()
 
void calculate_icoor (std::string const &child, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)
 calculate AtomICoor for an atom and set it More...
 
void set_ideal_xyz (std::string const &atm, Vector const &xyz_in)
 
void set_ideal_xyz (Size index, Vector const &xyz_in)
 
void add_orbital (std::string &orbital_name, std::string &orbital_type_name)
 add an orbital onto a residue based upon atom More...
 
void add_orbital_bond (std::string const &atom_name1, std::string const &orbital_name)
 add an orbital bond between an atom and an orbital. More...
 
orbitals::ICoorOrbitalData const & orbital_icoor_data (Size const orbital_index) const
 
orbitals::ICoorOrbitalData const & new_orbital_icoor_data (Size const orbital_index) const
 
void set_orbital_icoor_id (std::string const &orbital, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)
 set OrbitalICoor for an orbital More...
 
void add_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 add a chi angle defined by four atoms More...
 
void redefine_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 redefine a chi angle based on four atoms More...
 
void set_proton_chi (Size chino, utility::vector1< Real > dihedral_samples, utility::vector1< Real > extra_samples)
 
void add_chi_rotamer (Size const chino, Real const mean, Real const sdev)
 add a rotamer bin for a given chi More...
 
void finalize ()
 recalculate derived data, potentially reordering atom-indices More...
 
void require_final () const
 an assertion funtion to ensure an ResidueType has been finalized More...
 
Size add_residue_connection (std::string const &atom_name)
 add a ResidueConnection Doesnt set the ideal geometry – maybe it should? More...
 
utility::vector1< std::string >
const & 
properties () const
 acess specified properties More...
 
void add_property (std::string const &property)
 add properties More...
 
void delete_property (std::string const &property)
 delete properties More...
 
void add_actcoord_atom (std::string const &atom)
 add an atom to the list for calculating actcoord center More...
 
bool is_polymer () const
 is polymer? More...
 
bool is_protein () const
 is protein? More...
 
bool is_DNA () const
 is DNA? More...
 
bool is_RNA () const
 is RNA? More...
 
bool is_coarse () const
 is coarse? More...
 
bool is_NA () const
 is Nucleic Acid? More...
 
bool is_carbohydrate () const
 is carbohydrate? More...
 
bool is_ligand () const
 
bool is_surface () const
 is surface? (e.g. enamel) More...
 
bool has_sc_orbitals () const
 does this residue have sidechain orbitals? More...
 
bool is_polar () const
 is polar? More...
 
bool is_charged () const
 is charged? More...
 
bool is_aromatic () const
 is aromatic? More...
 
bool is_terminus () const
 is terminus? More...
 
bool is_lower_terminus () const
 is lower terminus? More...
 
bool is_upper_terminus () const
 is upper terminus? More...
 
bool is_acetylated_nterminus () const
 is acetylated n terminus More...
 
bool is_methylated_cterminus () const
 is methylated c terminus More...
 
bool is_branch_point () const
 is branch point for a branched polymer? More...
 
bool is_virtual (Size const &atomno) const
 Check if atom is virtual. More...
 
bool is_virtual_residue () const
 Check if residue is 'VIRTUAL_RESIDUE'. More...
 
bool is_adduct () const
 is an adduct-modified residue? More...
 
void set_adduct_flag (bool adduct_in)
 
bool has_property (std::string const &property) const
 Generic property access – SLOW!!!!! More...
 
bool has_variant_type (VariantType const &variant_type) const
 Generic variant access – SLOW!!!!! More...
 
utility::vector1< VariantType >
const & 
variant_types () const
 get all the variant types for this ResidueType More...
 
bool variants_match (ResidueType const &other) const
 Does this residue have exactly the same set of properties as residue other? phil – this code does not look correct to me should probably be other.has_variant_type not other.has_property. More...
 
bool nonadduct_variants_match (ResidueType const &other) const
 similar to variants_match(), but allows different adduct-modified states More...
 
void add_variant_type (VariantType const &variant_type)
 add one more variant type to this ResidueType More...
 
void aa (std::string const &type)
 set our aa-type (could be "UNK") More...
 
void rotamer_aa (std::string const &type)
 AA to use for rotamer library. More...
 
std::string const & name () const
 get our (unique) residue name More...
 
void name (std::string const &name_in)
 set our (unique) residue name More...
 
std::string const & name3 () const
 get our 3letter code More...
 
void name3 (std::string const &name_in)
 set our 3letter code More...
 
char name1 () const
 get our 1letter code More...
 
void name1 (char const code)
 set our 1letter code More...
 
void set_mol_data (sdf::MolData const &mol_data)
 set the MolData object More...
 
sdf::MolData get_mol_data () const
 
AA const & aa () const
 our traditional residue type, if any More...
 
AA const & rotamer_aa () const
 
void set_RotamerLibraryName (std::string const &filename)
 
std::string get_RotamerLibraryName () const
 A residue parameter file can refer to a set of "pdb rotamers" that can be superimposed onto a starting position for use in the packer. These rotamers are loaded into the pack::dunbrack::RotamerLibrary at the time of their first use. More...
 
dihedral_atom_set const & dihedral (Size const dihe) const
 dihedral methods More...
 
utility::vector1< Size > const & dihedrals_for_atom (Size atomno) const
 Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom. More...
 
Size ndihe () const
 Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms. More...
 
void print_dihedrals () const
 
bondangle_atom_set const & bondangle (Size const bondang) const
 Return the indices for the set of atoms that define a particular intraresidue angle. More...
 
utility::vector1< Size > const & bondangles_for_atom (Size atomno) const
 Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom. More...
 
Size num_bondangles () const
 get number of intraresidue bond angles More...
 
void print_bondangles () const
 print intraresidue bond angles to standard out More...
 
void print_pretty_path_distances () const
 print chemical-bond path distances to standard out More...
 
void set_ncaa_rotlib_path (std::string const &path)
 Sets the path for the NCAA rotlib for the ResidueType. More...
 
std::string const & get_ncaa_rotlib_path () const
 Returns the path to the NCAA rotlib for the residue type. More...
 
void set_use_ncaa_rotlib (bool flag)
 Sets whether we are using a NCAA rotlib for the residue type. More...
 
bool get_use_ncaa_rotlib () const
 Returns whether we are using a NCAA rotlib for the residue type. More...
 
void set_ncaa_rotlib_n_rotameric_bins (Size n_rots)
 Sets the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More...
 
Size set_ncaa_rotlib_n_rotameric_bins () const
 Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More...
 
void set_ncaa_rotlib_n_bin_per_rot (utility::vector1< Size > n_bins_per_rot)
 Sets the number of rotamers for each rotatable bond described by the NCAA rotlib. More...
 
Size get_ncaa_rotlib_n_bin_per_rot (Size n_rot)
 Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for a single bond. More...
 
utility::vector1< Size > const & get_ncaa_rotlib_n_bin_per_rot () const
 Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds. More...
 
utility::vector1< two_atom_set >
const & 
atoms_within_one_bond_of_a_residue_connection (Size resconn) const
 Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More...
 
utility::vector1< std::pair
< Size, Size > > const & 
within1bonds_sets_for_atom (Size atomid) const
 Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More...
 
utility::vector1
< three_atom_set > const & 
atoms_within_two_bonds_of_a_residue_connection (Size resconn) const
 Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn. More...
 
utility::vector1< std::pair
< Size, Size > > 
within2bonds_sets_for_atom (Size atomid) const
 Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More...
 
core::chemical::rna::RNA_ResidueType
const & 
RNA_type () const
 
core::chemical::carbohydrates::CarbohydrateInfoCOP carbohydrate_info () const
 Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More...
 
void force_nbr_atom_orient (bool force_orient)
 Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...
 
bool force_nbr_atom_orient () const
 Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...
 
void select_orient_atoms (Size &center, Size &nbr1, Size &nbr2) const
 Selects three atoms for orienting this residue type. More...
 
utility::vector1< Adduct > const & defined_adducts () const
 get the adducts defined for this residue More...
 
void add_adduct (Adduct &adduct_in)
 
void report_adducts ()
 
void nondefault (bool in)
 
void base_restype_name (std::string const &in)
 
std::string base_restype_name () const
 

Public Attributes

bool serialized_
 

Private Member Functions

void setup_atom_ordering (AtomIndices &old2new)
 set up atom ordering map old2new, called by finalize() More...
 
void reorder_primary_data (AtomIndices const &old2new)
 reorder primary data in ResidueType given the old2new map, called by finalize() More...
 
void update_derived_data ()
 update derived data in ResidueType, called by finalize() More...
 
void update_residue_connection_mapping ()
 
void update_last_controlling_chi ()
 compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom. More...
 
void note_chi_controls_atom (Size chi, Size atomno)
 Recursive subroutine invoked by update_last_controlling_chi(). More...
 
void assign_internal_coordinates (std::string const &current_atom)
 @ recursive function to assign internal coordinates More...
 

Private Attributes

AtomTypeSetCAP atom_types_
 AtomTypeSet Object. More...
 
ElementSetCAP elements_
 
MMAtomTypeSetCAP mm_atom_types_
 MMAtomTypeSet. More...
 
orbitals::OrbitalTypeSetCAP orbital_types_
 Orbital types. More...
 
ResidueTypeSetCAP residue_type_set_
 
utility::vector1< Atomatoms_
 vector of atoms: More...
 
utility::vector1< Orbitalorbitals_
 
Size natoms_
 number of atoms More...
 
Size nheavyatoms_
 number of heavy atoms More...
 
Size n_hbond_acceptors_
 number of hbond_acceptors More...
 
Size n_hbond_donors_
 number of hbond_donors More...
 
Size n_orbitals_
 number of orbitals More...
 
Size n_backbone_heavyatoms_
 number of backbone heavy atoms More...
 
Size first_sidechain_hydrogen_
 the index of first sidechain hydrogen atom More...
 
Size ndihe_
 number of dihedral angle atom sets More...
 
utility::vector1
< utility::vector1< core::Size > > 
orbital_bonded_neighbor_
 indices of the atoms psuedo bonded atoms. Used in orbital code More...
 
utility::vector1< AtomIndicesbonded_neighbor_
 indices of each atom's bonded neighbors More...
 
utility::vector1
< utility::vector1< BondName > > 
bonded_neighbor_type_
 indices of each atom's bonded neighbor type (uses the same indexing scheme and order as bonded_neighbor_ More...
 
utility::vector1< AtomIndicescut_bond_neighbor_
 indices of each atom's bonded neighbors More...
 
utility::vector1< Sizeatom_base_
 indices of each atom's base atom More...
 
utility::vector1< Sizeabase2_
 indices of each atom's second base atom, for acceptors atom only More...
 
utility::vector1< Sizeattached_H_begin_
 indices of each heavyatom's first attached hydrogen More...
 
utility::vector1< Sizeattached_H_end_
 indices of each heavyatom's last attached hydrogen More...
 
utility::vector1< Sizeparents_
 atom parents More...
 
utility::vector1
< dihedral_atom_set
dihedral_atom_sets_
 vector of sets of atoms that make up dihedral angles in the residue More...
 
utility::vector1
< utility::vector1< Size > > 
dihedrals_for_atom_
 all intra-residue dihedral angles that each atom "participates" in. More...
 
utility::vector1
< bondangle_atom_set
bondangle_atom_sets_
 vector of sets of atoms that make up bond angles in the residue More...
 
utility::vector1
< utility::vector1< Size > > 
bondangles_for_atom_
 all intra-residue bond angles that each atom "participates" in. More...
 
utility::vector1< Sizelast_controlling_chi_
 
utility::vector1< AtomIndicesatoms_last_controlled_by_chi_
 
AtomIndices atoms_with_orb_index_
 indices of Hbond acceptor positions More...
 
AtomIndices Haro_index_
 
AtomIndices Hpol_index_
 
AtomIndices accpt_pos_
 
AtomIndices Hpos_polar_
 indices of polar Hydrogens for Hbond donors More...
 
AtomIndices Hpos_apolar_
 indices of apolar hydrogens More...
 
AtomIndices accpt_pos_sc_
 
AtomIndices Hpos_polar_sc_
 
AtomIndices all_bb_atoms_
 Indices of all backbone atoms, hydrogens and heavyatoms. More...
 
AtomIndices all_sc_atoms_
 Indices of all sidechain atoms, hydrogens and heavyatoms. More...
 
utility::vector1< intheavyatom_has_polar_hydrogens_
 
utility::vector1< intheavyatom_is_an_acceptor_
 
utility::vector1< intatom_is_polar_hydrogen_
 
AtomIndices mainchain_atoms_
 indices of all mainchain atoms More...
 
AtomIndices actcoord_atoms_
 indices of action coordinate centers More...
 
utility::vector1< AtomIndiceschi_atoms_
 indices of four atoms to build each chi angle More...
 
utility::vector1< boolis_proton_chi_
 
utility::vector1< Sizeproton_chis_
 
utility::vector1< Sizechi_2_proton_chi_
 
utility::vector1
< utility::vector1< Real > > 
proton_chi_samples_
 
utility::vector1
< utility::vector1< Real > > 
proton_chi_extra_samples_
 
utility::vector1
< utility::vector1< int > > 
path_distance_
 number of bonds separated between any pair of atoms in this residue More...
 
std::map< std::string, intatom_index_
 atom index lookup by atom name string More...
 
std::map< std::string, intorbitals_index_
 atom index lookup by atom name string More...
 
utility::vector1
< utility::vector1< std::pair
< Real, Real > > > 
chi_rotamers_
 Additional non-dunbrack rotamer bins. More...
 
std::string rotamer_library_name_
 
bool use_ncaa_rotlib_
 
std::string ncaa_rotlib_path_
 path to the NCAA rotlib More...
 
Size ncaa_rotlib_n_rots_
 the number of non-hydrogen chi angles in the NCAA rotlib More...
 
utility::vector1< Sizencaa_rotlib_n_bins_per_rot_
 the number of rotamer bins for each chi angle in the NCAA rotlib More...
 
utility::vector1< std::string > properties_
 residue properties as defined in the residue param files More...
 
bool is_polymer_
 
bool is_protein_
 
bool is_charged_
 
bool is_polar_
 
bool has_sc_orbitals_
 
bool is_aromatic_
 
bool is_DNA_
 
bool is_RNA_
 
bool is_NA_
 
bool is_carbohydrate_
 
bool is_ligand_
 
bool is_surface_
 
bool is_terminus_
 
bool is_lower_terminus_
 
bool is_upper_terminus_
 
bool is_phosphonate_
 
bool is_phosphonate_upper_
 
bool is_acetylated_nterminus_
 
bool is_methylated_cterminus_
 
bool is_coarse_
 
bool is_adduct_
 
utility::vector1< VariantTypevariant_types_
 here we store the patch operations/variant types that describe this residue More...
 
AA aa_
 standard rosetta aa-type for knowledge-based potentials, may be aa_unk More...
 
AA rotamer_aa_
 
std::string name_
 unique residue id More...
 
std::string name3_
 pdb-file id, need not be unique More...
 
char name1_
 one-letter code, also not necessarily unique More...
 
Size nbr_atom_
 atom used for calculating residue-level neighbors More...
 
Real nbr_radius_
 radius cutoff to define neighors More...
 
bool force_nbr_atom_orient_
 
Real molecular_mass_
 
Real molar_mass_
 
Size n_actcoord_atoms_
 number of actcoord atoms More...
 
sdf::MolData mol_data_
 the unprocessed metadata More...
 
utility::vector1
< ResidueConnection
residue_connections_
 Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections. More...
 
utility::vector1
< utility::vector1< Size > > 
atom_2_residue_connection_map_
 
utility::vector1
< utility::vector1
< two_atom_set > > 
atoms_within_one_bond_of_a_residue_connection_
 For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More...
 
utility::vector1
< utility::vector1< std::pair
< Size, Size > > > 
within1bonds_sets_for_atom_
 For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. More...
 
utility::vector1
< utility::vector1
< three_atom_set > > 
atoms_within_two_bonds_of_a_residue_connection_
 For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i. More...
 
utility::vector1
< utility::vector1< std::pair
< Size, Size > > > 
within2bonds_sets_for_atom_
 For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. More...
 
Size lower_connect_id_
 Polymer lower connections. More...
 
Size upper_connect_id_
 Polymer upper connections. More...
 
Size n_non_polymeric_residue_connections_
 
Size n_polymeric_residue_connections_
 
utility::vector1< std::string > branch_point_atoms_
 
AtomIndices delete_atoms_
 a list of atom indices to be deleted More...
 
AtomIndices force_bb_
 atom indices forced to be considered backbone More...
 
core::chemical::rna::RNA_ResidueType rna_residuetype_
 
core::chemical::carbohydrates::CarbohydrateInfoOP carbohydrate_info_
 
bool finalized_
 status More...
 
utility::vector1< Adductdefined_adducts_
 
bool nondefault_
 
std::string base_restype_name_
 

Detailed Description

silly demo class – what would the most familiar residue look like?

Basically a slice of aaproperties pack!

This is an exercise to define the properties of an alternative Residue object, arising from frustration with the conformation::Residue hierarchy.

Properties:

Questions:

Constructor & Destructor Documentation

core::chemical::ResidueType::~ResidueType ( )
virtual

destructor

References core::chemical::tr().

core::chemical::ResidueType::ResidueType ( AtomTypeSetCAP  atom_types,
ElementSetCAP  element_types,
MMAtomTypeSetCAP  mm_atom_types,
orbitals::OrbitalTypeSetCAP  orbital_types 
)

constructor

We use the AtomTypeSet object to assign atom_types to atoms inside add_atom, and to identify (polar) hydrogens, acceptors, etc.

Referenced by clone().

Member Function Documentation

void core::chemical::ResidueType::aa ( std::string const &  type)
inline

set our aa-type (could be "UNK")

References aa_, and core::chemical::aa_from_name().

Referenced by protocols::simple_moves::MinimalRotamer::aa(), core::conformation::Residue::aa(), protocols::loops::add_loop(), protocols::motifs::add_motif_bb_constraints(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), protocols::motifs::backbone_stub_match(), core::io::pdb::build_pose_as_is1(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), core::scoring::methods::get_parallel_h_for_arg(), core::scoring::dna::get_y_axis_atoms(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::constraints::is_aromatic(), core::conformation::Residue::is_similar_aa(), core::conformation::Residue::is_similar_rotamer(), protocols::multistate_design::limit_rotamer_set(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::Selector_AA::operator[](), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::chemical::ResidueDatabaseIO::read_residue_type(), protocols::toolbox::pose_metric_calculators::ChargeCalculator::recompute(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::constraints::requires_CB_mapping(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), protocols::optimize_weights::IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy(), core::scoring::methods::residue_type_has_waters(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().

AA const& core::chemical::ResidueType::aa ( ) const
inline

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be "aa_unk"

Not clear what AA is – maybe an int, maybe an enum, maybe a "key"

References aa_.

Size core::chemical::ResidueType::abase2 ( Size const  atomno) const

get index of an atom's second base atom

References abase2_.

Referenced by core::conformation::Residue::abase2().

AtomIndices const& core::chemical::ResidueType::accpt_pos ( ) const
inline

indices of atoms as Hbond acceptors

References accpt_pos_.

Referenced by core::conformation::Residue::accpt_pos().

AtomIndices const& core::chemical::ResidueType::accpt_pos_sc ( ) const
inline

indices of atoms as Hbond acceptors

References accpt_pos_sc_.

Referenced by core::conformation::Residue::accpt_pos_sc().

AtomIndices const& core::chemical::ResidueType::actcoord_atoms ( ) const
inline

get indices for atoms used to define actcoord

References actcoord_atoms_.

Referenced by core::conformation::Residue::actcoord_atoms(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::add_actcoord_atom ( std::string const &  atom)

add an atom to the list for calculating actcoord center

References actcoord_atoms_, atom_index(), finalized_, is_protein(), n_actcoord_atoms_, name_, and core::chemical::tr().

void core::chemical::ResidueType::add_adduct ( Adduct adduct_in)
inline

References defined_adducts_.

void core::chemical::ResidueType::add_atom ( std::string const &  atom_name,
std::string const &  atom_type_name,
std::string const &  mm_atom_type_name,
Real const  charge 
)
void core::chemical::ResidueType::add_bond ( std::string const &  atom_name1,
std::string const &  atom_name2 
)

add a bond between atom1 and atom2, if bond type is not specified, default to SingleBond

add a bond between atom1 and atom2 and add a BondType object referencing the bond (default bond type of SingleBond) update bonded_neighbor_ and resize it as necessary

References atom_index_, bonded_neighbor_, bonded_neighbor_type_, finalized_, has(), and core::chemical::SingleBond.

Referenced by core::chemical::AddBond::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_bond().

void core::chemical::ResidueType::add_bond ( std::string const &  atom_name1,
std::string const &  atom_name2,
BondName  bondLabel 
)

add a bond between atom1 and atom2 and add a BondType object referencing the bond using the specified bondName

References atom_index_, bonded_neighbor_, bonded_neighbor_type_, finalized_, and has().

void core::chemical::ResidueType::add_chi ( Size const  chino,
std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)
void core::chemical::ResidueType::add_chi_rotamer ( Size const  chino,
Real const  mean,
Real const  sdev 
)

add a rotamer bin for a given chi

add a rotamer bin for a given chi a rotamer bin has the mean and standard deviation

References chi_rotamers_.

Referenced by core::chemical::AddChiRotamer::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi_rotamer().

void core::chemical::ResidueType::add_cut_bond ( std::string const &  atom_name1,
std::string const &  atom_name2 
)

add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond

add a cut_bond between atom1 and atom2, which disallows an atom-tree connection, though the atoms are really bonded. update cut_bond_ and resize it as necessary

References atom_index_, cut_bond_neighbor_, finalized_, and has().

Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_cut_bond().

void core::chemical::ResidueType::add_orbital ( std::string &  orbital_name,
std::string &  orbital_type_name 
)

add an orbital onto a residue based upon atom

Note
this does not set xyz coordiates for the added orbital but sets the index of the orbital and maps it to the type of orbital.

References finalized_, n_orbitals_, orbital_types_, orbitals_, orbitals_index_, and core::chemical::strip_whitespace().

void core::chemical::ResidueType::add_orbital_bond ( std::string const &  atom_name1,
std::string const &  orbital_name 
)

add an orbital bond between an atom and an orbital.

Note
NOTE!!!!! This is indexed based upon atoms, not orbitals. That means that in your params file you must have the atom as the first and orbital as the second.

References atom_index_, finalized_, has(), has_orbital(), orbital_bonded_neighbor_, and orbitals_index_.

void core::chemical::ResidueType::add_property ( std::string const &  property)
Size core::chemical::ResidueType::add_residue_connection ( std::string const &  atom_name)
void core::chemical::ResidueType::add_variant_type ( VariantType const &  variant_type)
inline

add one more variant type to this ResidueType

References has_variant_type(), and variant_types_.

Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_variant().

AtomIndices const& core::chemical::ResidueType::all_bb_atoms ( ) const
inline
AtomIndices const& core::chemical::ResidueType::all_sc_atoms ( ) const
inline
void core::chemical::ResidueType::assign_internal_coordinates ( )
void core::chemical::ResidueType::assign_internal_coordinates ( std::string const &  current_atom)
private
void core::chemical::ResidueType::assign_neighbor_atom ( )
Atom & core::chemical::ResidueType::atom ( Size const  atom_index)

References atom_index(), and atoms_.

Referenced by core::chemical::SetAtomicCharge::apply(), core::conformation::Residue::atomic_charge(), attached_H_begin(), attached_H_end(), protocols::match::bump_grid_to_enclose_pose(), calculate_icoor(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), debug_dump_icoor(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::mm_atom_name(), path_distance(), core::scoring::PQR::PQR(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::conformation::Residue::Residue(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::pack::task::operation::util::select_coord_for_residue(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

Atom const & core::chemical::ResidueType::atom ( Size const  atom_index) const

References atom_index(), and atoms_.

Atom & core::chemical::ResidueType::atom ( std::string const &  atom_name)

References atom_index(), and atoms_.

Atom const & core::chemical::ResidueType::atom ( std::string const &  atom_name) const

References atom_index(), and atoms_.

Size core::chemical::ResidueType::atom_base ( Size const  atomno) const
bool core::chemical::ResidueType::atom_forms_residue_connection ( Size const  atomid)
inline

Does an atom form any inter-residue chemical bonds?

References atom_2_residue_connection_map_.

Size core::chemical::ResidueType::atom_index ( std::string const &  name) const

get atom index by name

References atom_index_, is_protein(), name3(), show_all_atom_names(), and core::chemical::tr().

Referenced by add_actcoord_atom(), core::coarse::Translator::add_atom(), protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::hybridization::add_non_protein_cst(), add_residue_connection(), protocols::hybridization::TMalign::alignment2AtomMap(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::antibody2::GraftOneCDRLoop::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::antibody::GraftOneMover::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata(), assign_internal_coordinates(), atom(), core::conformation::Residue::atom_index(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::io::pdb::build_pose_as_is1(), calculate_icoor(), protocols::fldsgn::MatchResidues::compute_comb(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), protocols::match::Matcher::create_ds_builder(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), delete_atom(), protocols::topology_broker::fix_mainchain_connect(), protocols::loops::fix_with_coord_cst(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::forge::constraints::NtoC_RCG::generate_remodel_constraints(), protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::ICoorAtomID::ICoorAtomID(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), core::pose::named_atom_id_to_atom_id(), nbr_atom(), core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(), core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(), core::scoring::constraints::parse_NMR_name_old(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), protocols::constraints_additional::BindingSiteConstraint::read_def(), core::scoring::constraints::BigBinConstraint::read_def(), protocols::evaluation::PCA::read_structure(), core::scoring::constraints::requires_CB_mapping(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), core::pack::task::operation::util::select_coord_for_residue(), select_orient_atoms(), set_atom_type(), set_backbone_heavyatom(), set_ideal_xyz(), set_lower_connect_atom(), set_mm_atom_type(), set_upper_connect_atom(), protocols::rna::setup_base_pair_constraints(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), and protocols::fldsgn::MatchResidues::superimpose_comb().

bool core::chemical::ResidueType::atom_is_backbone ( Size const  atomno) const
inline
bool core::chemical::ResidueType::atom_is_hydrogen ( Size const  atomno) const
inline

quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last.

References finalized_, natoms_, and nheavyatoms_.

Referenced by assign_neighbor_atom(), core::conformation::Residue::atom_is_hydrogen(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), and core::scoring::is_protein_sidechain_heavyatom().

bool core::chemical::ResidueType::atom_is_polar_hydrogen ( Size  ind) const
inline
std::string const & core::chemical::ResidueType::atom_name ( Size const  index) const

get atom name by index

Get the atom name by index.

References atoms_.

Referenced by core::coarse::Translator::add_atom(), add_atom(), assign_internal_coordinates(), core::conformation::Residue::atom_name(), protocols::swa::rna::atom_square_deviation(), protocols::swa::rna::base_atoms_square_deviation(), core::io::pdb::build_pose_as_is1(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::swa::RigidBodySampler::check_num_hbonds(), protocols::swa::StepWiseScreener::copy_coords(), protocols::swa::protein::StepWiseProteinScreener::copy_coords(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), protocols::toolbox::AllowInsert::initialize(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_atom(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::MiniPose::MiniPose(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), protocols::swa::rna::print_atom_info(), protocols::ligand_docking::print_buried_unsat_Hbonds(), protocols::swa::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::swa::rna::Print_torsion_info(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::mm::score_atom_centrally(), core::scoring::methods::MMBondAngleEnergy::score_atom_centrally(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::swa::rna::setup_suite_atom_id_map(), core::scoring::methods::setup_water_builders_for_residue_type(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), and core::chemical::write_topology_file().

AtomType const & core::chemical::ResidueType::atom_type ( Size const  atomno) const
AtomTypeSet const& core::chemical::ResidueType::atom_type_set ( ) const
inline

access by reference the atomset for which this residue is constructed

References atom_types_.

Referenced by core::conformation::Residue::atom_type_set(), and protocols::features::AtomAtomPairFeatures::report_atom_pairs().

AtomTypeSetCAP core::chemical::ResidueType::atom_type_set_ptr ( ) const
inline
utility::vector1< AtomIndices > const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( ) const
inline
AtomIndices const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( Size  chi) const
inline

Read access to the Atoms last controlled by a particular chi.

References atoms_last_controlled_by_chi_.

AtomIndices const& core::chemical::ResidueType::atoms_with_orb_index ( ) const
inline
utility::vector1< two_atom_set > const& core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection ( Size  resconn) const
inline
utility::vector1< three_atom_set > const& core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection ( Size  resconn) const
inline

Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn.

References atoms_within_two_bonds_of_a_residue_connection_.

Referenced by core::scoring::methods::MMTorsionEnergy::residue_pair_energy().

Size core::chemical::ResidueType::attached_H_begin ( Size const  atom) const
inline
AtomIndices const& core::chemical::ResidueType::attached_H_begin ( ) const
inline

for all heavy atoms, index numbers of their first attached Hydrogen

References attached_H_begin_.

Size core::chemical::ResidueType::attached_H_end ( Size const  atom) const
inline
AtomIndices const& core::chemical::ResidueType::attached_H_end ( ) const
inline

for all heavy atoms, index numbers of their last attached Hydrogen

References attached_H_end_.

void core::chemical::ResidueType::base_restype_name ( std::string const &  in)
inline

References base_restype_name_.

std::string core::chemical::ResidueType::base_restype_name ( ) const
inline

References base_restype_name_.

bondangle_atom_set const& core::chemical::ResidueType::bondangle ( Size const  bondang) const
inline
utility::vector1< Size > const& core::chemical::ResidueType::bondangles_for_atom ( Size  atomno) const
inline

Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.

References bondangles_for_atom_.

Referenced by core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative().

AtomIndices const& core::chemical::ResidueType::bonded_neighbor ( Size const  atomno) const
inline
utility::vector1<BondName> const& core::chemical::ResidueType::bonded_neighbor_types ( Size const  atomno) const
inline
utility::vector1<core::Size> const& core::chemical::ResidueType::bonded_orbitals ( Size const  atomno) const
inline
void core::chemical::ResidueType::calculate_icoor ( std::string const &  child,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3 
)
core::chemical::carbohydrates::CarbohydrateInfoCOP core::chemical::ResidueType::carbohydrate_info ( ) const
Size core::chemical::ResidueType::chi_2_proton_chi ( Size  chi_index) const
inline
AtomIndices const& core::chemical::ResidueType::chi_atoms ( Size const  chino) const
inline
utility::vector1< AtomIndices > const& core::chemical::ResidueType::chi_atoms ( ) const
inline

indices of the atoms which are used to define all the chi angles

References chi_atoms_.

utility::vector1< std::pair< Real, Real > > const& core::chemical::ResidueType::chi_rotamers ( Size const  chino) const
inline
ResidueTypeOP core::chemical::ResidueType::clone ( ) const
AtomIndices const& core::chemical::ResidueType::cut_bond_neighbor ( Size const  atomno) const
inline
void core::chemical::ResidueType::debug_dump_icoor ( )

Dump out atomnames and icoor values.

References atom(), atom_name(), core::chemical::Atom::ideal_xyz(), name3(), natoms(), and core::chemical::tr().

utility::vector1< Adduct > const& core::chemical::ResidueType::defined_adducts ( ) const
inline
void core::chemical::ResidueType::delete_atom ( std::string const &  name)
inline

flag an atom for deletion by adding its index to the delete_atom_ list

References atom_index(), delete_atoms_, finalized_, and has().

Referenced by core::chemical::DeleteAtom::apply().

void core::chemical::ResidueType::delete_property ( std::string const &  property)
dihedral_atom_set const& core::chemical::ResidueType::dihedral ( Size const  dihe) const
inline
utility::vector1< Size > const& core::chemical::ResidueType::dihedrals_for_atom ( Size  atomno) const
inline

Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.

References dihedrals_for_atom_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().

ElementSet const& core::chemical::ResidueType::element_set ( ) const
inline

access by reference the atomset for which this residue is constructed

References elements_.

void core::chemical::ResidueType::finalize ( )

recalculate derived data, potentially reordering atom-indices

This routine updates all the derived data.
Atom order will probably change after this call, so if you add a new property that depends on atom-indices that will have to be updated below.

References delete_atoms_, finalized_, force_bb_, reorder_primary_data(), setup_atom_ordering(), and update_derived_data().

Size core::chemical::ResidueType::first_sidechain_atom ( ) const
inline
Size core::chemical::ResidueType::first_sidechain_hydrogen ( ) const
inline

index of the first sidehchain hydrogen

References finalized_, and first_sidechain_hydrogen_.

Referenced by core::conformation::Residue::first_sidechain_hydrogen().

void core::chemical::ResidueType::force_nbr_atom_orient ( bool  force_orient)
inline

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

Referenced by core::chemical::SetOrientAtom::apply(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::force_nbr_atom_orient ( ) const
inline

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

Referenced by select_orient_atoms().

sdf::MolData core::chemical::ResidueType::get_mol_data ( ) const
inline

References mol_data_.

Size core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot ( Size  n_rot)
inline

Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for a single bond.

References ncaa_rotlib_n_bins_per_rot_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary().

utility::vector1<Size> const& core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot ( ) const
inline

Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds.

References ncaa_rotlib_n_bins_per_rot_.

std::string const& core::chemical::ResidueType::get_ncaa_rotlib_path ( ) const
inline

Returns the path to the NCAA rotlib for the residue type.

References ncaa_rotlib_path_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary().

std::string core::chemical::ResidueType::get_RotamerLibraryName ( ) const

A residue parameter file can refer to a set of "pdb rotamers" that can be superimposed onto a starting position for use in the packer. These rotamers are loaded into the pack::dunbrack::RotamerLibrary at the time of their first use.

References rotamer_library_name_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library(), and core::chemical::ResidueDatabaseIO::report_residue_type().

bool core::chemical::ResidueType::get_use_ncaa_rotlib ( ) const
inline

Returns whether we are using a NCAA rotlib for the residue type.

References use_ncaa_rotlib_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library().

AtomIndices const& core::chemical::ResidueType::Haro_index ( ) const
inline

return indices of aromatic Hydrogens

References Haro_index_.

Referenced by core::conformation::Residue::Haro_index().

bool core::chemical::ResidueType::has ( std::string const &  atom_name) const
inline

is this atom present in this residue?

References atom_index_.

Referenced by core::coarse::Translator::add_atom(), add_bond(), add_chi(), add_cut_bond(), protocols::hybridization::add_non_protein_cst(), add_orbital_bond(), core::pack::task::operation::util::any_atoms_within_cutoff(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddConnect::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), core::io::pdb::build_pose_as_is1(), protocols::hybridization::InsertChunkMover::check_overlap(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), delete_atom(), protocols::swa::protein::do_set_xyz(), core::conformation::Residue::has(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::pose::named_atom_id_to_atom_id(), core::conformation::Residue::place(), redefine_chi(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::pack::task::operation::util::select_coord_for_residue(), set_atom_base(), set_icoor(), protocols::rna::setup_coarse_chainbreak_constraints(), and core::coarse::Translator::Translator().

bool core::chemical::ResidueType::has_atom_name ( std::string const &  name) const

Check if residue type has an atom by a given atomname.

References atom_index_.

Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::is_disulfide_bond(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), and core::scoring::setup_matching_atoms_with_given_names().

bool core::chemical::ResidueType::has_orbital ( std::string const &  orbital_name) const
inline

is this orbital present in this residue?

References orbitals_index_.

Referenced by add_orbital_bond().

bool core::chemical::ResidueType::has_property ( std::string const &  property) const
inline
bool core::chemical::ResidueType::has_sc_orbitals ( ) const
inline

does this residue have sidechain orbitals?

References has_sc_orbitals_.

Referenced by core::conformation::Residue::has_sc_orbitals().

bool core::chemical::ResidueType::has_variant_type ( VariantType const &  variant_type) const
inline

Generic variant access – SLOW!!!!!

References variant_types_.

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), add_variant_type(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants(), core::io::pdb::build_pose_as_is1(), protocols::swa::InputStreamWithResidueInfo::cleanup_pose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::swa::Figure_out_moving_residues(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::conformation::Residue::has_variant_type(), core::scoring::rna::is_cutpoint_open(), is_virtual_residue(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::make_pose_from_sequence(), nonadduct_variants_match(), core::chemical::Selector_VARIANT_TYPE::operator[](), core::chemical::Selector_MATCH_VARIANTS::operator[](), protocols::swa::protein::StepWiseProteinPoseMinimizer::pose_has_chainbreak(), protocols::swa::rna::remove_all_variant_types(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::swa::rna::Remove_virtual_O2Star_hydrogen(), core::scoring::methods::pHEnergy::residue_energy(), core::pose::residue_types_from_sequence(), protocols::swa::StepWisePoseSetup::setup_disulfides(), protocols::swa::protein::setup_protein_backbone_atom_id_map(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), and variants_match().

bool core::chemical::ResidueType::heavyatom_has_polar_hydrogens ( Size  ind) const
inline
bool core::chemical::ResidueType::heavyatom_is_an_acceptor ( Size  ind) const
inline
AtomIndices const& core::chemical::ResidueType::Hpol_index ( ) const
inline

return indices of polar Hydrogens

References Hpol_index_.

Referenced by core::conformation::Residue::Hpol_index().

AtomIndices const& core::chemical::ResidueType::Hpos_apolar ( ) const
inline

indices of non-polar hydrogens as potential carbon Hbond donors

References Hpos_apolar_.

Referenced by core::conformation::Residue::Hpos_apolar().

AtomIndices const& core::chemical::ResidueType::Hpos_polar ( ) const
inline

indices of polar hydrogens as Hbond donors

References Hpos_polar_.

Referenced by core::conformation::Residue::Hpos_polar().

AtomIndices const& core::chemical::ResidueType::Hpos_polar_sc ( ) const
inline
AtomICoor const & core::chemical::ResidueType::icoor ( Size const  atm) const
bool core::chemical::ResidueType::is_acetylated_nterminus ( ) const
inline

is acetylated n terminus

References is_acetylated_nterminus_.

bool core::chemical::ResidueType::is_adduct ( ) const
inline

is an adduct-modified residue?

References is_adduct_.

bool core::chemical::ResidueType::is_aromatic ( ) const
inline
bool core::chemical::ResidueType::is_branch_point ( ) const
inline

is branch point for a branched polymer?

References branch_point_atoms_.

bool core::chemical::ResidueType::is_carbohydrate ( ) const
inline
bool core::chemical::ResidueType::is_charged ( ) const
inline
bool core::chemical::ResidueType::is_coarse ( ) const
inline
bool core::chemical::ResidueType::is_DNA ( ) const
inline
bool core::chemical::ResidueType::is_ligand ( ) const
inline
bool core::chemical::ResidueType::is_lower_terminus ( ) const
inline
bool core::chemical::ResidueType::is_methylated_cterminus ( ) const
inline

is methylated c terminus

References is_methylated_cterminus_.

bool core::chemical::ResidueType::is_NA ( ) const
inline
bool core::chemical::ResidueType::is_polar ( ) const
inline
bool core::chemical::ResidueType::is_polymer ( ) const
inline
bool core::chemical::ResidueType::is_protein ( ) const
inline

is protein?

References is_protein_.

Referenced by add_actcoord_atom(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::motifs::add_motif_sc_constraints(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), atom_index(), protocols::toolbox::CA_superimpose(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::simple_moves::ConsensusDesignMover::create_sequence_profile_constraints(), core::scoring::methods::dfire::DFIRE_Energy::defines_residue_pair_energy(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::loops::extract_secondary_structure_chunks(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::surface_docking::FullatomRelaxMover::FinalizeMovers(), protocols::loops::find_non_protein_chunks(), protocols::match::BfactorMPM::get_ca_bfactors(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::fldsgn::topology::SS_Info2::initialize(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::features::ResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), protocols::match::AddAllPositionsMPM::modified_match_positions(), protocols::match::RemoveNorCTermMPM::modified_match_positions(), protocols::loops::native_loop_core_CA_rmsd(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::motifs::MotifSearch::position_vector_setup(), protocols::motifs::LigandMotifSearch::position_vector_setup(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::hybridization::TMalign::read_pose(), protocols::toolbox::pose_metric_calculators::HPatchCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SurfaceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::ChargeCalculator::recompute(), protocols::toolbox::pose_metric_calculators::PackstatCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::pose::set_ss_from_phipsi(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::swa::protein::setup_protein_backbone_atom_id_map(), protocols::swa::protein::setup_protein_CA_atom_id_map(), core::pose::transfer_phi_psi(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_proton_chi ( Size const  chino) const
inline
bool core::chemical::ResidueType::is_RNA ( ) const
inline
bool core::chemical::ResidueType::is_surface ( ) const
inline

is surface? (e.g. enamel)

References is_surface_.

Referenced by core::conformation::Residue::is_surface(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_terminus ( ) const
inline
bool core::chemical::ResidueType::is_upper_terminus ( ) const
inline
bool core::chemical::ResidueType::is_virtual ( Size const &  atomno) const
bool core::chemical::ResidueType::is_virtual_residue ( ) const

Check if residue is 'VIRTUAL_RESIDUE'.

References has_variant_type().

Referenced by core::conformation::Residue::is_virtual_residue().

Size core::chemical::ResidueType::last_backbone_atom ( ) const
inline
utility::vector1< Size > const& core::chemical::ResidueType::last_controlling_chi ( ) const
inline

Read access to the last_controlling_chi_ array.

References last_controlling_chi_.

Referenced by protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type().

Size core::chemical::ResidueType::last_controlling_chi ( Size  atomno) const
inline

The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.

References last_controlling_chi_.

ResidueConnection const & core::chemical::ResidueType::lower_connect ( ) const
Size core::chemical::ResidueType::lower_connect_atom ( ) const
Size core::chemical::ResidueType::lower_connect_id ( ) const
inline
Size core::chemical::ResidueType::mainchain_atom ( Size const  atm) const
inline
AtomIndices const& core::chemical::ResidueType::mainchain_atoms ( ) const
inline
MMAtomType const & core::chemical::ResidueType::mm_atom_type ( Size const  atomno) const

Get the MM atom_type for this atom by its index number in this residue.

References atoms_, and mm_atom_types_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParam::init(), print_bondangles(), print_dihedrals(), and core::chemical::write_topology_file().

core::Real const& core::chemical::ResidueType::molar_mass ( ) const
inline

get the molecular weight of this residue

References molar_mass_.

Referenced by core::pose::molar_mass().

core::Real const& core::chemical::ResidueType::molecular_mass ( ) const
inline

get the molecular weight of this residue

References molecular_mass_.

Referenced by core::pose::molecular_mass().

Size core::chemical::ResidueType::n_hbond_acceptors ( ) const
inline

number of hbond_acceptors

References n_hbond_acceptors_.

Referenced by core::conformation::Residue::n_hbond_acceptors().

Size core::chemical::ResidueType::n_hbond_donors ( ) const
inline

number of hbond_donors

References n_hbond_donors_.

Referenced by core::conformation::Residue::n_hbond_donors().

Size core::chemical::ResidueType::n_non_polymeric_residue_connections ( ) const
inline
Size core::chemical::ResidueType::n_orbitals ( ) const
inline

number of orbitals

References n_orbitals_.

Referenced by core::conformation::Residue::n_orbitals().

Size core::chemical::ResidueType::n_polymeric_residue_connections ( ) const
inline
Size core::chemical::ResidueType::n_proton_chi ( ) const
inline
Size core::chemical::ResidueType::n_residue_connections ( ) const
Size core::chemical::ResidueType::n_residue_connections_for_atom ( Size const  atomid) const
inline
std::string const& core::chemical::ResidueType::name ( ) const
inline

get our (unique) residue name

References name_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::chemical::Patch::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::chemical::apply_adducts_to_residue(), assign_neighbor_atom(), core::io::pdb::build_pose_as_is1(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::relax::delete_virtual_residues(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::import_pose::atom_tree_diffs::dump_reference_pose(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::conformation::Residue::fill_missing_atoms(), core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::loops::get_tenA_neighbor_residues(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::methods::LKB_ResidueInfo::initialize_residue_type(), protocols::features::HBondFeatures::insert_site_row(), core::pack::dunbrack::load_unboundrot(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::conformation::Residue::name(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::coarse::CoarseEtable::print_residue_info(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::pose::remove_virtual_residues(), reorder_primary_data(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::ResidueDatabaseIO::report_residue_type_properties(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::loops::select_loop_residues(), select_orient_atoms(), core::import_pose::set_reasonable_fold_tree(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), core::scoring::methods::setup_water_builders_for_residue_type(), core::util::switch_to_residue_type_set(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), core::io::serialization::write_binary(), core::chemical::ResidueDatabaseIO::write_residuetype_to_database(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::name ( std::string const &  name_in)
inline

set our (unique) residue name

References name_.

char core::chemical::ResidueType::name1 ( ) const
inline
void core::chemical::ResidueType::name1 ( char const  code)
inline

set our 1letter code

References name1_.

std::string const& core::chemical::ResidueType::name3 ( ) const
inline

get our 3letter code

References name3_.

Referenced by protocols::loops::add_loop(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::dna::WatsonCrickRotamerCouplings::apply(), core::pack::task::operation::OptCysHG::apply(), protocols::match::MatcherMover::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), core::chemical::SetIO_String::apply(), atom_index(), core::scoring::automorphic_rmsd(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), protocols::ligand_docking::MoveMapBuilder::build(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::flxbb::constraints_sheet(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), debug_dump_icoor(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::RotamerSet_::different_resgroup(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::frac_atoms_within(), protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), core::scoring::methods::get_restag(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), core::conformation::Residue::is_similar_rotamer(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), core::conformation::Residue::name3(), core::pack::task::operation::ResidueName3Is::operator()(), core::chemical::Selector_NAME3::operator[](), orbital_index(), core::scoring::constraints::parse_NMR_name_old(), protocols::dna::DnaChains::print(), protocols::ligand_docking::print_buried_unsat_Hbonds(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::viewer::print_node(), protocols::dna::DnaInterfacePacker::protein_scan(), core::chemical::ResidueDatabaseIO::read_residue_type(), report_adducts(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::conformation::setup_corresponding_atoms(), core::scoring::hbonds::HBond::show(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_residue_type_set(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::name3 ( std::string const &  name_in)
inline

set our 3letter code

References name3_.

Size core::chemical::ResidueType::natoms ( ) const
inline

Get the chemical atom_type index number for this atom by its index number in this residue.

number of atoms

References natoms_.

Referenced by core::conformation::annotated_atom_graph_from_conformation(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::seeded_abinitio::PlaceFragments::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::apply_transform_Rx_plus_v(), protocols::hybridization::apply_transformation(), core::conformation::atom_graph_from_conformation(), core::scoring::automorphic_rmsd(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::io::pdb::build_pose_as_is1(), protocols::toolbox::CA_superimpose(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::toolbox::AllowInsert::calculate_atom_id_domain_map(), protocols::toolbox::AllowInsert::calculate_atom_id_map(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::swa::StepWiseScreener::copy_coords(), protocols::swa::protein::StepWiseProteinScreener::copy_coords(), core::pose::copy_dofs(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::io::silent::BinaryRNASilentStruct::fill_pose(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::ligand_docking::frac_atoms_within(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::get_residue_path_distances(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::toolbox::AllowInsert::initialize(), core::pose::initialize_atomid_map(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::natoms(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), core::conformation::symmetry::recenter(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), protocols::fibril::reorient_extended_fibril(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::conformation::Residue::Residue(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), protocols::swa::rotate(), select_orient_atoms(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), core::scoring::methods::setup_water_builders_for_residue_type(), core::scoring::superimpose_pose(), protocols::swa::translate(), core::chemical::write_topology_file(), protocols::sic_dock::xform_pose(), core::fragment::xform_pose(), and protocols::sic_dock::xform_pose_rev().

void core::chemical::ResidueType::nbr_atom ( std::string const &  atom_name)
inline
Size core::chemical::ResidueType::nbr_atom ( ) const
inline

get nbr_atom used to define residue-level neighbors

References nbr_atom_.

Referenced by assign_neighbor_atom(), and select_orient_atoms().

void core::chemical::ResidueType::nbr_radius ( Real const  radius)
inline
Real core::chemical::ResidueType::nbr_radius ( ) const
inline

get nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

AtomIndices const& core::chemical::ResidueType::nbrs ( Size const  atomno) const
inline
Size core::chemical::ResidueType::nchi ( ) const
inline

number of chi angles

References chi_atoms_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::MinimalRotamer::atom_is_ideal(), protocols::comparative_modeling::chis_from_pose(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::conformation::Residue::nchi(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::simple_moves::MinimalRotamer::record_chi(), protocols::swa::protein::StepWiseProteinPacker::reinstate_side_chain_angles(), protocols::swa::protein::StepWiseProteinResidueSampler::reinstate_side_chain_angles(), protocols::swa::protein::reinstate_side_chain_angles(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::conformation::Residue::Residue(), update_last_controlling_chi(), and core::chemical::write_topology_file().

Size core::chemical::ResidueType::ndihe ( ) const
inline

Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms.

References ndihe_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions().

orbitals::ICoorOrbitalData const & core::chemical::ResidueType::new_orbital_icoor_data ( Size const  orbital_index) const
Size core::chemical::ResidueType::nheavyatoms ( ) const
inline
bool core::chemical::ResidueType::nonadduct_variants_match ( ResidueType const &  other) const

similar to variants_match(), but allows different adduct-modified states

References core::chemical::ADDUCT, has_variant_type(), and variant_types_.

Referenced by core::pack::task::ResidueLevelTask_::ResidueLevelTask_().

void core::chemical::ResidueType::nondefault ( bool  in)
inline

References nondefault_.

void core::chemical::ResidueType::note_chi_controls_atom ( Size  chi,
Size  atomno 
)
private

Recursive subroutine invoked by update_last_controlling_chi().

O(N) recursive algorithm for determining the last chi for each atom. Each atom is visited at most twice.

References atom_base_, bonded_neighbor_, last_controlling_chi_, and nbrs().

Referenced by update_last_controlling_chi().

Size core::chemical::ResidueType::num_bondangles ( ) const
inline
Size core::chemical::ResidueType::number_bonded_heavyatoms ( Size const  atomno) const
inline

indicates how many heavyatom bonded neighbors an atom has

References bonded_neighbor_, and number_bonded_hydrogens().

Size core::chemical::ResidueType::number_bonded_hydrogens ( Size const  atomno) const
inline
Orbital const & core::chemical::ResidueType::orbital ( Size const  orbital_index) const
Orbital const & core::chemical::ResidueType::orbital ( std::string const &  orbital_name) const

References orbital_index(), and orbitals_.

orbitals::ICoorOrbitalData const & core::chemical::ResidueType::orbital_icoor_data ( Size const  orbital_index) const

References orbital_index(), and orbitals_.

core::Size core::chemical::ResidueType::orbital_index ( std::string const &  name) const

orbital name by index

get orbital index by name

References name3(), and orbitals_index_.

Referenced by new_orbital_icoor_data(), orbital(), orbital_icoor_data(), orbital_type(), reorder_primary_data(), and set_orbital_icoor_id().

orbitals::OrbitalType const & core::chemical::ResidueType::orbital_type ( int const  orbital_index) const

Get the MM atom_type index number for this atom by its index number in this residue.

References orbital_index(), orbital_types_, and orbitals_.

Referenced by core::conformation::Residue::orbital_type().

int core::chemical::ResidueType::path_distance ( Size  at1,
Size  at2 
) const
inline

path distance (number of bonds separated) between a pair of atoms

References path_distance_.

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::conformation::Residue::path_distance().

utility::vector1< int > const& core::chemical::ResidueType::path_distance ( Size  atom) const
inline

shortest path distance for an atom to all other residue atoms

References atom(), and path_distance_.

utility::vector1< utility::vector1< int > > const& core::chemical::ResidueType::path_distances ( ) const
inline

accessor of path_distance_ data for this residue, which is a 2D array

References path_distance_.

Referenced by core::conformation::Residue::path_distances(), and update_derived_data().

void core::chemical::ResidueType::print_bondangles ( ) const
void core::chemical::ResidueType::print_dihedrals ( ) const

as non-member so it has not to show up in the header

this might return 0, so please check for that

References atom_type(), atoms_, dihedral_atom_sets_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), ndihe_, and core::chemical::tr().

void core::chemical::ResidueType::print_pretty_path_distances ( ) const

print chemical-bond path distances to standard out

References atoms_, natoms_, path_distance_, and core::chemical::tr().

utility::vector1< std::string > const & core::chemical::ResidueType::properties ( ) const

acess specified properties

get all specified properties for this residue type

References properties_.

Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_properties().

Size core::chemical::ResidueType::proton_chi_2_chi ( Size  proton_chi_id) const
inline

translate proton_chi to global chi

References proton_chis_.

Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().

utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_extra_samples ( Size  proton_chi) const
inline
utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_samples ( Size  proton_chi) const
inline
void core::chemical::ResidueType::redefine_chi ( Size const  chino,
std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

redefine a chi angle based on four atoms

References atom_index_, chi_2_proton_chi_, chi_atoms_, finalized_, has(), and is_proton_chi_.

Referenced by core::chemical::RedefineChi::apply().

void core::chemical::ResidueType::reorder_primary_data ( AtomIndices const &  old2new)
private
void core::chemical::ResidueType::report_adducts ( )
void core::chemical::ResidueType::require_final ( ) const
inline

an assertion funtion to ensure an ResidueType has been finalized

References finalized_.

bool core::chemical::ResidueType::requires_actcoord ( ) const
inline
Size core::chemical::ResidueType::residue_connect_atom_index ( Size const  resconn_id) const
ResidueConnection const & core::chemical::ResidueType::residue_connection ( Size const  i) const
ResidueConnection & core::chemical::ResidueType::residue_connection ( Size const  i)

References residue_connections_.

Size core::chemical::ResidueType::residue_connection_id_for_atom ( Size const  atomid) const
inline
bool core::chemical::ResidueType::residue_connection_is_polymeric ( Size const  resconn_id) const
inline
utility::vector1< Size > const& core::chemical::ResidueType::residue_connections_for_atom ( Size const  atomid) const
inline
ResidueTypeSet const & core::chemical::ResidueType::residue_type_set ( ) const
void core::chemical::ResidueType::residue_type_set ( ResidueTypeSetCAP  set_in)

set the residue type set of origin.

References residue_type_set_.

core::chemical::rna::RNA_ResidueType const& core::chemical::ResidueType::RNA_type ( ) const
inline
void core::chemical::ResidueType::rotamer_aa ( std::string const &  type)
inline
AA const& core::chemical::ResidueType::rotamer_aa ( ) const
inline
void core::chemical::ResidueType::select_orient_atoms ( Size center,
Size nbr1,
Size nbr2 
) const
void core::chemical::ResidueType::set_adduct_flag ( bool  adduct_in)
inline

References is_adduct_.

void core::chemical::ResidueType::set_atom_base ( std::string const &  atom_name1,
std::string const &  atom_name2 
)

sets atom_base[ atom1 ] = atom2

sets atom_base_[atom1] = atom2 resize atom_base_ vector as necessary

References atom_base_, atom_index_, bonded_neighbor_, cut_bond_neighbor_, finalized_, has(), and natoms_.

Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), and set_icoor().

void core::chemical::ResidueType::set_atom_type ( std::string const &  atom_name,
std::string const &  atom_type_name 
)

set atom type

References atom_index(), atom_types_, and atoms_.

Referenced by core::chemical::SetAtomType::apply().

void core::chemical::ResidueType::set_backbone_heavyatom ( std::string const &  name)

set an atom as backbone heavy atom

backbone stuff is a little tricky if we want to allow newly added atoms, eg in patching, to be backbone atoms. We move any exsiting backbone heavy atoms back into force_bb_ list and add the new one. Afterwards, the new backbone heavy atom list will be generated in finalize() using info from force_bb_.

References atom_index(), finalized_, force_bb_, and n_backbone_heavyatoms_.

Referenced by core::chemical::SetBackboneHeavyatom::apply().

void core::chemical::ResidueType::set_icoor ( std::string const &  atm,
Real const  phi,
Real const  theta,
Real const  d,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3,
bool const  update_xyz = false 
)
void core::chemical::ResidueType::set_icoor ( Size const &  index,
std::string const &  atm,
Real const  phi,
Real const  theta,
Real const  d,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3,
bool const  update_xyz = false 
)
void core::chemical::ResidueType::set_ideal_xyz ( std::string const &  atm,
Vector const &  xyz_in 
)
void core::chemical::ResidueType::set_ideal_xyz ( Size  index,
Vector const &  xyz_in 
)

References atoms_.

void core::chemical::ResidueType::set_lower_connect_atom ( std::string const &  atm_name)
void core::chemical::ResidueType::set_mainchain_atoms ( AtomIndices const &  mainchain)
inline

set indices of all mainchain atoms

References mainchain_atoms_.

Referenced by core::chemical::PrependMainchainAtom::apply(), and core::chemical::AppendMainchainAtom::apply().

void core::chemical::ResidueType::set_mm_atom_type ( std::string const &  atom_name,
std::string const &  mm_atom_type_name 
)

set mm atom type

References atom_index(), atoms_, and mm_atom_types_.

Referenced by core::chemical::SetMMAtomType::apply().

void core::chemical::ResidueType::set_mol_data ( sdf::MolData const &  mol_data)
inline

set the MolData object

References mol_data_.

void core::chemical::ResidueType::set_ncaa_rotlib_n_bin_per_rot ( utility::vector1< Size n_bins_per_rot)

Sets the number of rotamers for each rotatable bond described by the NCAA rotlib.

References ncaa_rotlib_n_bins_per_rot_, and ncaa_rotlib_n_rots_.

void core::chemical::ResidueType::set_ncaa_rotlib_n_rotameric_bins ( Size  n_rots)
inline

Sets the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)

References ncaa_rotlib_n_rots_.

Size core::chemical::ResidueType::set_ncaa_rotlib_n_rotameric_bins ( ) const
inline

Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)

References ncaa_rotlib_n_rots_.

void core::chemical::ResidueType::set_ncaa_rotlib_path ( std::string const &  path)
inline

Sets the path for the NCAA rotlib for the ResidueType.

References ncaa_rotlib_path_.

Referenced by core::chemical::NCAARotLibPath::apply().

void core::chemical::ResidueType::set_orbital_icoor_id ( std::string const &  orbital,
Real const  phi,
Real const  theta,
Real const  d,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3 
)

set OrbitalICoor for an orbital

References atom_index_, icoor(), orbital_index(), and orbitals_.

void core::chemical::ResidueType::set_proton_chi ( Size  chino,
utility::vector1< Real dihedral_samples,
utility::vector1< Real extra_samples 
)

Describe proton behavior for residue type; where should rotamer samples be considered, and if expanded rotamers are desired, what deviations from the original rotamer samples should be included. E.g. dihedral_samples of 60, -60, and 180 could have an extra_sample of 20 which would produce rotamers at 40 60 & 80, -40 -60 & -80, and -160, 180 & 160. Extra_samples at 10 and 20 would produce 15 different rotamer samples.

References chi_2_proton_chi_, is_proton_chi_, proton_chi_extra_samples_, proton_chi_samples_, and proton_chis_.

Referenced by core::chemical::AddProtonChi::apply().

void core::chemical::ResidueType::set_RotamerLibraryName ( std::string const &  filename)
void core::chemical::ResidueType::set_upper_connect_atom ( std::string const &  atm_name)
void core::chemical::ResidueType::set_use_ncaa_rotlib ( bool  flag)
inline

Sets whether we are using a NCAA rotlib for the residue type.

References use_ncaa_rotlib_.

Referenced by core::chemical::NCAARotLibPath::apply().

void core::chemical::ResidueType::setup_atom_ordering ( AtomIndices old2new)
private

set up atom ordering map old2new, called by finalize()

set up atom ordering map old2new, called by finalize() because some new heavy atoms are added by patching, some are flagged to be deleted in delete_atoms_ and some are forced to be backbon atoms as in force_bb_

old2new[old_atom_index] = new_atom_index

sets natoms_, nheavyatoms_, and n_backbone_heavyatoms_

also fills attached_H_begin, attached_H_end

References atom_type(), atom_types_, atoms_, attached_H_begin_, attached_H_end_, bonded_neighbor_, delete_atoms_, force_bb_, core::scoring::is_heavyatom(), n_backbone_heavyatoms_, natoms_, nbrs(), nheavyatoms_, and core::chemical::tr().

Referenced by finalize().

void core::chemical::ResidueType::show_all_atom_names ( std::ostream &  out) const

References atoms_, and core::sequence::end.

Referenced by atom_index().

void core::chemical::ResidueType::update_actcoord ( conformation::Residue rot) const

update actcoord

update actcoord average geometrical center of the set of actcoord_atoms_

References core::conformation::Residue::actcoord(), actcoord_atoms_, core::conformation::Residue::atoms(), and n_actcoord_atoms_.

Referenced by core::conformation::Residue::update_actcoord().

void core::chemical::ResidueType::update_derived_data ( )
private

update derived data in ResidueType, called by finalize()

update derived data in ResidueType, called by finalize() after primary data have been reordered, update derived data acoordingly, including
, Hbond donor and acceptors, path_distance etc.

References abase2_, accpt_pos_, accpt_pos_sc_, all_bb_atoms_, all_sc_atoms_, atom_base_, core::chemical::AtomType::atom_has_orbital(), atom_is_polar_hydrogen_, atom_types_, atoms_, atoms_last_controlled_by_chi_, atoms_with_orb_index_, atoms_within_one_bond_of_a_residue_connection_, atoms_within_two_bonds_of_a_residue_connection_, attached_H_begin_, attached_H_end_, bondangle_atom_sets_, bondangles_for_atom_, bonded_neighbor_, carbohydrate_info_, dihedral_atom_sets_, dihedrals_for_atom_, first_sidechain_hydrogen_, core::chemical::get_residue_path_distances(), Haro_index_, heavyatom_has_polar_hydrogens_, heavyatom_is_an_acceptor_, Hpol_index_, Hpos_apolar_, Hpos_polar_, Hpos_polar_sc_, core::chemical::AtomType::is_acceptor(), is_carbohydrate_, core::chemical::AtomType::is_haro(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_polar_hydrogen(), is_RNA_, last_controlling_chi_, n_backbone_heavyatoms_, natoms_, ndihe_, nheavyatoms_, path_distance_, path_distances(), residue_connections_, rna_residuetype_, core::chemical::rna::RNA_ResidueType::rna_update_last_controlling_chi(), core::chemical::rna::RNA_ResidueType::update_derived_rna_data(), update_last_controlling_chi(), within1bonds_sets_for_atom_, and within2bonds_sets_for_atom_.

Referenced by finalize().

void core::chemical::ResidueType::update_last_controlling_chi ( )
private

compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom.

References atom_base_, atoms_last_controlled_by_chi_, bonded_neighbor_, chi_atoms_, last_controlling_chi_, natoms_, nchi(), and note_chi_controls_atom().

Referenced by update_derived_data().

void core::chemical::ResidueType::update_residue_connection_mapping ( )
private
ResidueConnection const & core::chemical::ResidueType::upper_connect ( ) const
Size core::chemical::ResidueType::upper_connect_atom ( ) const
Size core::chemical::ResidueType::upper_connect_id ( ) const
inline
utility::vector1< VariantType > const& core::chemical::ResidueType::variant_types ( ) const
inline
bool core::chemical::ResidueType::variants_match ( ResidueType const &  other) const

Does this residue have exactly the same set of properties as residue other? phil – this code does not look correct to me should probably be other.has_variant_type not other.has_property.

References core::chemical::DEPROTONATED, has_variant_type(), core::chemical::PROTONATED, and variant_types_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), and core::pack::task::ResidueLevelTask_::ResidueLevelTask_().

utility::vector1< std::pair< Size, Size > > const& core::chemical::ResidueType::within1bonds_sets_for_atom ( Size  atomid) const
inline

Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

References within1bonds_sets_for_atom_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), and core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative().

utility::vector1< std::pair< Size, Size > > core::chemical::ResidueType::within2bonds_sets_for_atom ( Size  atomid) const
inline

Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

References within2bonds_sets_for_atom_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().

Member Data Documentation

AA core::chemical::ResidueType::aa_
private

standard rosetta aa-type for knowledge-based potentials, may be aa_unk

Referenced by aa(), and rotamer_aa().

utility::vector1< Size > core::chemical::ResidueType::abase2_
private

indices of each atom's second base atom, for acceptors atom only

Referenced by abase2(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_
private

Referenced by accpt_pos(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_sc_
private

indices of Hbond acceptor positions that are part of the sidechain must be a subset of the atoms listed in the accpt_pos_ array

Referenced by accpt_pos_sc(), and update_derived_data().

AtomIndices core::chemical::ResidueType::actcoord_atoms_
private

indices of action coordinate centers

the geometric center of the atoms listed defined the residue's "action coordinate"

Referenced by actcoord_atoms(), add_actcoord_atom(), reorder_primary_data(), and update_actcoord().

AtomIndices core::chemical::ResidueType::all_bb_atoms_
private

Indices of all backbone atoms, hydrogens and heavyatoms.

Referenced by all_bb_atoms(), and update_derived_data().

AtomIndices core::chemical::ResidueType::all_sc_atoms_
private

Indices of all sidechain atoms, hydrogens and heavyatoms.

Referenced by all_sc_atoms(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::atom_2_residue_connection_map_
private
utility::vector1< Size > core::chemical::ResidueType::atom_base_
private
std::map< std::string, int > core::chemical::ResidueType::atom_index_
private
utility::vector1< int > core::chemical::ResidueType::atom_is_polar_hydrogen_
private
AtomTypeSetCAP core::chemical::ResidueType::atom_types_
private

AtomTypeSet Object.

used to define the set of allowed atomtypes for this residue and their properties

Referenced by add_atom(), atom_type(), atom_type_set(), atom_type_set_ptr(), set_atom_type(), setup_atom_ordering(), and update_derived_data().

utility::vector1< Atom > core::chemical::ResidueType::atoms_
private

vector of atoms:

Note
not pointers but Atom objects currently each Atom holds coords, atom_type, count_pair array index

Atom order rules: (1) heavyatoms before hydrogens (2) backbone heavyatoms before sidechain heavyatoms (3) hydrogens are grouped by the heavyatom they are attached to and come in the order of those heavyatoms (4) as a consequence of (2)+(3) –> backbone hydrogens come before sidechain hydrogens (5) atom order in the residue file is preserved subject to rules 1-4 see finalize() for the logic to determine the atom order

WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING

If you add new properties that are associated with atoms and therefore depend on the atom order, and that get set during Residue creation before the call to finalize(), then you have to make sure to update them in finalize() if the atom order changes

in general, anything that might be sensitive to atom order should be updated in finalize using the old2new mapping

WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING

Referenced by add_atom(), assign_neighbor_atom(), atom(), atom_name(), atom_type(), icoor(), mm_atom_type(), print_bondangles(), print_dihedrals(), print_pretty_path_distances(), reorder_primary_data(), set_atom_type(), set_icoor(), set_ideal_xyz(), set_mm_atom_type(), setup_atom_ordering(), show_all_atom_names(), and update_derived_data().

utility::vector1< AtomIndices > core::chemical::ResidueType::atoms_last_controlled_by_chi_
private

for chi i, the list of atoms last controlled by i. E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1

Referenced by atoms_last_controlled_by_chi(), update_derived_data(), and update_last_controlling_chi().

AtomIndices core::chemical::ResidueType::atoms_with_orb_index_
private

indices of Hbond acceptor positions

Referenced by atoms_with_orb_index(), and update_derived_data().

utility::vector1< utility::vector1< two_atom_set > > core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection_
private

For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.

Referenced by atoms_within_one_bond_of_a_residue_connection(), and update_derived_data().

utility::vector1< utility::vector1< three_atom_set > > core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection_
private

For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i.

Referenced by atoms_within_two_bonds_of_a_residue_connection(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::attached_H_begin_
private

indices of each heavyatom's first attached hydrogen

Referenced by attached_H_begin(), number_bonded_hydrogens(), setup_atom_ordering(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::attached_H_end_
private

indices of each heavyatom's last attached hydrogen

Referenced by attached_H_end(), number_bonded_hydrogens(), setup_atom_ordering(), and update_derived_data().

std::string core::chemical::ResidueType::base_restype_name_
private

Referenced by base_restype_name().

utility::vector1< bondangle_atom_set > core::chemical::ResidueType::bondangle_atom_sets_
private

vector of sets of atoms that make up bond angles in the residue

Referenced by bondangle(), num_bondangles(), print_bondangles(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::bondangles_for_atom_
private

all intra-residue bond angles that each atom "participates" in.

Referenced by bondangles_for_atom(), and update_derived_data().

utility::vector1< AtomIndices > core::chemical::ResidueType::bonded_neighbor_
private
utility::vector1<utility::vector1<BondName> > core::chemical::ResidueType::bonded_neighbor_type_
private

indices of each atom's bonded neighbor type (uses the same indexing scheme and order as bonded_neighbor_

Referenced by add_atom(), add_bond(), bonded_neighbor_types(), and reorder_primary_data().

utility::vector1<std::string> core::chemical::ResidueType::branch_point_atoms_
private

Referenced by is_branch_point().

core::chemical::carbohydrates::CarbohydrateInfoOP core::chemical::ResidueType::carbohydrate_info_
private
utility::vector1< Size > core::chemical::ResidueType::chi_2_proton_chi_
private
utility::vector1< AtomIndices > core::chemical::ResidueType::chi_atoms_
private

indices of four atoms to build each chi angle

Referenced by add_chi(), chi_atoms(), nchi(), redefine_chi(), reorder_primary_data(), and update_last_controlling_chi().

utility::vector1< utility::vector1< std::pair< Real, Real > > > core::chemical::ResidueType::chi_rotamers_
private

Additional non-dunbrack rotamer bins.

pair<Real,Real> ==> mean,sdev for each chi angle i and rotamer j: chi_rotamers_[i][j]

Referenced by add_chi(), add_chi_rotamer(), and chi_rotamers().

utility::vector1< AtomIndices > core::chemical::ResidueType::cut_bond_neighbor_
private

indices of each atom's bonded neighbors

Referenced by add_atom(), add_cut_bond(), cut_bond_neighbor(), reorder_primary_data(), and set_atom_base().

utility::vector1< Adduct > core::chemical::ResidueType::defined_adducts_
private
AtomIndices core::chemical::ResidueType::delete_atoms_
private

a list of atom indices to be deleted

in the next call to finalize(), used in delete_atom which is called during patching

Referenced by delete_atom(), finalize(), and setup_atom_ordering().

utility::vector1< dihedral_atom_set > core::chemical::ResidueType::dihedral_atom_sets_
private

vector of sets of atoms that make up dihedral angles in the residue

Referenced by dihedral(), print_dihedrals(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::dihedrals_for_atom_
private

all intra-residue dihedral angles that each atom "participates" in.

Referenced by dihedrals_for_atom(), and update_derived_data().

ElementSetCAP core::chemical::ResidueType::elements_
private

Referenced by add_atom(), and element_set().

bool core::chemical::ResidueType::finalized_
private
Size core::chemical::ResidueType::first_sidechain_hydrogen_
private

the index of first sidechain hydrogen atom

Referenced by atom_is_backbone(), first_sidechain_hydrogen(), and update_derived_data().

AtomIndices core::chemical::ResidueType::force_bb_
private

atom indices forced to be considered backbone

Referenced by finalize(), set_backbone_heavyatom(), and setup_atom_ordering().

bool core::chemical::ResidueType::force_nbr_atom_orient_
private

Referenced by force_nbr_atom_orient().

AtomIndices core::chemical::ResidueType::Haro_index_
private

Referenced by Haro_index(), and update_derived_data().

bool core::chemical::ResidueType::has_sc_orbitals_
private
utility::vector1< int > core::chemical::ResidueType::heavyatom_has_polar_hydrogens_
private

Vectors of booleans, represented as integers for speed (since vector1<bool> is optimized for space and is slow to read from) 1 for true, 0 for false

Referenced by heavyatom_has_polar_hydrogens(), and update_derived_data().

utility::vector1< int > core::chemical::ResidueType::heavyatom_is_an_acceptor_
private
AtomIndices core::chemical::ResidueType::Hpol_index_
private

Referenced by Hpol_index(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_apolar_
private

indices of apolar hydrogens

Referenced by Hpos_apolar(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_polar_
private

indices of polar Hydrogens for Hbond donors

Referenced by Hpos_polar(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_polar_sc_
private

indices of polar Hydrogens for Hbond donors that are part of the sidechain must be a subset of the atoms listed in the Hpos_polar_ array

Referenced by Hpos_polar_sc(), and update_derived_data().

bool core::chemical::ResidueType::is_acetylated_nterminus_
private
bool core::chemical::ResidueType::is_adduct_
private

Referenced by is_adduct(), and set_adduct_flag().

bool core::chemical::ResidueType::is_aromatic_
private
bool core::chemical::ResidueType::is_carbohydrate_
private
bool core::chemical::ResidueType::is_charged_
private
bool core::chemical::ResidueType::is_coarse_
private
bool core::chemical::ResidueType::is_DNA_
private
bool core::chemical::ResidueType::is_ligand_
private
bool core::chemical::ResidueType::is_lower_terminus_
private
bool core::chemical::ResidueType::is_methylated_cterminus_
private
bool core::chemical::ResidueType::is_NA_
private

Referenced by add_property(), and is_NA().

bool core::chemical::ResidueType::is_phosphonate_
private

Referenced by add_property(), and delete_property().

bool core::chemical::ResidueType::is_phosphonate_upper_
private

Referenced by add_property(), and delete_property().

bool core::chemical::ResidueType::is_polar_
private
bool core::chemical::ResidueType::is_polymer_
private
bool core::chemical::ResidueType::is_protein_
private
utility::vector1< bool > core::chemical::ResidueType::is_proton_chi_
private
bool core::chemical::ResidueType::is_RNA_
private
bool core::chemical::ResidueType::is_surface_
private
bool core::chemical::ResidueType::is_terminus_
private
bool core::chemical::ResidueType::is_upper_terminus_
private
utility::vector1< Size > core::chemical::ResidueType::last_controlling_chi_
private

for each atom, the last controlling chi angle for that atom. a chi of 0 represents an atom whose location is not determined by any chi.

Referenced by last_controlling_chi(), note_chi_controls_atom(), update_derived_data(), and update_last_controlling_chi().

Size core::chemical::ResidueType::lower_connect_id_
private

Polymer lower connections.

Note
ResidueConnection objects store the ideal internal coordinates for the connected atom

Referenced by lower_connect(), lower_connect_atom(), lower_connect_id(), residue_connection_is_polymeric(), set_icoor(), set_lower_connect_atom(), and set_upper_connect_atom().

AtomIndices core::chemical::ResidueType::mainchain_atoms_
private

indices of all mainchain atoms

mainchain_atoms are those atoms on the shortest path from polymer lower_connect to upper_connect. For protein, this will be N, CA and C.

Referenced by mainchain_atom(), mainchain_atoms(), reorder_primary_data(), and set_mainchain_atoms().

MMAtomTypeSetCAP core::chemical::ResidueType::mm_atom_types_
private
sdf::MolData core::chemical::ResidueType::mol_data_
private

the unprocessed metadata

Referenced by get_mol_data(), and set_mol_data().

Real core::chemical::ResidueType::molar_mass_
private

Referenced by add_atom(), and molar_mass().

Real core::chemical::ResidueType::molecular_mass_
private

Referenced by add_atom(), and molecular_mass().

Size core::chemical::ResidueType::n_actcoord_atoms_
private

number of actcoord atoms

the geometric center of the atoms listed defined the residue's "action coordinate"

Referenced by add_actcoord_atom(), reorder_primary_data(), requires_actcoord(), and update_actcoord().

Size core::chemical::ResidueType::n_backbone_heavyatoms_
private
Size core::chemical::ResidueType::n_hbond_acceptors_
private

number of hbond_acceptors

Referenced by add_atom(), and n_hbond_acceptors().

Size core::chemical::ResidueType::n_hbond_donors_
private

number of hbond_donors

Referenced by add_atom(), and n_hbond_donors().

Size core::chemical::ResidueType::n_non_polymeric_residue_connections_
private
Size core::chemical::ResidueType::n_orbitals_
private

number of orbitals

Referenced by add_orbital(), and n_orbitals().

Size core::chemical::ResidueType::n_polymeric_residue_connections_
private
char core::chemical::ResidueType::name1_
private

one-letter code, also not necessarily unique

Referenced by name1().

std::string core::chemical::ResidueType::name3_
private

pdb-file id, need not be unique

Referenced by name3().

std::string core::chemical::ResidueType::name_
private

unique residue id

Referenced by add_actcoord_atom(), and name().

Size core::chemical::ResidueType::natoms_
private
Size core::chemical::ResidueType::nbr_atom_
private

atom used for calculating residue-level neighbors

Referenced by assign_internal_coordinates(), nbr_atom(), and reorder_primary_data().

Real core::chemical::ResidueType::nbr_radius_
private

radius cutoff to define neighors

Referenced by nbr_radius().

utility::vector1< Size > core::chemical::ResidueType::ncaa_rotlib_n_bins_per_rot_
private

the number of rotamer bins for each chi angle in the NCAA rotlib

Referenced by get_ncaa_rotlib_n_bin_per_rot(), and set_ncaa_rotlib_n_bin_per_rot().

Size core::chemical::ResidueType::ncaa_rotlib_n_rots_
private

the number of non-hydrogen chi angles in the NCAA rotlib

Referenced by set_ncaa_rotlib_n_bin_per_rot(), and set_ncaa_rotlib_n_rotameric_bins().

std::string core::chemical::ResidueType::ncaa_rotlib_path_
private

path to the NCAA rotlib

Referenced by get_ncaa_rotlib_path(), and set_ncaa_rotlib_path().

Size core::chemical::ResidueType::ndihe_
private

number of dihedral angle atom sets

Referenced by ndihe(), print_dihedrals(), and update_derived_data().

Size core::chemical::ResidueType::nheavyatoms_
private
bool core::chemical::ResidueType::nondefault_
private

Referenced by nondefault().

utility::vector1< utility::vector1<core::Size > > core::chemical::ResidueType::orbital_bonded_neighbor_
private

indices of the atoms psuedo bonded atoms. Used in orbital code

Referenced by add_atom(), add_orbital_bond(), bonded_orbitals(), and reorder_primary_data().

orbitals::OrbitalTypeSetCAP core::chemical::ResidueType::orbital_types_
private

Orbital types.

Referenced by add_orbital(), and orbital_type().

utility::vector1< Orbital > core::chemical::ResidueType::orbitals_
private
std::map< std::string, int > core::chemical::ResidueType::orbitals_index_
private

atom index lookup by atom name string

Referenced by add_orbital(), add_orbital_bond(), has_orbital(), and orbital_index().

utility::vector1< Size > core::chemical::ResidueType::parents_
private
utility::vector1< utility::vector1< int > > core::chemical::ResidueType::path_distance_
private

number of bonds separated between any pair of atoms in this residue

Referenced by path_distance(), path_distances(), print_pretty_path_distances(), and update_derived_data().

utility::vector1< std::string > core::chemical::ResidueType::properties_
private

residue properties as defined in the residue param files

Referenced by add_property(), delete_property(), has_property(), and properties().

utility::vector1< utility::vector1< Real > > core::chemical::ResidueType::proton_chi_extra_samples_
private
utility::vector1< utility::vector1< Real > > core::chemical::ResidueType::proton_chi_samples_
private
utility::vector1< Size > core::chemical::ResidueType::proton_chis_
private
utility::vector1< ResidueConnection > core::chemical::ResidueType::residue_connections_
private

Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections.

Note
ResidueConnection objects store the ideal internal coordinates for the connected atom
Much of the code assumes at most one residue connection per atom. The pseudobond code has been partially written to handle cases where multiple connections to a single atom can exist, but much of the standard residue connection code assumes a simple correspondence between atoms and residue connections. That code will have to be updated to support single-atom "backbones."

Referenced by add_residue_connection(), lower_connect(), lower_connect_atom(), n_residue_connections(), reorder_primary_data(), residue_connect_atom_index(), residue_connection(), set_icoor(), set_lower_connect_atom(), set_upper_connect_atom(), update_derived_data(), update_residue_connection_mapping(), upper_connect(), and upper_connect_atom().

ResidueTypeSetCAP core::chemical::ResidueType::residue_type_set_
private

Referenced by residue_type_set().

core::chemical::rna::RNA_ResidueType core::chemical::ResidueType::rna_residuetype_
private

Referenced by RNA_type(), and update_derived_data().

AA core::chemical::ResidueType::rotamer_aa_
private

Referenced by rotamer_aa().

std::string core::chemical::ResidueType::rotamer_library_name_
private
bool core::chemical::ResidueType::serialized_
mutable
Size core::chemical::ResidueType::upper_connect_id_
private

Polymer upper connections.

Note
ResidueConnection objects store the ideal internal coordinates for the connected atom

Referenced by residue_connection_is_polymeric(), set_icoor(), set_lower_connect_atom(), set_upper_connect_atom(), upper_connect(), upper_connect_atom(), and upper_connect_id().

bool core::chemical::ResidueType::use_ncaa_rotlib_
private

NCAA rotlib stuff some of this is hardcoded elsewhere for the CAAs whether or not we should use the NCAA rotlib if it exists

Referenced by get_use_ncaa_rotlib(), and set_use_ncaa_rotlib().

utility::vector1< VariantType > core::chemical::ResidueType::variant_types_
private

here we store the patch operations/variant types that describe this residue

Referenced by add_variant_type(), has_variant_type(), nonadduct_variants_match(), variant_types(), and variants_match().

utility::vector1< utility::vector1< std::pair< Size, Size > > > core::chemical::ResidueType::within1bonds_sets_for_atom_
private

For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array.

Referenced by update_derived_data(), and within1bonds_sets_for_atom().

utility::vector1< utility::vector1< std::pair< Size, Size > > > core::chemical::ResidueType::within2bonds_sets_for_atom_
private

For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array.

Referenced by update_derived_data(), and within2bonds_sets_for_atom().


The documentation for this class was generated from the following files: