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core::chemical::ResidueType Class Reference

A class for defining a type of residue. More...

#include <ResidueType.hh>

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

 ~ResidueType () override
 destructor More...
 
 ResidueType (AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types)
 constructor More...
 
 ResidueType (ResidueType const &residue_type)
 
ResidueTypeOP clone () const
 make a copy More...
 
ResidueTypeOP placeholder_clone () const
 make a copy More...
 
ResidueTypeoperator= (ResidueType const &src)
 Copies <src> into the ResidueType. More...
 
ResidueTypeCOP get_self_ptr () const
 self pointers More...
 
ResidueTypeOP get_self_ptr ()
 
ResidueTypeCAP get_self_weak_ptr () const
 
ResidueTypeAP get_self_weak_ptr ()
 
TypeSetMode mode () const
 
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 element set for which this residue is constructed More...
 
ElementSetCOP element_set_ptr () const
 access by const pointer the element set for which this residue is constructed More...
 
AtomTypeSetCOP 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
 
Atomatom (VD const atom_vd)
 
Atom const & atom (VD const atom_vd) const
 
Orbital const & orbital (Size const orbital_index) const
 
Orbital const & orbital (std::string const &orbital_name) const
 
Bondbond (ED const ed)
 
Bond const & bond (ED const ed) const
 
Bondbond (VD vd1, VD vd2)
 
Bond const & bond (VD vd1, VD vd2) const
 
Bondbond (std::string const &atom1, std::string const &atom2)
 
Bond const & bond (std::string const &atom1, std::string const &atom2) 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...
 
AtomType const & atom_type (VD const vd) const
 Get the chemical atom_type for this atom by it index number in this residue. More...
 
Size natoms () const
 number of atoms 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 nbonds () const
 number of bonds More...
 
Size nbonds (Size atom) const
 number of bonds for given atom More...
 
Size nbonds (VD atom) const
 number of bonds for given atom 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 n_virtual_atoms () const
 Counts the number of virtual atoms and returns the count. 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...
 
AdjacentIterPair bonded_neighbor_iterators (VD const &atom) const
 
bool atoms_are_bonded (core::Size const atomindex1, core::Size const atomindex2) const
 Indicates whether or not two atom indices have a chemical bond linking them. 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...
 
VDs const & chi_atom_vds (Size const chino) const
 VDs 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 & nu_atoms (core::uint const nu_index) const
 Return indices of the atoms used to define a given nu (internal ring) angle. More...
 
utility::vector1< AtomIndices >
const & 
nu_atoms () const
 Return list of indices of the atoms used to define all the nu (internal ring) angles. More...
 
AtomIndices const & ring_atoms (uint const ring_num) const
 Return list of indices of the atoms within this residue's nth cycle, not counting virtual atoms. More...
 
utility::vector1< AtomIndices >
const & 
ring_atoms () const
 Return list of indices of the atoms within this residue's cycles, not counting virtual atoms. More...
 
bool is_ring_atom (uint const ring_num, uint const atom_id) const
 Return whether this atom is in a particular ring. More...
 
void get_metal_binding_atoms (AtomIndices &metal_binding_indices) const
 Gets indices of all atoms that can form bonds to metals. More...
 
utility::vector1< std::string > get_metal_binding_atoms () const
 
std::string get_disulfide_atom_name () const
 Gets disulfide atom name. More...
 
utility::vector1< std::string > get_anomeric_pseudotorsion () const
 @ brief Gets atom names used for alternate anomeric pseudotorsion. More...
 
utility::vector1< std::string > get_anomeric_sidechain () const
 @ brief Gets atom names that are part of the anomeric side chain. More...
 
void set_disulfide_atom_name (std::string const &n)
 Sets disulfide atom name. 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 atomno) const
 
bool heavyatom_is_an_acceptor (Size atomno) const
 
bool atom_is_polar_hydrogen (Size atomno) 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...
 
bool has (VD const vd) const
 is this vertex descriptor present in this residue? More...
 
Size atom_base (Size const atomno) const
 get index of an atom's base atom More...
 
VD atom_base (VD const atomno) const
 get vd 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...
 
std::string const & atom_name (VD const vd) const
 get atom name by vertex descriptor More...
 
Size atom_index (std::string const &name) const
 get atom index by name More...
 
std::map< std::string,
std::string > 
atom_aliases () const
 returns atom aliases More...
 
std::map< std::string,
std::string > 
canonical_atom_aliases () const
 returns atom aliases More...
 
Size atom_index (VD const &vd) const
 get atom index by vertex descriptor More...
 
VD atom_vertex (std::string const &name) const
 get the vertex descriptor from the name of the atom. More...
 
VD atom_vertex (Size const &atomno) const
 Get the vertex descriptor from the atom index. More...
 
ResidueGraph const & graph () const
 Constant access to the underlying graph. More...
 
void dump_vd_info () const
 
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...
 
VIterPair atom_iterators () const
 
EIterPair bond_iterators () const
 
OutEdgeIterPair bond_iterators (VD const &atom) const
 
bool atom_is_backbone (Size const atomno) const
 is a backbone atom (heavy or hydrogen)? More...
 
bool atom_is_sidechain (Size const atomno) const
 
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...
 
bool is_virtual (Size const atomno) const
 Check if atom is virtual. More...
 
bool is_repulsive (Size const atomno) const
 Check if atom is repulsive. 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...
 
MMAtomTypeSetCOP mm_atom_types_ptr () const
 Get the MM atom_type for this atom by its index number in this residue. More...
 
gasteiger::GasteigerAtomTypeDataCOP gasteiger_atom_type (Size const atomno) const
 Get the MM atom_type index number for this atom by its index number in this residue. More...
 
gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_typeset () const
 
chemical::orbitals::OrbitalType
const & 
orbital_type (int const orbital_index) const
 
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
 get orbital index by name More...
 
orbitals::OrbitalTypeSetCOP orbital_types_ptr () const
 Get the MM atom_type for this atom by its index number in this residue. More...
 
core::chemical::rings::RingConformerSetCOP ring_conformer_set (core::uint ring_num) const
 Return a pointer to the object containing the set of ring conformers possible for this residue's nth cycle. More...
 
core::Size n_ring_conformer_sets () const
 
Size nchi () const
 number of chi angles More...
 
Size n_nus () const
 Return number of nu (internal ring) angles. More...
 
Size n_rings () const
 Return the number of rings in this residue. 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...
 
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
 
utility::vector1< std::pair
< Real, Real > > const & 
chi_rotamers (Size const chino) const
 all rotamers bins (mean, std) for a given chi angle More...
 
ResidueConnection const & lower_connect () const
 
Size lower_connect_id () const
 
Size lower_connect_atom () const
 index number of the atom which connects to the lower connection More...
 
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
 
Size upper_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< uintbranch_connect_atoms () const
 Return a list of indices of atoms at non-polymer connections. More...
 
utility::vector1< std::string > branch_connect_atom_names () const
 Return a list of names of atoms at non-polymer connections. More...
 
Size n_possible_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)
 Get a ResidueConection. More...
 
bool atom_forms_residue_connection (Size const atomid) const
 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 real_to_virtual ()
 make all atoms virtual, set variant of this residue type as VIRTUAL Virtual residues are exactly the same, but they are not not scored! Please use Pose.freal_to_virtual, unless you know what you are doing! More...
 
VD 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 Will return the vertex descriptor of the added atom. More...
 
VD add_atom (std::string const &atom_name="")
 add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom. More...
 
VD add_atom (Atom const &atom, AtomICoor const &icoor)
 
void delete_atom (std::string const &name)
 flag an atom for deletion by adding its index to the delete_atom_ list More...
 
void delete_atom (Size const index)
 flag an atom for deletion by adding its index to the delete_atom_ list More...
 
void add_atom_alias (std::string const &rosetta_atom, std::string const &alias)
 Add an alias name for an atom. More...
 
void add_canonical_atom_alias (std::string const &rosetta_atom, std::string const &alias)
 store canonical to alias mapping More...
 
void delete_atom_alias (std::string const &alias, bool error=true)
 Remove a given alias name for an atom. More...
 
void set_atom_type (std::string const &atom_name, std::string const &atom_type_name)
 set atom type More...
 
void set_atom_type (VD atom, 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 set_gasteiger_typeset (gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types)
 Manually set the gasteiger typeset - will use the default set otherwise. More...
 
void set_gasteiger_atom_type (std::string const &atom_name, std::string const &gasteiger_atom_type_name)
 set gasteiger atom type More...
 
void set_gasteiger_atom_type (VD atom, std::string const &gasteiger_atom_type_name)
 set gasteiger atom type More...
 
void add_metalbinding_atom (std::string const &atom_name)
 Add an atom to the list of atoms that can potentially form a bond to a metal ion. Note that the atom must exist in the residue type (the function checks for this at runtime). More...
 
void delete_metalbinding_atom (std::string const &atom_name)
 Remove an atom from the list of atoms that can potentially form a bond to a metal ion (used in patching when it kills the valence that is thus used) More...
 
void delete_act_coord_atom (std::string const &atom_name)
 Remove an atom from the list of act coord atoms (used in patching when it kills the valence that is thus used) More...
 
void add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond)
 add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond) More...
 
void add_bond (VD atom1, VD atom2, BondName bondLabel=SingleBond)
 add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond) More...
 
void change_bond_type (std::string const &atom_name1, std::string const &atom_name2, BondName const old_bond_label, BondName const new_bond_label)
 Change the bond type of the given bond from one type to another. More...
 
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...
 
VD root_atom () const
 get root_atom used as the base of the icoor tree. More...
 
void nbr_atom (std::string const &atom_name)
 set nbr_atom used to define residue-level neighbors More...
 
void nbr_atom (VD vertex)
 set nbr_atom used to define residue-level neighbors More...
 
Size nbr_atom () const
 get nbr_atom used to define residue-level neighbors More...
 
VD nbr_vertex () const
 get VD 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 & 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_atom_base (VD const &atom1, VD const &atom2)
 sets atom_base[ atom1 ] = atom2, vertex descriptor version More...
 
void set_backbone_heavyatom (std::string const &name)
 set an atom as backbone heavy atom More...
 
void debug_dump_icoor () const
 Dump out atomnames and icoor values. More...
 
AtomICoor const & icoor (Size const atm) const
 AtomICoord of an atom. More...
 
AtomICoor const & icoor (VD 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 (VD const &atm, Real const phi, Real const theta, Real const d, VD const &stub_atom1, VD const &stub_atom2, VD const &stub_atom3, bool const update_xyz=false)
 set AtomICoor for an atom, vertex descriptor version More...
 
void set_icoor (std::string const &atm, Real const phi, Real const theta, Real const d, ICoorAtomID const &stub_atom1, ICoorAtomID const &stub_atom2, ICoorAtomID const &stub_atom3, bool const update_xyz=false)
 set AtomICoor for an atom More...
 
void reset_bond_distance_to_atom (std::string const &atm, core::Distance const d)
 Reset the bond distance to an atom whose internal coordinates have already been set. More...
 
void assign_neighbor_atom ()
 
void assign_internal_coordinates ()
 Assign internal coordinates from the set ideal xyz coordinates. Note that it currently does not obey mainchain designations or cut bonds. More...
 
void assign_internal_coordinates (core::chemical::VD new_root)
 
void set_ideal_xyz (std::string const &atm, Vector const &xyz_in)
 
void set_ideal_xyz (Size index, Vector const &xyz_in)
 
void set_ideal_xyz (VD atm, Vector const &xyz_in)
 
void fill_ideal_xyz_from_icoor ()
 
void set_shadowing_atom (std::string const &atom, std::string const &atom_being_shadowed)
 
void clear_orbitals ()
 clear orbitals More...
 
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...
 
const HeavyAtomGraph heavy_atoms ()
 
const AcceptorAtomGraph acceptor_atoms ()
 
const
HeavyAtomWithPolarHydrogensGraph 
heavy_atom_with_polar_hydrogens ()
 
const HeavyAtomWithHydrogensGraph heavy_atom_with_hydrogens ()
 
const HydrogenAtomGraph hydrogens ()
 
const PolarHydrogenGraph polar_hydrogens ()
 
const APolarHydrogenGraph apolar_hydrogens ()
 
const AromaticAtomGraph aromatic_atoms ()
 
void add_chi (Size const chino, VD atom1, VD atom2, VD atom3, VD atom4)
 Add a chi (side-chain) angle defined by four atoms. More...
 
void add_chi (VD atom1, VD atom2, VD atom3, VD atom4)
 Add a chi (side-chain) angle defined by four atoms. 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 (side-chain) angle defined by four atoms. More...
 
void add_chi (std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 Add a chi (side-chain) angle defined by four atoms to the end of the list of chis. More...
 
void add_nu (core::uint const nu_index, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 Add a nu (internal cyclic) angle defined by four atoms. More...
 
void set_anomeric_pseudotorsion (utility::vector1< std::string > const &alternate_atoms)
 Set atoms to use for anomeric pseudotorsion (if not using defaults, lower, C1, C5, C6) More...
 
void set_anomeric_sidechain (utility::vector1< std::string > const &anomeric_sidechain)
 Sets the atoms to use in the anomeric side hain. More...
 
void add_ring (core::uint const ring_num, utility::vector1< std::string > const &ring_atoms)
 Add a ring definition. More...
 
void set_lowest_energy_ring_conformer (core::uint const ring_num, std::string const &conformer)
 Set this cyclic residue's lowest-energy ring conformer for the nth ring by IUPAC name. More...
 
void set_low_energy_ring_conformers (core::uint const ring_num, utility::vector1< std::string > const &conformers)
 Set this cyclic residue's low-energy ring conformers for the nth ring by IUPAC name. 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 delete_terminal_chi ()
 delete terminal chi angle More...
 
void delete_child_proton (std::string const &atom)
 
void add_metapatch_connect (std::string const &atom)
 
void set_proton_chi (Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples)
 Annotate a given chi as a proton chi, and set the sampling behavior If the chi is already listed as a proton chi, change the sampling behavior. More...
 
void add_chi_rotamer (Size const chino, Real const mean, Real const sdev)
 Add a rotamer bin for a given chi. More...
 
void add_chi_rotamer_to_last_chi (core::Angle const mean, core::Angle const sdev)
 Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType. More...
 
void clear_chi_rotamers (core::uint const chi_no)
 Delete all of the chi rotamer bins from the specified chi for this ResidueType. More...
 
void autodetermine_chi_bonds (core::Size max_proton_chi_samples=500)
 Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all. More...
 
void finalize ()
 recalculate derived data, potentially reordering atom-indices More...
 
bool finalized () const
 finalized? should always be true, except in very special case early in on-the-fly ResidueTypeSet. More...
 
void require_final () const
 an assertion function to ensure an ResidueType has been finalized More...
 
Size add_residue_connection (std::string const &atom_name)
 add a non-polymeric ResidueConnection More...
 
void add_actcoord_atom (std::string const &atom)
 add an atom to the list for calculating actcoord center More...
 
ResidueProperties const & properties () const
 Access the collection of properties for this ResidueType. More...
 
void set_properties (ResiduePropertiesOP properties)
 Set the collection of properties for this ResidueType. More...
 
void add_property (std::string const &property)
 Add a property to this ResidueType. More...
 
void set_adduct_flag (bool adduct_in)
 
void add_numeric_property (std::string const &tag, core::Real value)
 Add a numeric property. More...
 
void add_string_property (std::string const &tag, std::string value)
 Add a string property. More...
 
void delete_property (std::string const &property)
 Add a property of this ResidueType. More...
 
bool is_base_type () const
 Is this ResidueType a base type? More...
 
ResidueTypeCOP get_base_type_cop () const
 Get a pointer to this ResidueType's base ResidueType. More...
 
void reset_base_type_cop ()
 Reset the base type COP to be null. This implies that this ResidueType is a base type. More...
 
void set_base_type_cop (ResidueTypeCOP new_base_type)
 Set the base type COP. This implies that this ResidueType is NOT a base type. More...
 
bool is_polymer () const
 is polymer? More...
 
bool is_sidechain_thiol () const
 is thiol? More...
 
bool is_disulfide_bonded () const
 is disulfide? More...
 
bool is_sidechain_amine () const
 is sidechain amine? More...
 
bool is_protein () const
 is protein? More...
 
bool is_alpha_aa () const
 Is this an alpha-amino acid? More...
 
bool is_beta_aa () const
 Is this a beta-amino acid? More...
 
bool is_gamma_aa () const
 Is this a gamma-amino acid? More...
 
bool is_water () const
 is this a water residue type? More...
 
bool is_oligourea () const
 Is this an oligourea? More...
 
bool is_aramid () const
 Is this an aramid? More...
 
bool has_polymer_dependent_groups () const
 Does this type have groups (not just single atoms) that are polymer-bond dependent? More...
 
bool atom_depends_on_lower_polymeric_connection (core::Size const atom_index) const
 Does an atom with a given index have an icoor that depends, directly or indirectly, on the lower polymeric connection? More...
 
bool atom_depends_on_upper_polymeric_connection (core::Size const atom_index) const
 Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper polymeric connection? More...
 
bool atom_depends_on_polymeric_connection (core::Size const atom_index) const
 Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper or lower polymeric connection? More...
 
bool atom_depends_on_connection (core::Size const atom_index, core::Size const connection_id) const
 Does an atom with a given index have an icoor that depends, directly or indirectly, on a particular connection ID? More...
 
signed long int net_formal_charge () const
 Get the net formal charge on this residue type. More...
 
void net_formal_charge (signed long int charge_in)
 Set the net formal charge on this residue type. More...
 
bool is_sri () const
 Is this one of SRI's special heteropolymer building blocks? More...
 
bool is_triazolemer () const
 Is this a triazolemer? More...
 
bool is_d_aa () const
 is this a d-amino acid? More...
 
bool is_l_aa () const
 is this an l-amino acid? More...
 
bool is_d_rna () const
 is this a d-RNA? More...
 
bool is_l_rna () const
 is this an l-RNA? More...
 
bool is_achiral_backbone () const
 is this an achiral backbone? More...
 
bool is_DNA () const
 is DNA? More...
 
bool is_RNA () const
 is RNA? More...
 
bool is_TNA () const
 is TNA? More...
 
bool is_PNA () const
 is PNA? More...
 
bool is_coarse () const
 is coarse? More...
 
bool is_NA () const
 is Nucleic Acid? More...
 
bool is_purine () const
 is purine? More...
 
bool is_pyrimidine () const
 is pyrimidine? More...
 
bool is_solvent () const
 Is this a solvent molecule (SOLVENT property)? More...
 
bool is_canonical_nucleic () const
 Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)? More...
 
bool is_canonical_aa () const
 Is this a canonical amino acid (CANONICAL_AA property)? More...
 
bool is_canonical () const
 Is this a canonical residue type (nucleic acid or amino acid)? More...
 
bool is_peptoid () const
 is peptoid? More...
 
bool is_carbohydrate () const
 is carbohydrate? More...
 
bool is_ligand () const
 is ligand? More...
 
bool is_lipid () const
 is lipid? More...
 
bool is_metal () const
 Return true if this residue type is a metal ion, false otherwise. More...
 
bool is_metalbinding () const
 Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.), false otherwise. More...
 
bool is_membrane () const
 is membrane? More...
 
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_cyclic () const
 is cyclic? 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_branch_point () const
 is a branch-point residue? More...
 
bool is_acetylated_nterminus () const
 is acetylated n terminus More...
 
bool is_methylated_cterminus () const
 is methylated c terminus More...
 
bool is_virtual_residue () const
 Check if residue is 'VIRTUAL_RESIDUE' This ONLY checks the VIRTUAL_RESIDUE PROPERTY! More...
 
bool is_inverted_virtual_residue () const
 Check if atom is an inverted virtual. More...
 
bool is_adduct () const
 is an adduct-modified residue? More...
 
bool has_property (std::string const &property) const
 Generic property access. More...
 
bool has_property (ResidueProperty const property) const
 Generic property access, by ResidueProperty. More...
 
core::Real get_numeric_property (std::string const &tag) const
 Get a numeric property, if it exists. More...
 
std::string get_string_property (std::string const &tag) const
 Get a string property, if it exists. More...
 
void add_variant_type (VariantType const variant_type)
 Add a variant type to this ResidueType. More...
 
void add_variant_type (std::string const &variant_type)
 Add a variant type to this ResidueType by string. More...
 
void remove_variant_type (VariantType const variant_type)
 Remove a variant type to this ResidueType. More...
 
void remove_variant_type (std::string const &variant_type)
 Remove a variant type to this ResidueType by string. More...
 
bool has_variant_type (VariantType const variant_type) const
 Generic variant access. More...
 
bool has_variant_type (std::string const &variant_type) const
 Generic variant access by string. More...
 
void enable_custom_variant_types ()
 Turn on the ability to create VariantTypes "on-the-fly". More...
 
utility::vector1< std::string > variant_types () const
 get all the variant types for this ResidueType More...
 
utility::vector1< VariantTypevariant_type_enums () const
 Get a vector of VariantType enums for this ResidueType. More...
 
utility::vector1< std::string >
const & 
custom_variant_types () const
 Get a list of custom VariantType strings for this ResidueType (by const reference). More...
 
void aa (AA const &type)
 set our aa-type (could be "UNK") More...
 
void aa (std::string const &type)
 set our aa-type (could be "UNK") More...
 
void backbone_aa (std::string const &type)
 AA to use for backbone scoring. More...
 
void base_analogue (std::string const &type)
 NA to use for base-specific generalization (can be more forgiving than na_analogue for new NA backbones) More...
 
void na_analogue (std::string const &type)
 NA to use for fragment sampling and some scoring purposes. More...
 
void rotamer_aa (std::string const &type)
 AA to use for rotamer scoring. More...
 
void nondefault (bool const in)
 
std::string const & base_name () const
 Get this ResidueType's base name (shared with other residue types with the same base type). More...
 
std::string const & name () const
 get our (unique) residue name More...
 
void base_name (std::string const &base_name_in)
 Set this ResidueType's base name (shared with other residue types with the same base type). More...
 
void name (std::string const &name_in)
 set our (unique) residue name More...
 
std::string const & name3 () const
 get our 3letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...
 
void name3 (std::string const &name_in)
 set our 3letter code More...
 
char name1 () const
 get our 1letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name3 string. More...
 
void name1 (char const code)
 set our 1letter code More...
 
std::string interchangeability_group () const
 get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypes ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypes .params file with the INTERCHANGEABILITY_GROUP tag. More...
 
void interchangeability_group (std::string setting)
 set our interchangeability-group id More...
 
void remap_pdb_atom_names (bool rename)
 Turn on geometry-based atom renaming when loading this residue type from PDB files. More...
 
bool remap_pdb_atom_names () const
 Are we using geometry-based atom renaming when loading this residue type from PDB. More...
 
AA const & aa () const
 our traditional residue type, if any More...
 
AA const & backbone_aa () const
 Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp). More...
 
AA const & base_analogue () const
 Returns the nucleic acid type to be used for base features. More...
 
AA const & na_analogue () const
 Returns the nucleic acid type to be used for fragment sampling/scoring. More...
 
void rotamer_library_specification (rotamers::RotamerLibrarySpecificationOP)
 
rotamers::RotamerLibrarySpecificationCOP rotamer_library_specification () const
 
rotamers::RotamerLibrarySpecificationOP rotamer_library_specification_nonconst ()
 Nonconst access to the RotamerLibrarySpecification. More...
 
void strip_rotamer_library_specification ()
 Remove any rotamer library specifications attached to this ResidueType. More...
 
dihedral_atom_set const & dihedral (Size const dihe) const
 dihedral methods More...
 
dihedral_atom_set const & improper_dihedral (Size const dihe) const
 Return the indices for the set of atoms that define a particular intraresidue improper dihedral. 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...
 
utility::vector1< Size > const & improper_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...
 
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...
 
bool has_shadow_atoms () const
 Returns true if this residue has shadow atoms, false otherwise. More...
 
Size atom_being_shadowed (Size atom_shadowing) const
 Return the index of the atom that the "atom_shadowing" atom is shadowing; returns zero if the "atom_shadowing" atom is not shadowing anyone. 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...
 
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_Info
const & 
RNA_info () 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...
 
std::tuple< Size, Size, Sizeselect_orient_atoms () const
 Selects three atoms for orienting this residue type. More...
 
core::Size smallest_ring_size (VD const &atom, core::Size const &max_size=999999) const
 A graph-based function to determine the size of the smallest ring that involves a given atom. More...
 
std::list< utility::vector1
< ED > > const & 
rings ()
 
std::string const & get_rama_prepro_mainchain_torsion_potential_name (bool const pre_proline_position) const
 Get the key name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
bool mainchain_potentials_match (ResidueType const &other) const
 Do the rama_prepro mainchain torsion potentials of this residue match another? More...
 
void set_rama_prepro_mainchain_torsion_potential_name (std::string const &name_in, bool const pre_proline_position)
 Set the key name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
std::string const & get_rama_prepro_map_file_name (bool const pre_proline_position) const
 Get the file name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
void set_rama_prepro_map_file_name (std::string const &filename_in, bool const pre_proline_position)
 Set the file name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
bool defines_custom_rama_prepro_map (bool const pre_proline_position) const
 Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_ defined for this ResidueType (which is presumably different from that of the base type). More...
 
void reset_mainchain_torsion_potential_names ()
 Set the names of the mainchain torsion potential maps to use to "". More...
 
void show (std::ostream &output=std::cout, bool output_atomic_details=false) const
 Generate string representation of ResidueType for debugging purposes. More...
 
void set_atom_type_set (AtomTypeSetCOP setting)
 Change which atom type set this ResidueType points to WARNING - While this tries to switch over the atom types, it will null out any that don't have exact name correspondences. You NEED to go through and manually reset the types on all atoms. Exposed for black-magic use only. 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 ()
 
template<typename MemFn , typename Ptr >
utility::signals::Link attach_destruction_obs (MemFn fn, Ptr ptr) const
 attach RestypeDestructionEvent observer function More...
 
template<typename MemFn , typename Ptr >
bool detach_destruction_obs (MemFn fn, Ptr ptr) const
 detach RestypeDestructionEvent observer function More...
 

Static Public Attributes

static VD const null_vertex = boost::graph_traits<ResidueGraph>::null_vertex()
 

Private Member Functions

 ResidueType ()
 
void update_icoors_after_connection_deletion (core::Size const conn_id_deleted)
 After deleting a connection, update the icoors of any atoms dependent on HIGHER-numbered connections. More...
 
void setup_atom_ordering ()
 set up atom ordering map old2new, called by finalize() More...
 
void order_atoms ()
 GRAPH FUNCTION to provide backward compatibility ////////. More...
 
void generate_atom_indices ()
 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_polymer_dependent_groups ()
 Determine which atoms are polymer bond-dependent. More...
 
void update_nonpolymer_dependent_groups ()
 Determine which atoms are nonpolymer bond-dependent. More...
 
void update_ncaa_rotamer_library_specification_if_present ()
 If there is an NCAARotamerLibrarySpecification, ensure that the rotamer backbone dependicies have been set. If they have not, set them to all mainchain torsions except omega (the final, inter-residue torsion). More...
 
void perform_checks ()
 Final check of ResidueType data, 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 set_icoor_private (std::string const &atm, ICoorAtomID const &id, AtomICoor const &ic, bool update_xyz)
 

Private Attributes

AtomTypeSetCOP atom_types_
 The type set for Rosetta Atom types. – Primary used to define the set of allowed atomtypes for this residue and their properties Needs to be non-null by the time finalize() is called. More...
 
utility::vector1< AtomTypevec_atom_types_
 
ElementSetCOP elements_
 The set for element objects. – Primary, can be null. More...
 
MMAtomTypeSetCOP mm_atom_types_
 The set for MMAtomTypes. – Primary, can be null. More...
 
gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types_
 The set for GasteigerAtomTypes. – Primary, can be null. More...
 
orbitals::OrbitalTypeSetCOP orbital_types_
 The set for OrbitalTypes. – Primary, can be null. More...
 
utility::vector1
< rings::RingConformerSetOP
conformer_sets_
 The sets of all possible ring conformers, one per ring – Derived, can be null. More...
 
TypeSetMode mode_ = INVALID_t
 The TypeSet mode for this ResidueType – Primary, should be valid. More...
 
ResidueGraph graph_
 The Atoms and Bonds of the ResidueType, stored as Nodes and Edges. – Primary. More...
 
std::map< VD, Sizevd_to_index_
 A map of graph VDs to vector indexes. – Derived, valid during Mutable. More...
 
std::map< VD, VDatom_base_
 The atom "one up" in the atom tree. – Derived, valid during Mutable. Updated in set_icoor. (also set_atom_base - TODO: Fix redundancy issue. More...
 
std::map< VD, VDabase2_
 The base of the atom base – Derived. More...
 
VDs ordered_atoms_
 Vector of atoms for index->vd mapping. More...
 
utility::vector1< Orbitalorbitals_
 The orbitals on the ResidueType, if any. – Primary. More...
 
Size nheavyatoms_
 The number of heavy atoms – Derived. More...
 
Size n_hbond_acceptors_
 The number of hbond_acceptors – Derived. More...
 
Size n_hbond_donors_
 number of hbond_donors – Derived. More...
 
Size n_backbone_heavyatoms_
 number of backbone heavy atoms – Derived. More...
 
Size first_sidechain_hydrogen_
 the index of first sidechain hydrogen atom – Derived. More...
 
utility::vector1< AtomIndicesbonded_neighbor_
 indices of the atoms psuedo bonded atoms. Used in orbital code – Derived More...
 
utility::vector1
< utility::vector1< BondName > > 
bonded_neighbor_type_
 ??? – Derived More...
 
std::map< VD, utility::vector1
< VD > > 
cut_bond_neighbor_
 ??? – Derived More...
 
utility::vector1< Sizeattached_H_begin_
 indices of each heavyatom's first attached hydrogen – Derived. More...
 
utility::vector1< Sizeattached_H_end_
 indices of each heavyatom's last attached hydrogen – Derived. More...
 
std::map< VD, AtomICooricoor_
 Internal coordinates on how to build the given atom – Primary. More...
 
utility::vector1
< dihedral_atom_set
dihedral_atom_sets_
 Data for the mm potentials. – Derived List all of the intra-residue dihedral angles and bond angles. vector of sets of atoms that make up dihedral angles in the residue Data for the mm potentials. More...
 
utility::vector1
< utility::vector1< Size > > 
dihedrals_for_atom_
 all intra-residue dihedral angles that each atom "participates" in – Derived More...
 
utility::vector1
< dihedral_atom_set
improper_dihedral_atom_sets_
 
utility::vector1
< utility::vector1< Size > > 
improper_dihedrals_for_atom_
 
utility::vector1
< bondangle_atom_set
bondangle_atom_sets_
 vector of sets of atoms that make up bond angles in the residue – Derived More...
 
utility::vector1
< utility::vector1< Size > > 
bondangles_for_atom_
 ??? – Derived More...
 
std::map< VD, VDatom_shadowed_
 Data to describe virtual atoms that should shadow other atoms for the sake of keeping intraresidue cycles closed when working with an atom tree, e.g. NV shadows N on proline. For each atom, the following vector lists the index of the atom it is shadowing. – Primary. More...
 
utility::vector1< Sizelast_controlling_chi_
 Data for controlling chi. – Derived. Computed in update_last_controlling_chi() for each atom 0 means an atom whose location is not determined by any chi. More...
 
utility::vector1< AtomIndicesatoms_last_controlled_by_chi_
 for chi i, the list of atoms last controlled by i – Derived E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1 More...
 
AtomIndices atoms_with_orb_index_
 indices of atoms with orbitals – Derived More...
 
AtomIndices Haro_index_
 indices of haro hydrogens – Derived More...
 
AtomIndices Hpol_index_
 indices of hpolar hydrogens – Derived More...
 
AtomIndices accpt_pos_
 indices of Hbond acceptor positions – Derived More...
 
AtomIndices Hpos_polar_
 indices of polar Hydrogens for Hbond donors – Derived More...
 
AtomIndices Hpos_apolar_
 indices of apolar hydrogens – Derived More...
 
AtomIndices accpt_pos_sc_
 indices of Hbond acceptor positions that are part of the sidechain – Derived must be a subset of the atoms listed in the accpt_pos_ array More...
 
AtomIndices Hpos_polar_sc_
 indices of polar Hydrogens for Hbond donors that are part of the sidechain – Derived must be a subset of the atoms listed in the Hpos_polar_ array More...
 
AtomIndices all_bb_atoms_
 Indices of all backbone atoms, hydrogens and heavyatoms – Derived. More...
 
AtomIndices all_sc_atoms_
 Indices of all sidechain atoms, hydrogens and heavyatoms – Derived. More...
 
utility::vector1< std::string > metal_binding_atoms_
 Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types. More...
 
utility::vector1< std::string > anomeric_pseudotorsion_
 Atoms used to determine the anomeric pseudotorsion of glycans. – Primary. More...
 
utility::vector1< std::string > anomeric_sidechain_
 Atoms to use in the anomeric side chain of glycans. – Primary. More...
 
std::string disulfide_atom_name_
 Name of the disulfide-forming atom, if any. More...
 
utility::vector1< VDmainchain_atoms_
 Verticies of all mainchain atoms – Primary. More...
 
utility::vector1< VDactcoord_atoms_
 indices of action coordinate centers – Primary More...
 
utility::vector1
< utility::vector1< VD > > 
chi_atoms_
 the four atoms to build each chi angle – Primary. More...
 
utility::vector1< boolis_proton_chi_
 Is the corresponding chi in chi_atoms_ a proton chi? – Primary. More...
 
utility::vector1< Sizeproton_chis_
 Indices of the chi_atoms_ vector for proton chis – Derived, valid during Mutable. More...
 
utility::vector1< Sizechi_2_proton_chi_
 A "map" of chi indices to proteon_chi indices – Derived, valid during Mutable. More...
 
utility::vector1
< utility::vector1< Real > > 
proton_chi_samples_
 For a proton chi, the primary samples to diversify the rotamer library with – Primary. More...
 
utility::vector1
< utility::vector1< Real > > 
proton_chi_extra_samples_
 For a proton chi, how to handle extra ex_ levels – Primary. More...
 
utility::vector1
< utility::vector1< VD > > 
nu_atoms_
 VDs of four atoms to build each nu angle – Primary. More...
 
utility::vector1
< utility::vector1< VD > > 
ring_atoms_
 VDs of all ring atoms, not counting virtual atoms – Primary. More...
 
utility::vector1
< utility::vector1< int > > 
path_distance_
 number of bonds separated between any pair of atoms in this residue – Derived. More...
 
std::map< std::string, VDatom_name_to_vd_
 atom index lookup by atom name string – Derived, valid during Mutable, with caveats More...
 
std::map< std::string,
std::string > 
atom_aliases_
 A mapping of alias atom names to canonical atom names – Primary Will be added to atom_name_to_vd_ during finalization. More...
 
std::map< std::string,
std::string > 
canonical_atom_aliases_
 A map of canonical atom names to atom aliases (white space included) More...
 
std::map< std::string, int > orbitals_index_
 index lookup for orbitals based on atom name – Derived, valid during Mutable Updated in add_orbital() More...
 
utility::vector1
< utility::vector1< std::pair
< Real, Real > > > 
chi_rotamers_
 Additional non-Dunbrack rotamer bins – Primary. More...
 
rotamers::RotamerLibrarySpecificationOP rotamer_library_specification_
 How to construct a rotamer library for this ResidueType – Primary. More...
 
utility::vector1< Sizering_sizes_
 The size of each ring in this residue – Primary. More...
 
utility::vector1< std::string > lowest_ring_conformer_
 Lowest-energy ring conformer for each ring – Primary. More...
 
utility::vector1
< utility::vector1
< std::string > > 
low_ring_conformers_
 Low-energy ring conformers for each ring – Primary. More...
 
ResiduePropertiesOP properties_
 Residue properties as defined in the residue topology (.params) files – Primary. More...
 
AA aa_
 standard rosetta aa-type for knowledge-based potentials, may be aa_unk – Primary More...
 
AA rotamer_aa_
 
AA backbone_aa_
 
AA na_analogue_
 
AA base_analogue_
 
std::string base_name_
 Residue id for the base type (i.e. sans variants). More...
 
ResidueTypeCOP base_type_cop_
 Const-access owning pointer to the base residue type. More...
 
std::string name_
 Residue id – Primary, should be unique. More...
 
std::string name3_
 PDB-file id, need not be unique – Primary NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...
 
char name1_
 one-letter code, also not necessarily unique – Primary More...
 
std::string interchangeability_group_
 interchangeability group lets a ResidueType claim to be functionally interchangeable with any other ResidueType in the same group. This is used by the packer to decide which ResidueType from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueType and build rotamers for it. Primary. More...
 
VD root_atom_
 Atom at the nominal root of the ICOOR tree. More...
 
VD nbr_atom_
 atom used for calculating residue-level neighbors – Primary More...
 
Real nbr_radius_
 radius cutoff to define neighbors – Primary More...
 
bool force_nbr_atom_orient_
 
bool remap_pdb_atom_names_
 Should we attempt to rename atoms for this residue type when we read in PDB files? – Primary. More...
 
Real mass_
 The isotopically averaged mass of the residue – Derived. More...
 
utility::vector1
< ResidueConnection
residue_connections_
 Vector of inter-residue connections expected for this residuetype – Primary NOW includes the polymer connections, as well as disulf-type connections. More...
 
utility::vector1
< utility::vector1< Size > > 
atom_2_residue_connection_map_
 Mapping of atom indicies to residue connections – Derived. More...
 
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. – Derived. 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. – Derived. 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. – Derived. 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. – Derived. More...
 
Size lower_connect_id_
 Polymer lower connections – Derived, valid during Mutable Updated in set_lower_connect_atom() More...
 
Size upper_connect_id_
 Polymer upper connections – Derived valid during Mutable Updated in set_upper_connect_atom() More...
 
Size n_non_polymeric_residue_connections_
 Number of non-polymeric residue connections – Derived. More...
 
Size n_polymeric_residue_connections_
 Number of polymeric residue connections – Derived. More...
 
utility::vector1< VDforce_bb_
 atom indices forced to be considered backbone – Primary More...
 
core::chemical::rna::RNA_InfoOP rna_info_
 A container for properties unique to RNA. – Derived, can be null. More...
 
core::chemical::carbohydrates::CarbohydrateInfoOP carbohydrate_info_
 A container for residue properties unique to carbohydrates. – Derived, can be null. More...
 
std::list< utility::vector1< ED > > rings_and_their_edges_
 All the rings and the edges. Defaulted to null until defined – Derived. More...
 
utility::vector1< Sizeatom_base_indices_
 Index version of atom_base_ – Derived. More...
 
utility::vector1< Sizeabase2_indices_
 Index version of abase2_ – Derived. More...
 
utility::vector1< AtomIndiceschi_atoms_indices_
 Index version of chi_atoms_ – Derived. More...
 
utility::vector1< AtomIndicesnu_atoms_indices_
 Index version of nu_atoms_ – Derived. More...
 
utility::vector1< AtomIndicesring_atoms_indices_
 Index version of ring_atoms_ – Derived. More...
 
AtomIndices mainchain_atoms_indices_
 Index version of mainchain_atoms_ – Derived. More...
 
Size nbr_atom_indices_
 Index version of nbr_atom_ – Derived. More...
 
AtomIndices actcoord_atoms_indices_
 Index version of actcoord_atoms_ – Derived. More...
 
utility::vector1< AtomIndicescut_bond_neighbor_indices_
 Index version of cut_bond_neighbor_ – Primary - will be converted to derived (from Bond.cut_bond()) More...
 
utility::vector1< Sizeatom_shadowed_indices_
 Index version of atom_shadowed_ – Derived. More...
 
std::string rama_prepro_mainchain_torsion_potential_name_
 The name of the mainchain torsion potential used by this ResidueType for the RamaPrePro score term. More...
 
std::string rama_prepro_mainchain_torsion_potential_name_beforeproline_
 The name of the mainchain torsion potential used by this ResidueType for the RamaPrePro score term. More...
 
std::string rama_prepro_map_file_name_
 The filename of the mainchain torsion potential used by this ResidueType for the RamaPrePro score term. More...
 
std::string rama_prepro_map_file_name_beforeproline_
 The filename of the mainchain torsion potential used by this ResidueType for the RamaPrePro score term. More...
 
bool has_polymer_dependent_groups_
 Does this ResidueType have groups with icoors that depend, directly or indirectly, on polymeric bonds? More...
 
utility::vector1< boolatom_depends_on_lower_polymeric_connection_
 vector of length corresponding to number of atoms indicating whether each atom is dependent on the lower polymer bond. More...
 
utility::vector1< boolatom_depends_on_upper_polymeric_connection_
 vector of length corresponding to number of atoms indicating whether each atom is dependent on the upper polymer bond. More...
 
bool has_nonpolymer_connection_dependent_groups_
 Does this ResidueType have groups with icoors that depend, directly or indirectly, on non-polymeric bonds? More...
 
utility::vector1
< utility::vector1< bool > > 
atom_depends_on_connection_
 An outer vector indexed to connection ID, and an inner vector indexed to atom ids. "True" means that the atom id for the inner vector depends on the connection ID for the outer. More...
 
signed long int net_formal_charge_
 The formal charge on this residue. More...
 
bool finalized_
 Is all the derived data appropriately updated? More...
 
utility::vector1< Adductdefined_adducts_
 Adducts defined for this residue – Primary. More...
 
bool nondefault_
 
utility::signals::BufferedSignalHub
< void,
RestypeDestructionEvent
destruction_obs_hub_
 Who needs to be told if this ResidueType is destroyed? More...
 

Detailed Description

A class for defining a type of residue.

This class contains the "chemical" information for residues as well as the ideal xyz and internal coordinates for a residue (generated xyz coordinates are found in core/conformation/Residue.hh). A ResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. ResidueTypes are generated through .params files, which are read from the database chemical/residue_types. For ligands, a parameter has to be provided to rosetta through the -extra_res_fa flag. Primary data are set through the residue_io.cc class. The primary data that are set are: atoms, mmatoms, orbitals, and properties of the particular ResidueType. These properties can be modified through patches, which create new ResidueTypes, and are controlled through PatchOperations.cc.

The data structure of a ResidueType is based on a boost::graph implementation. Vertex descriptors (VD, yeah, I know, the name is kind of bad) are the atoms, while the edge descriptors (ED, yet another bad name) are the bonds. Initially, when a ResidueType is constructed, the following primary data are set:

atom_base_; chi_atoms_; nu_atoms_; ring_atoms_; mainchain_atoms_; nbr_atom_; actcoord_atoms_; cut_bond_neighbor_; atom_shadowed_;

When this data is set, it is set based on vertex descriptors. Because vertex descriptors never change, like atom indices, there is no need to reorder this primary data; however, because Rosetta relies heavily on atom indices to access data, atom indices for the above data have to be generated. To do this, when finalized is called, a function specifically designed to generate the atom indices for the primary data is called: generate_atom_indices. This function iterates over the vertex descriptors assigned in the primary data and creates private data based on atom indices. For example, atom_base_ has atom_base_indices_. When the function atom_base(atomno) is called, the private datum atom_base_indices_ is called. This allows for the external interface of ResidueType to be accessed by atom indices while the internal functions in ResidueType work off of vertex descriptors. This also removes the need to have the former old2new reordering scheme.

Atoms: Setting of atoms includes indexing the atoms into vectors, saving their names into vectors/maps, saving the associated mm_atom_type into a vector, saving bond connections into vectors, etc, etc. On any given residue, the heavy atoms are put into the vector first, (their indices are first,) and hydrogens are put in last.

Properties: Properties of a residue include things like DNA, PROTEIN, CHARGED, etc. These properties indicate the type of residue it is and what properties are associated with the residue. They are set when read in. To add new ResidueProperties, add them to core/chemical/residue_properties/general_properties.list.

Orbitals: Orbitals are indexed separately from atoms. They function much the same way as atoms, except for some key differences. To find atoms bonded to orbitals, you must provide the atom index, not the orbital index. (I haven't figured out how to get the reverse to work because of the separate indices.) Orbital xyz coordinates are not updated when atom coordinates are. This is to keep speed consistent with just having atoms. To output the orbitals, use the flag -output_orbitals.

Constructor & Destructor Documentation

core::chemical::ResidueType::~ResidueType ( )
override

destructor

References destruction_obs_hub_.

core::chemical::ResidueType::ResidueType ( )
privatedefault

Referenced by clone(), and placeholder_clone().

core::chemical::ResidueType::ResidueType ( AtomTypeSetCOP  atom_types,
ElementSetCOP  element_types,
MMAtomTypeSetCOP  mm_atom_types,
orbitals::OrbitalTypeSetCOP  orbital_types 
)

constructor

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

References mode_.

core::chemical::ResidueType::ResidueType ( ResidueType const &  residue_type)

Member Function Documentation

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

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

References aa_.

Referenced by protocols::minimization_packing::MinimalRotamer::aa(), core::conformation::Residue::aa(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::loops::add_loop(), protocols::motifs::add_motif_bb_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), core::select::residue_selector::NumNeighborsSelector::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), core::chemical::Set_AA::apply(), core::chemical::ChiralFlipNaming::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), protocols::motifs::backbone_stub_match(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_single_edge_waters(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::matdes::OligomericAverageDegreeFilter::compute(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::rna::movers::RNAIdealizeMover::constrain_to_ideal(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::pack::dunbrack::RotamerLibrary::create_srdl(), core::scoring::constraints::SequenceProfileConstraint::dist(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(), protocols::stepwise::modeler::find_downstream_connection_res(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::chemical::Patch::generates_aa(), core::chemical::rna::get_base_pair_atoms(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_last_sidechain_carbon_name(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_max_sidechain_length(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_amide_name(), core::scoring::dna::get_y_axis_atoms(), protocols::metal_interface::MatchGrafter::graft(), protocols::magnesium::MgHydrater::hydrate_magnesium(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose(), protocols::cyclic_peptide::crosslinker::TMA_Helper::is_allowed_residue_type(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::is_allowed_type(), core::scoring::constraints::is_aromatic(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::is_counted(), core::conformation::Residue::is_similar_aa(), core::conformation::Residue::is_similar_rotamer(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::liganding_atom_from_restype(), 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(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), protocols::denovo_design::DisulfidizeMover::noncanonical_disulfide(), core::import_pose::libraries::one_letter_from_rt(), core::chemical::Selector_AA::operator[](), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::chemical::ResidueDatabaseIO::read_residue_type(), protocols::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(), protocols::match::upstream::DunbrackSCSampler::samples(), core::scoring::ProQPotential::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::chemical::setup_patch_atomic_charge_reassignments_from_commandline(), protocols::stepwise::modeler::rna::suite_square_deviation(), core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_last_virtual_residue(), protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(), core::scoring::rna::RNA_AtomVDW::vdw_atom_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), and core::chemical::write_topology_file().

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().

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".

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

References aa_.

Referenced by placeholder_clone().

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

get index of an atom's second base atom

References abase2_indices_, and ordered_atoms_.

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

const AcceptorAtomGraph core::chemical::ResidueType::acceptor_atoms ( )

References atom_types_, graph(), and graph_.

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_indices_.

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

add an atom to the list for calculating actcoord center

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

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

References defined_adducts_.

VD 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 
)
VD core::chemical::ResidueType::add_atom ( std::string const &  atom_name = "")

add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom.

References atom_2_residue_connection_map_, atom_base_, atom_name(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, icoor_, ordered_atoms_, core::chemical::strip_whitespace(), and vd_to_index_.

VD core::chemical::ResidueType::add_atom ( Atom const &  atom,
AtomICoor const &  icoor 
)
void core::chemical::ResidueType::add_atom_alias ( std::string const &  rosetta_atom,
std::string const &  alias 
)

Add an alias name for an atom.

References atom_aliases_, finalized_, has(), and core::chemical::strip_whitespace().

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

void core::chemical::ResidueType::add_bond ( std::string const &  atom_name1,
std::string const &  atom_name2,
BondName  bondLabel = SingleBond 
)
void core::chemical::ResidueType::add_bond ( VD  atom1,
VD  atom2,
BondName  bondLabel = SingleBond 
)

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

References atom_index(), bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, has(), and protocols::mean_field::max().

void core::chemical::ResidueType::add_canonical_atom_alias ( std::string const &  rosetta_atom,
std::string const &  alias 
)

store canonical to alias mapping

store map of canonical name to atom alias

References canonical_atom_aliases_.

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

void core::chemical::ResidueType::add_chi ( Size const  chino,
VD  atom1,
VD  atom2,
VD  atom3,
VD  atom4 
)
void core::chemical::ResidueType::add_chi ( VD  atom1,
VD  atom2,
VD  atom3,
VD  atom4 
)

Add a chi (side-chain) angle defined by four atoms.

References add_chi(), and nchi().

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 
)

Add a chi (side-chain) angle defined by four atoms.

References add_chi(), and atom_vertex().

void core::chemical::ResidueType::add_chi ( std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

Add a chi (side-chain) angle defined by four atoms to the end of the list of chis.

This method is needed for combinatorial patching of ResidueTypes for which the number of chis is variable. Its primary purpose is to be used with add_chi_rotamer_to_last_chi() that adds rotamer bins to the last chi in the list. In this way, a new chi can be added by a patch file and its rotamer bins set without needing to designate a chi index.

Note
See also add_chi_rotamer_to_last_chi().
Author
Labonte

References add_chi(), and nchi().

void core::chemical::ResidueType::add_chi_rotamer ( Size const  chino,
Real const  mean,
Real const  sdev 
)
void core::chemical::ResidueType::add_chi_rotamer_to_last_chi ( core::Angle const  mean,
core::Angle const  sdev 
)

Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType.

This method is needed for combinatorial patching of ResidueTypes for which the number of chis is variable. Its primary purpose is to be used with the overloaded version of add_chi() that adds a new chi to the end of the list. In this way, a new chi can be added by a patch file and its rotamer bins set without needing to designate a chi index.

Note
See also add_chi().
Author
Labonte

References add_chi_rotamer(), and nchi().

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

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_name_to_vd_, cut_bond_neighbor_, finalized_, graph_, has(), and core::chemical::tr().

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

void core::chemical::ResidueType::add_metalbinding_atom ( std::string const &  atom_name)

Add an atom to the list of atoms that can potentially form a bond to a metal ion. Note that the atom must exist in the residue type (the function checks for this at runtime).

Add an atom to the list of atoms that can potentially form a bond to a metal ion.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References has(), metal_binding_atoms_, and name3().

void core::chemical::ResidueType::add_metapatch_connect ( std::string const &  atom)
void core::chemical::ResidueType::add_nu ( core::uint const  nu_index,
std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

Add a nu (internal cyclic) angle defined by four atoms.

References atom_index(), finalized_, has(), nu_atoms_, and ordered_atoms_.

void core::chemical::ResidueType::add_numeric_property ( std::string const &  tag,
core::Real  value 
)

Add a numeric property.

References properties_.

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 coordinates for the added orbital but sets the index of the orbital and maps it to the type of orbital.

References finalized_, 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(), atom_name_to_vd_, finalized_, graph_, has(), has_orbital(), orbitals_index_, and ordered_atoms_.

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

add a non-polymeric ResidueConnection

For polymeric connections, see set_lower_connect() and set_upper_connect() Doesn't set the ideal geometry – maybe it should?

References atom_index(), finalized_, n_non_polymeric_residue_connections_, ordered_atoms_, residue_connections_, and update_residue_connection_mapping().

Referenced by add_metapatch_connect(), core::chemical::AddConnect::apply(), and core::chemical::AddConnectAndTrackingVirt::apply().

void core::chemical::ResidueType::add_ring ( core::uint const  ring_num,
utility::vector1< std::string > const &  ring_atoms 
)
void core::chemical::ResidueType::add_string_property ( std::string const &  tag,
std::string  value 
)

Add a string property.

References properties_.

Referenced by core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::add_variant_type ( VariantType const  variant_type)
void core::chemical::ResidueType::add_variant_type ( std::string const &  variant_type)

Add a variant type to this ResidueType by string.

References finalized_, and properties_.

AtomIndices const& core::chemical::ResidueType::all_bb_atoms ( ) const
inline
AtomIndices const& core::chemical::ResidueType::all_sc_atoms ( ) const
inline
const APolarHydrogenGraph core::chemical::ResidueType::apolar_hydrogens ( )

References atom_types_, and graph_.

const AromaticAtomGraph core::chemical::ResidueType::aromatic_atoms ( )

References atom_types_, and graph_.

void core::chemical::ResidueType::assign_internal_coordinates ( )

Assign internal coordinates from the set ideal xyz coordinates. Note that it currently does not obey mainchain designations or cut bonds.

References nbr_atom_, null_vertex, ordered_atoms_, and root_atom_.

void core::chemical::ResidueType::assign_internal_coordinates ( core::chemical::VD  new_root)

@ recursive function to assign internal coordinates Note that it currently does not work well with polymers.

References graph_, n_possible_residue_connections(), name(), null_vertex, core::chemical::reroot_restype(), root_atom_, and core::chemical::tr().

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

References atom_index(), graph_, and ordered_atoms_.

Referenced by add_atom(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::ChiralFlipAtoms::apply(), core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), core::chemical::AddConnectDeleteChildProton::apply(), core::chemical::VirtualizeAll::apply(), core::chemical::VirtualizeSidechain::apply(), core::chemical::RenameAtom::apply(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::conformation::Residue::atomic_charge(), attached_H_begin(), attached_H_end(), autodetermine_chi_bonds(), protocols::match::bump_grid_to_enclose_pose(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::AutomorphismIterator::can_pair(), core::chemical::AddConnectDeleteChildProton::changes_connections_on(), core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_chirality(), core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_outgroup(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::sdf::MolWriter::compose_properties(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), debug_dump_icoor(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::determine_max_accepted_hbond_count(), protocols::md::CartesianMD::do_initialize(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::RigidDistanceVisitor::examine_vertex(), core::chemical::find_chi_bonds(), core::chemical::find_nbr_dist(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::chemical::RerootRestypeVisitor::initialize_vertex(), core::chemical::RigidDistanceVisitor::is_nub(), core::chemical::make_centroid(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_hbonds(), core::chemical::Metapatch::meets_requirements(), core::conformation::Residue::mm_atom_name(), path_distance(), core::scoring::PQR::PQR(), core::pose::rna::print_torsion_info(), real_to_virtual(), core::chemical::rename_atoms(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::conformation::Residue::Residue(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::rosetta_recharge_fullatom(), core::io::pose_from_sfr::score_mapping(), core::select::util::select_coord_for_residue(), set_atom_type(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), set_gasteiger_atom_type(), show(), update_derived_data(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::chemical::ResidueTypeKinWriter::write_restype(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

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

References atom_index(), graph_, and ordered_atoms_.

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

References atom_name(), atom_name_to_vd_, and graph_.

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

References atom_name_to_vd_, and graph_.

Atom & core::chemical::ResidueType::atom ( VD const  atom_vd)

References graph_, and has().

Atom const & core::chemical::ResidueType::atom ( VD const  atom_vd) const

References graph_, and has().

std::map< std::string, std::string > core::chemical::ResidueType::atom_aliases ( ) const
inline

returns atom aliases

References atom_aliases_.

Size core::chemical::ResidueType::atom_base ( Size const  atomno) const
VD core::chemical::ResidueType::atom_base ( VD const  atomno) const

get vd of an atom's base atom

References atom_base_, and has().

Size core::chemical::ResidueType::atom_being_shadowed ( Size  atom_shadowing) const
inline

Return the index of the atom that the "atom_shadowing" atom is shadowing; returns zero if the "atom_shadowing" atom is not shadowing anyone.

References atom_shadowed_indices_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), and core::scoring::methods::RingClosureEnergy::residue_energy().

bool core::chemical::ResidueType::atom_depends_on_connection ( core::Size const  atom_index,
core::Size const  connection_id 
) const

Does an atom with a given index have an icoor that depends, directly or indirectly, on a particular connection ID?

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References atom_depends_on_connection_, atom_index(), n_possible_residue_connections(), and natoms().

bool core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection ( core::Size const  atom_index) const

Does an atom with a given index have an icoor that depends, directly or indirectly, on the lower polymeric connection?

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References atom_depends_on_lower_polymeric_connection_, atom_index(), is_polymer(), and natoms().

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

bool core::chemical::ResidueType::atom_depends_on_polymeric_connection ( core::Size const  atom_index) const

Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper or lower polymeric connection?

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References atom_depends_on_lower_polymeric_connection_, atom_depends_on_upper_polymeric_connection_, atom_index(), is_polymer(), and natoms().

bool core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection ( core::Size const  atom_index) const

Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper polymeric connection?

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References atom_depends_on_upper_polymeric_connection_, atom_index(), is_polymer(), and natoms().

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

bool core::chemical::ResidueType::atom_forms_residue_connection ( Size const  atomid) const
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_name_to_vd_, graph_, is_membrane(), is_protein(), name(), name3(), ordered_atoms_, show_all_atom_names(), and core::chemical::tr().

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), add_actcoord_atom(), add_bond(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), add_metapatch_connect(), protocols::hybridization::add_non_protein_cst(), add_nu(), add_orbital_bond(), add_residue_connection(), add_ring(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), protocols::hybridization::TMalign::alignment2AtomMap(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::CreateTorsionConstraint::apply(), protocols::cyclic_peptide::CreateAngleConstraint::apply(), protocols::cyclic_peptide::CreateDistanceConstraint::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::antibody_legacy::GraftOneMover::apply(), core::chemical::ChangeAncestory::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::ReplaceMainchainAtom::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), core::chemical::RenameAtom::apply(), protocols::stepwise::legacy::modeler::rna::apply_chi_cst(), protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata(), core::chemical::gasteiger::assign_gasteiger_atom_types(), atom(), atom_depends_on_connection(), atom_depends_on_lower_polymeric_connection(), atom_depends_on_polymeric_connection(), atom_depends_on_upper_polymeric_connection(), core::conformation::Residue::atom_index(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), autodetermine_chi_bonds(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), change_bond_type(), core::chemical::SetPolymerConnectAtom::changes_connections_on(), core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(), core::chemical::AddConnectAndTrackingVirt::changes_connections_on(), core::chemical::AddConnectDeleteChildProton::changes_connections_on(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::fldsgn::MatchResidues::compute_comb(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), protocols::fldsgn::SheetConstraintGenerator::create_bb_dihedral_constraint(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), protocols::match::Matcher::create_ds_builder(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), delete_act_coord_atom(), delete_atom(), delete_child_proton(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::RigidDistanceVisitor::examine_vertex(), protocols::constraint_generator::existing_atoms(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor(), core::chemical::find_nbr_dist(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::loops::fix_with_coord_cst(), generate_atom_indices(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::pose::motif::get_AIDs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::elec::CountPairRepMap::get_map(), get_metal_binding_atoms(), core::conformation::get_root_atomno(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::chemical::ICoorAtomID::ICoorAtomID(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::chemical::RerootRestypeVisitor::initialize_vertex(), core::conformation::Conformation::insert_residue_by_bond(), 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::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), core::scoring::constraints::BigBinConstraint::read_def(), protocols::constraints_additional::COMCoordinateConstraint::read_def(), protocols::constraints_additional::BindingSiteConstraint::read_def(), protocols::evaluation::PCA::read_structure(), redefine_chi(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::scoring::constraints::requires_CB_mapping(), reset_bond_distance_to_atom(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::symmetry::SymmetrySlider::rg(), core::chemical::RigidDistanceVisitor::RigidDistanceVisitor(), core::select::util::select_coord_for_residue(), select_orient_atoms(), set_ideal_xyz(), set_lower_connect_atom(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), set_orbital_icoor_id(), set_shadowing_atom(), set_upper_connect_atom(), core::pose::rna::setup_base_pair_constraints(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), core::scoring::methods::GoapRsdType::setup_connectivity(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::denovo_design::movers::RotateSegmentMover::target_atoms(), protocols::chemically_conjugated_docking::ubq_ras_distance(), and protocols::chemically_conjugated_docking::ubq_ras_rotation_angle().

Size core::chemical::ResidueType::atom_index ( VD const &  vd) const

get atom index by vertex descriptor

References vd_to_index_.

bool core::chemical::ResidueType::atom_is_backbone ( Size const  atomno) const
inline
bool core::chemical::ResidueType::atom_is_hydrogen ( Size const  atomno) const
inline
bool core::chemical::ResidueType::atom_is_polar_hydrogen ( Size  atomno) const
inline
bool core::chemical::ResidueType::atom_is_sidechain ( Size const  atomno) const
inline
VIterPair core::chemical::ResidueType::atom_iterators ( ) 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 graph_, and ordered_atoms_.

Referenced by add_atom(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), core::chemical::ReplaceMainchainAtom::apply(), core::chemical::SetAllAtomsRepulsive::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::VirtualizeAll::apply(), core::chemical::VirtualizeSidechain::apply(), core::chemical::gasteiger::assign_gasteiger_atom_types(), atom(), core::conformation::Residue::atom_name(), core::chemical::Metapatch::atoms(), autodetermine_chi_bonds(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), bond(), branch_connect_atom_names(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::calculate_rigid_matrix(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), core::scoring::rna::data::RNA_DMS_Potential::check_hbonded(), core::chemical::rna::chi1_torsion_atom(), core::chemical::complex_ring_detection(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraint_atom_id_map(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::chemical::rna::default_jump_atom(), delete_act_coord_atom(), delete_atom(), delete_child_proton(), delete_metalbinding_atom(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), dump_vd_info(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::chemical::fill_ideal_xyz_from_icoor(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), core::io::silent::BinarySilentStruct::fill_struct(), core::chemical::find_best_match(), core::chemical::find_chi_bonds(), core::chemical::find_nbr_dist(), core::chemical::rna::first_base_atom(), core::conformation::form_disulfide(), core::chemical::formatted_icoord_tree(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::chemical::rna::get_rna_base_centroid(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), core::chemical::heavy_atom_names_match(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::pose::toolbox::AtomID_Mapper::initialize_from_pose(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::pose::rna::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::chemical::make_centroid(), core::pose::MiniPose::MiniPose(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::conformation::Residue::orient_onto_residue(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), perform_checks(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::ligand_docking::print_buried_unsat_Hbonds(), core::chemical::print_chis(), protocols::rna::denovo::print_hbonds(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), core::pose::rna::print_torsion_info(), core::chemical::quick_ring_detection(), real_to_virtual(), protocols::denovo_design::rebuild_missing_atoms(), core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::reroot_restype(), core::scoring::mm::score_atom_centrally(), core::scoring::methods::MMBondAngleEnergy::score_atom_centrally(), core::io::pose_from_sfr::score_mapping(), set_atom_base(), set_atom_type(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), set_icoor_private(), set_mm_atom_type(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::methods::GoapRsdType::setup_connectivity(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::lkball::setup_water_builders_for_residue_type(), show(), core::chemical::RerootRestypeVisitor::start_vertex(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), and core::chemical::write_topology_file().

std::string const & core::chemical::ResidueType::atom_name ( VD const  vd) const

get atom name by vertex descriptor

Get atom name by vertex descriptor.

References graph_, and has().

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

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

If we want the atom_type index (integer), we get this from the conformation::Atom itself, as seen in the code below

References ordered_atoms_, and vec_atom_types_.

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Residue::atom_type(), core::scoring::elec::GroupElec::build_groupinfo(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::sdf::MolWriter::compose_typeinfo(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_repulsive(), is_repulsive(), core::conformation::Residue::is_virtual(), is_virtual(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), print_bondangles(), print_dihedrals(), protocols::match::output::print_node(), core::conformation::print_node(), core::pose::rna::print_torsion_info(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

AtomType const & core::chemical::ResidueType::atom_type ( VD const  vd) const

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

References atom_types_, graph_, and ordered_atoms_.

AtomTypeSet const& core::chemical::ResidueType::atom_type_set ( ) const
inline
AtomTypeSetCOP core::chemical::ResidueType::atom_type_set_ptr ( ) const
inline

access by const pointer the atomset for which this residue is constructed

References atom_types_.

Referenced by placeholder_clone(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), and core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_().

VD core::chemical::ResidueType::atom_vertex ( std::string const &  name) const
VD core::chemical::ResidueType::atom_vertex ( Size const &  atomno) const

Get the vertex descriptor from the atom index.

References ordered_atoms_.

bool core::chemical::ResidueType::atoms_are_bonded ( core::Size const  atom_index1,
core::Size const  atom_index2 
) const

Indicates whether or not two atom indices have a chemical bond linking them.

Note that this assumes that the Rosetta machinery is set up so that if atom 1 is bonded to atom 2, atom 2 is bonded to atom 1. This function breaks if that assumption breaks.

Author
Vikram K. Mulligan

References nbrs().

Referenced by core::conformation::get_second_atom_from_connection().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( ) const
inline

Read access to the atoms_last_controlled_by_chi_ array.

References atoms_last_controlled_by_chi_.

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

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::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), and core::scoring::methods::MMTorsionEnergy::residue_pair_energy().

template<typename MemFn , typename Ptr >
utility::signals::Link core::chemical::ResidueType::attach_destruction_obs ( MemFn  fn,
Ptr  ptr 
) const
inline

attach RestypeDestructionEvent observer function

Parameters
fnpointer to observer's unary member function with signature void( RestypeDestructionEvent const & )
ptrRAW pointer to observer object
Returns
Link that can be used to manage the connection.
Remarks
RestypeDestructionEvent observers will only be notified upon destruction of the ResidueType

References destruction_obs_hub_.

Referenced by core::scoring::elec::CountPairRepMap::get_map(), core::scoring::FACTSRsdTypeMap::get_type_info(), core::scoring::lkball::LKBallDatabase::initialize_residue_type(), core::scoring::methods::IdealParametersDatabase::parameters_for_restype(), and core::scoring::custom_pair_distance::PairFuncMap::set_atom_pair_func().

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_.

Referenced by add_metapatch_connect(), and delete_child_proton().

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_.

Referenced by delete_child_proton().

void core::chemical::ResidueType::autodetermine_chi_bonds ( core::Size  max_proton_chi_samples = 500)

Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all.

Requires that Icoor and atom base records are up-to-date, and that ring bonds have been annotated.

References add_chi(), atom(), atom_index(), atom_name(), atom_vertex(), chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, core::chemical::find_chi_bonds(), core::chemical::rna::first_base_atom(), core::chemical::element::H, has(), is_protein(), is_proton_chi_, is_RNA(), core::chemical::is_sp2_proton_chi(), name(), nchi(), proton_chi_extra_samples_, proton_chi_samples_, proton_chis_, set_backbone_heavyatom(), set_proton_chi(), and core::chemical::tr().

Referenced by core::chemical::reroot_restype().

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

AA to use for backbone scoring.

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

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

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

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

References aa_, core::chemical::aa_unk, and backbone_aa_.

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

Returns the nucleic acid type to be used for base features.

References aa_, core::chemical::aa_unp, and base_analogue_.

std::string const& core::chemical::ResidueType::base_name ( ) const
inline
void core::chemical::ResidueType::base_name ( std::string const &  base_name_in)
inline

Set this ResidueType's base name (shared with other residue types with the same base type).

References base_name_.

Bond & core::chemical::ResidueType::bond ( ED const  ed)
Bond const & core::chemical::ResidueType::bond ( ED const  ed) const

References graph_.

Bond & core::chemical::ResidueType::bond ( VD  vd1,
VD  vd2 
)

References atom_name(), graph_, and name().

Bond const & core::chemical::ResidueType::bond ( VD  vd1,
VD  vd2 
) const

References atom_name(), graph_, and name().

Bond & core::chemical::ResidueType::bond ( std::string const &  atom1,
std::string const &  atom2 
)

References atom_vertex(), and bond().

Bond const & core::chemical::ResidueType::bond ( std::string const &  atom1,
std::string const &  atom2 
) const

References atom_vertex(), and bond().

EIterPair core::chemical::ResidueType::bond_iterators ( ) const
inline
OutEdgeIterPair core::chemical::ResidueType::bond_iterators ( VD const &  atom) const
inline

References graph_.

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
AdjacentIterPair core::chemical::ResidueType::bonded_neighbor_iterators ( VD const &  atom) const
utility::vector1< BondName > const & core::chemical::ResidueType::bonded_neighbor_types ( Size const  atomno) const
utility::vector1<core::Size> const& core::chemical::ResidueType::bonded_orbitals ( Size const  atomno) const
inline
utility::vector1< std::string > core::chemical::ResidueType::branch_connect_atom_names ( ) const

Return a list of names of atoms at non-polymer connections.

References atom_name(), and branch_connect_atoms().

Referenced by show().

utility::vector1< uint > core::chemical::ResidueType::branch_connect_atoms ( ) const
std::map< std::string, std::string > core::chemical::ResidueType::canonical_atom_aliases ( ) const
inline
core::chemical::carbohydrates::CarbohydrateInfoCOP core::chemical::ResidueType::carbohydrate_info ( ) const

Return the CarbohydrateInfo object containing sugar-specific properties for this residue.

References carbohydrate_info_.

Referenced by core::conformation::Residue::carbohydrate_info(), core::pose::Pose::chain_sequence(), and core::chemical::Selector_UPPER_POSITION::operator[]().

void core::chemical::ResidueType::change_bond_type ( std::string const &  atom_name1,
std::string const &  atom_name2,
BondName const  old_bond_label,
BondName const  new_bond_label 
)

Change the bond type of the given bond from one type to another.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_index(), atom_name_to_vd_, bonded_neighbor_type_, core::sequence::end, finalized_, graph_, and has().

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

Size core::chemical::ResidueType::chi_2_proton_chi ( Size  chi_index) const
inline
VDs const& core::chemical::ResidueType::chi_atom_vds ( Size const  chino) const
inline

VDs of the atoms which are used to define a given chi angle (chino)

References chi_atoms_.

Referenced by core::chemical::is_sp2_proton_chi(), and core::chemical::reroot_restype().

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_indices_.

Referenced by delete_child_proton(), generate_atom_indices(), perform_checks(), and update_last_controlling_chi().

utility::vector1< std::pair< Real, Real > > const& core::chemical::ResidueType::chi_rotamers ( Size const  chino) const
inline
void core::chemical::ResidueType::clear_chi_rotamers ( core::uint const  chi_no)

Delete all of the chi rotamer bins from the specified chi for this ResidueType.

This method is useful if one has redefined a chi within a patch file such that the old rotamer bins need to be regenerated.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References chi_rotamers_.

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

void core::chemical::ResidueType::clear_orbitals ( )

clear orbitals

References graph_, natoms(), orbitals_, orbitals_index_, and ordered_atoms_.

ResidueTypeOP core::chemical::ResidueType::clone ( ) const
utility::vector1< std::string > const & core::chemical::ResidueType::custom_variant_types ( ) const

Get a list of custom VariantType strings for this ResidueType (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References properties_.

Referenced by protocols::cyclic_peptide::RamaMutationSelector::apply().

AtomIndices const& core::chemical::ResidueType::cut_bond_neighbor ( Size const  atomno) const
inline
void core::chemical::ResidueType::debug_dump_icoor ( ) const
utility::vector1< Adduct > const& core::chemical::ResidueType::defined_adducts ( ) const
inline
bool core::chemical::ResidueType::defines_custom_rama_prepro_map ( bool const  pre_proline_position) const

Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_ defined for this ResidueType (which is presumably different from that of the base type).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

References is_base_type(), rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

void core::chemical::ResidueType::delete_act_coord_atom ( std::string const &  atom_name)

Remove an atom from the list of act coord atoms (used in patching when it kills the valence that is thus used)

Author
Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu)

References actcoord_atoms_, actcoord_atoms_indices_, atom_index(), atom_name(), atom_name_to_vd_, has(), and name3().

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

void core::chemical::ResidueType::delete_atom ( std::string const &  name)
void core::chemical::ResidueType::delete_atom ( Size const  index)

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

References atom_aliases_, atom_name(), delete_atom_alias(), finalized_, graph_, ordered_atoms_, and core::chemical::strip_whitespace().

void core::chemical::ResidueType::delete_atom_alias ( std::string const &  alias,
bool  error = true 
)

Remove a given alias name for an atom.

If error is true, raise error if the alias can't be found

References atom_aliases_, finalized_, and core::chemical::strip_whitespace().

Referenced by delete_atom().

void core::chemical::ResidueType::delete_child_proton ( std::string const &  atom)
void core::chemical::ResidueType::delete_metalbinding_atom ( std::string const &  atom_name)

Remove an atom from the list of atoms that can potentially form a bond to a metal ion (used in patching when it kills the valence that is thus used)

Author
Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu)

References atom_name(), has(), metal_binding_atoms_, and name3().

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

void core::chemical::ResidueType::delete_property ( std::string const &  property)

Add a property of this ResidueType.

This is needed for deleting properties, which occurs in certain PTMs.

References finalized_, and properties_.

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

void core::chemical::ResidueType::delete_terminal_chi ( )

delete terminal chi angle

Author
Andrew M. Watkins (April 2015)

References chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, is_proton_chi_, and proton_chis_.

Referenced by core::chemical::DeleteTerminalChi::apply(), and delete_child_proton().

template<typename MemFn , typename Ptr >
bool core::chemical::ResidueType::detach_destruction_obs ( MemFn  fn,
Ptr  ptr 
) const
inline

detach RestypeDestructionEvent observer function

Parameters
fnpointer to observer's unary member function with signature void( RestypeDestructionEvent const & )
ptrRAW pointer to observer object
Returns
true if disconnect successful, false if connection does not exist
Remarks
RestypeDestructionEvent observers will only be notified upon destruction of the ResidueType

References destruction_obs_hub_.

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().

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

access by reference the element set for which this residue is constructed

References elements_.

ElementSetCOP core::chemical::ResidueType::element_set_ptr ( ) const
inline

access by const pointer the element set for which this residue is constructed

References elements_.

Referenced by placeholder_clone().

void core::chemical::ResidueType::enable_custom_variant_types ( )

Turn on the ability to create VariantTypes "on-the-fly".

"Custom" VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

References properties_.

Referenced by add_metapatch_connect(), core::chemical::AddConnectAndTrackingVirt::apply(), and delete_child_proton().

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

recalculate derived data, potentially reordering atom-indices

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 destruction_obs_hub_, finalized_, generate_atom_indices(), graph_, perform_checks(), core::chemical::regenerate_graph_vertex_index(), setup_atom_ordering(), update_derived_data(), and update_ncaa_rotamer_library_specification_if_present().

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

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

finalized? should always be true, except in very special case early in on-the-fly ResidueTypeSet.

References finalized_.

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

gasteiger::GasteigerAtomTypeDataCOP core::chemical::ResidueType::gasteiger_atom_type ( Size const  atomno) const

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

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

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

References graph_, and ordered_atoms_.

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueType::gasteiger_atom_typeset ( ) const
void core::chemical::ResidueType::generate_atom_indices ( )
private

reorder primary data in ResidueType given the old2new map, called by finalize()

The private data for ResidueType is based on vertex descriptors (VD). Rosetta relies on atom indices to access the private data. In order to keep this interface, the VDs must be converted into atom indices. These are called *_indices, where the primary data is a VD but the indices_data is the atom indices. Because the atom indices change during the setup atom ordering, we must regenerate the cached data. This would not have to occur if Rosetta relied on VDs instead of atom indices.

First, the private data that relies on atom ordering, atom_name_to_vd_ and vd_to_index_ is created by iterating over the total number of atoms in the graph.

Second, the bonded neighbors are generated based on the graph structure.

Finally, all the cached data is generated by iterating over the VDs.

– Assumes that ordered_atoms_ is updated appropriately. Derived data set in this method: atom_name_to_vd_ vd_to_index_ atom_base_indices_ chi_atoms_indices_ nu_atoms_indices_ ring_atoms_indices_ mainchain_atoms_indices_ nbr_atom_indices_ actcoord_atoms_indices_ cut_bond_neighbor_indices_ atom_shadowed_indices_ bonded_neighbor_ bonded_neighbor_type_ atom_2_residue_connection_map_

References actcoord_atoms_, actcoord_atoms_indices_, atom_2_residue_connection_map_, atom_aliases_, atom_base_, atom_base_indices_, atom_index(), atom_name_to_vd_, atom_shadowed_, atom_shadowed_indices_, core::chemical::ICoorAtomID::atomno(), bond(), bonded_neighbor_, bonded_neighbor_type_, bonded_orbitals(), chi_atoms(), chi_atoms_, chi_atoms_indices_, cut_bond_neighbor_, cut_bond_neighbor_indices_, graph_, icoor_, core::chemical::ICoorAtomID::INTERNAL, mainchain_atoms_, mainchain_atoms_indices_, name(), natoms(), nbr_atom_, nbr_atom_indices_, nu_atoms_, nu_atoms_indices_, orbitals_, ordered_atoms_, core::chemical::pretty_print_atomicoor(), residue_connections_, ring_atoms_, ring_atoms_indices_, core::chemical::strip_whitespace(), core::chemical::AtomICoor::stub_atom(), core::chemical::tr(), core::chemical::ICoorAtomID::type(), update_residue_connection_mapping(), vd_to_index_, and core::chemical::ICoorAtomID::vertex().

Referenced by finalize().

utility::vector1<std::string> core::chemical::ResidueType::get_anomeric_pseudotorsion ( ) const
inline
utility::vector1<std::string> core::chemical::ResidueType::get_anomeric_sidechain ( ) const
inline

@ brief Gets atom names that are part of the anomeric side chain.

References anomeric_sidechain_.

Referenced by protocols::carbohydrates::IdealizeAnomericHydrogens::apply().

ResidueTypeCOP core::chemical::ResidueType::get_base_type_cop ( ) const

Get a pointer to this ResidueType's base ResidueType.

Returns the base_type_cop_ pointer if not null, self pointer if null.

References base_type_cop_, and get_self_ptr().

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), and get_rama_prepro_map_file_name().

std::string core::chemical::ResidueType::get_disulfide_atom_name ( ) const
inline
void core::chemical::ResidueType::get_metal_binding_atoms ( AtomIndices metal_binding_indices) const
inline

Gets indices of all atoms that can form bonds to metals.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References atom_index(), has(), and metal_binding_atoms_.

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

utility::vector1< std::string > core::chemical::ResidueType::get_metal_binding_atoms ( ) const
inline

References metal_binding_atoms_.

core::Real core::chemical::ResidueType::get_numeric_property ( std::string const &  tag) const

Get a numeric property, if it exists.

References name3_, and properties_.

Referenced by protocols::qsar::scoring_grid::LigandPropertyScore::score().

std::string const & core::chemical::ResidueType::get_rama_prepro_mainchain_torsion_potential_name ( bool const  pre_proline_position) const

Get the key name for the mainchain torsion potential used by the RamaPrePro score term.

Get the key name for the mainchain torsion potential.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueType), though this can be overridden.

Note
Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueType), though this can be overridden.

References get_base_type_cop(), is_base_type(), rama_prepro_mainchain_torsion_potential_name_, and rama_prepro_mainchain_torsion_potential_name_beforeproline_.

std::string const & core::chemical::ResidueType::get_rama_prepro_map_file_name ( bool const  pre_proline_position) const

Get the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueType), though this can be overridden.

Note
Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueType), though this can be overridden.

References get_base_type_cop(), is_base_type(), rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

ResidueTypeCOP core::chemical::ResidueType::get_self_ptr ( ) const
inline
ResidueTypeOP core::chemical::ResidueType::get_self_ptr ( )
inline
ResidueTypeCAP core::chemical::ResidueType::get_self_weak_ptr ( ) const
inline

Referenced by update_derived_data().

ResidueTypeAP core::chemical::ResidueType::get_self_weak_ptr ( )
inline
std::string core::chemical::ResidueType::get_string_property ( std::string const &  tag) const

Get a string property, if it exists.

References name3_, and properties_.

ResidueGraph const& core::chemical::ResidueType::graph ( ) const
inline
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_name_to_vd_.

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), add_atom_alias(), add_bond(), add_chi(), add_cut_bond(), add_metalbinding_atom(), add_metapatch_connect(), add_nu(), add_orbital_bond(), add_ring(), core::select::util::any_atoms_within_cutoff(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddConnect::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddAtom::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::ResetBondLength::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::ReplaceMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::AddConnectDeleteChildProton::apply(), core::chemical::DeleteChildProton::apply(), core::chemical::SetVirtualShadow::apply(), core::chemical::SetDisulfideAtomName::apply(), atom(), atom_base(), atom_name(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), autodetermine_chi_bonds(), core::scoring::elec::GroupElec::build_groupinfo(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps(), change_bond_type(), core::chemical::SetPolymerConnectAtom::changes_connections_on(), core::chemical::AddConnect::changes_connections_on(), core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(), core::chemical::AddConnectAndTrackingVirt::changes_connections_on(), core::chemical::AddConnectDeleteChildProton::changes_connections_on(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::simple_filters::AtomicDistanceFilter::compute(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), delete_act_coord_atom(), delete_atom(), delete_metalbinding_atom(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::stepwise::sampler::protein::do_set_xyz(), dump_vd_info(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor(), core::chemical::find_best_match(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::rna::movers::find_nearby_res(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::pose::motif::get_AIDs(), core::scoring::elec::CountPairRepMap::get_map(), get_metal_binding_atoms(), core::conformation::Residue::has(), core::chemical::has_assigned_coords(), icoor(), core::chemical::ICoorAtomID::ICoorAtomID(), core::chemical::sdf::MolFileIOMolecule::index_valid(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::is_disulfide_bond(), core::pose::named_atom_id_to_atom_id(), core::chemical::Selector_HAS_ATOMS::operator[](), core::conformation::Residue::orient_onto_residue(), protocols::hybridization::MRMover::pack_missing_sidechains(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), redefine_chi(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::chemical::reroot_restype(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::select::util::select_coord_for_residue(), set_atom_base(), set_atom_type(), set_backbone_heavyatom(), set_icoor(), set_ideal_xyz(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), core::scoring::setup_matching_atoms_with_given_names(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), core::chemical::RerootRestypeVisitor::start_vertex(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd().

bool core::chemical::ResidueType::has ( VD const  vd) const
inline

is this vertex descriptor present in this residue?

References graph_, and core::chemical::has().

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_polymer_dependent_groups ( ) const

Does this type have groups (not just single atoms) that are polymer-bond dependent?

Always returns false for non-polymeric residue types.

References has_polymer_dependent_groups_, and is_polymer().

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

Generic property access, by ResidueProperty.

References properties_.

bool core::chemical::ResidueType::has_sc_orbitals ( ) const

does this residue have sidechain orbitals?

References properties_, and core::chemical::SC_ORBITALS.

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

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

Returns true if this residue has shadow atoms, false otherwise.

References atom_shadowed_.

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

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

Generic variant access.

References properties_.

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), add_metapatch_connect(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover::apply(), protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), core::pack::task::operation::OptCysHG::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply_Aform_torsions_to_five_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply_Aform_torsions_to_three_prime_phosphate(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_phosphate_variants(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::rna::movers::RNA_LoopCloser::check_closure(), protocols::stepwise::modeler::rna::check_instantiated_O2Prime_hydrogen(), protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::cleanup_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints(), delete_child_proton(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::figure_out_loop(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::modeler::figure_out_moving_partition_res(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::methods::find_relevant_connections(), core::scoring::methods::find_relevant_connections_onersd(), protocols::stepwise::modeler::find_root_without_virtual_ribose(), core::pose::fix_up_residue_type_variants_at_floating_base(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed(), protocols::rna::denovo::get_default_allowed_bulge_res(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::conformation::get_root_atomno(), core::conformation::Residue::has_variant_type(), core::pose::rna::has_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), protocols::stepwise::modeler::is_cutpoint_closed(), core::pose::rna::is_cutpoint_closed_torsion(), core::pose::rna::is_cutpoint_open(), core::pose::rna::is_torsion_valid(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::make_pose_from_sequence(), protocols::stepwise::modeler::make_variants_match(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), core::chemical::Selector_VARIANT_TYPE::operator[](), core::chemical::Selector_MATCH_VARIANTS::operator[](), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_has_chainbreak(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), core::import_pose::remove_cutpoints_closed(), protocols::stepwise::modeler::rna::remove_virtual_O2Prime_hydrogen(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), core::import_pose::setup_fold_trees(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), core::pose::rna::setup_three_prime_phosphate_based_on_next_residue(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants(), protocols::stepwise::modeler::split_pose(), core::pose::update_block_stack_variants(), protocols::rna::denovo::movers::RNA_FragmentMover::update_insert_map(), core::pose::toolbox::AtomLevelDomainMap::update_to_move_internal_phosphates(), core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_o2prime(), core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_phosphates(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), core::pose::rna::virtualize_5prime_phosphates(), protocols::rna::denovo::virtualize_bulges(), and core::pose::rna::virtualize_free_rna_moieties().

bool core::chemical::ResidueType::has_variant_type ( std::string const &  variant_type) const

Generic variant access by string.

References properties_.

const HeavyAtomWithHydrogensGraph core::chemical::ResidueType::heavy_atom_with_hydrogens ( )

References atom_types_, graph(), and graph_.

const HeavyAtomWithPolarHydrogensGraph core::chemical::ResidueType::heavy_atom_with_polar_hydrogens ( )

References atom_types_, graph(), and graph_.

const HeavyAtomGraph core::chemical::ResidueType::heavy_atoms ( )

References atom_types_, and graph_.

bool core::chemical::ResidueType::heavyatom_has_polar_hydrogens ( Size  atomno) const
inline
bool core::chemical::ResidueType::heavyatom_is_an_acceptor ( Size  atomno) 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(), and perform_checks().

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
AtomIndices const& core::chemical::ResidueType::Hpos_polar_sc ( ) const
inline
const HydrogenAtomGraph core::chemical::ResidueType::hydrogens ( )

References atom_types_, and graph_.

Referenced by setup_atom_ordering().

AtomICoor const & core::chemical::ResidueType::icoor ( Size const  atm) const

AtomICoord of an atom.

References icoor_, and ordered_atoms_.

Referenced by add_atom(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), add_metapatch_connect(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), core::chemical::ChangeAncestory::apply(), core::chemical::ChiralFlipAtoms::apply(), core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), delete_child_proton(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::chemical::fill_ideal_xyz_from_icoor(), core::chemical::formatted_icoord_tree(), core::conformation::Residue::icoor(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), reset_bond_distance_to_atom(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), update_nonpolymer_dependent_groups(), update_polymer_dependent_groups(), and core::chemical::write_topology_file().

AtomICoor const & core::chemical::ResidueType::icoor ( VD const  atm) const

AtomICoord of an atom.

References has(), and icoor_.

dihedral_atom_set const& core::chemical::ResidueType::improper_dihedral ( Size const  dihe) const
inline

Return the indices for the set of atoms that define a particular intraresidue improper dihedral.

References improper_dihedral_atom_sets_.

utility::vector1< Size > const& core::chemical::ResidueType::improper_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 improper_dihedrals_for_atom_.

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

get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypes ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypes .params file with the INTERCHANGEABILITY_GROUP tag.

References interchangeability_group_.

Referenced by core::chemical::SetInterchangeabilityGroup_String::apply(), core::chemical::ChiralFlipNaming::apply(), placeholder_clone(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::interchangeability_group ( std::string  setting)
inline

set our interchangeability-group id

References interchangeability_group_.

bool core::chemical::ResidueType::is_acetylated_nterminus ( ) const

is acetylated n terminus

References core::chemical::ACETYLATED_NTERMINUS, and properties_.

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

is an adduct-modified residue?

References core::chemical::ADDUCT, and properties_.

bool core::chemical::ResidueType::is_alpha_aa ( ) const

Is this an alpha-amino acid?

References core::chemical::ALPHA_AA, and properties_.

Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::SetTorsion::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), core::select::residue_selector::BinSelector::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_dihedral_bbg(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::conformation::check_good_cutpoint_neighbour(), protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), core::conformation::form_disulfide_helper(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_residues_recursively(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_torsion_sets().

bool core::chemical::ResidueType::is_aramid ( ) const
bool core::chemical::ResidueType::is_aromatic ( ) const
bool core::chemical::ResidueType::is_base_type ( ) const

Is this ResidueType a base type?

Checks the base_type_cop_ pointer. If it's null, this is assumed to be a base type.

References base_type_cop_.

Referenced by defines_custom_rama_prepro_map(), get_rama_prepro_mainchain_torsion_potential_name(), get_rama_prepro_map_file_name(), and update_derived_data().

bool core::chemical::ResidueType::is_beta_aa ( ) const

Is this a beta-amino acid?

References core::chemical::BETA_AA, and properties_.

Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::conformation::check_good_cutpoint_neighbour(), protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::conformation::form_disulfide_helper(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_residues_recursively(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_torsion_sets().

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

is a branch-point residue?

References core::chemical::BRANCH_POINT, and properties_.

Referenced by core::conformation::Residue::is_branch_point(), and show().

bool core::chemical::ResidueType::is_canonical ( ) const
bool core::chemical::ResidueType::is_canonical_aa ( ) const

Is this a canonical amino acid (CANONICAL_AA property)?

Only the standard amino acid types (ACDEFGHIKLMNPQRSTVWY) are canonical.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::CANONICAL_AA, and properties_.

Referenced by is_canonical(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), and core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary().

bool core::chemical::ResidueType::is_canonical_nucleic ( ) const

Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)?

Only the standard nucliec acid types (dA, dC, dG, dT, A, C, G, U) are canonical.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::CANONICAL_NUCLEIC, and properties_.

Referenced by is_canonical().

bool core::chemical::ResidueType::is_carbohydrate ( ) const

is carbohydrate?

References core::chemical::CARBOHYDRATE, and properties_.

Referenced by core::conformation::Conformation::append_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), core::select::residue_selector::GlycanLayerSelector::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::calculate(), core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), core::conformation::Residue::carbohydrate_info(), core::conformation::check_good_cutpoint_neighbour(), core::chemical::rna::default_jump_atom(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::scoring::methods::get_restag(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_residue_level_screeners(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), core::conformation::Conformation::insert_polymer_residue(), core::conformation::Residue::is_carbohydrate(), protocols::stepwise::modeler::is_protein(), core::chemical::Selector_UPPER_POSITION::operator[](), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().

bool core::chemical::ResidueType::is_charged ( ) const
bool core::chemical::ResidueType::is_coarse ( ) const
bool core::chemical::ResidueType::is_cyclic ( ) const
bool core::chemical::ResidueType::is_d_aa ( ) const

is this a d-amino acid?

References core::chemical::D_AA, and properties_.

Referenced by protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::denovo_design::movers::FastDesign::apply(), core::fragment::IndependentBBTorsionSRFD::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), protocols::simple_filters::ResidueChiralityFilter::compute(), protocols::denovo_design::construct_poly_ala_pose(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector_bbdep(), core::conformation::form_disulfide_helper(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static_voronoi(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::denovo_design::DisulfidizeMover::mixed_disulfide(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv_bbdep(), and core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide().

bool core::chemical::ResidueType::is_d_rna ( ) const
bool core::chemical::ResidueType::is_disulfide_bonded ( ) const

is disulfide?

References core::chemical::DISULFIDE_BONDED, and properties_.

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), core::conformation::break_disulfide(), protocols::denovo_design::construct_poly_ala_pose(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), core::conformation::get_disulf_partner(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::is_allowed_type(), core::conformation::is_disulfide_bond(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), protocols::loops::select_loop_residues(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), and core::pose::full_model_info::update_disulfides_from_full_model_info().

bool core::chemical::ResidueType::is_DNA ( ) const
bool core::chemical::ResidueType::is_gamma_aa ( ) const
bool core::chemical::ResidueType::is_inverted_virtual_residue ( ) const

Check if atom is an inverted virtual.

Check if residue is 'INVERTING_VIRTUAL_RESIDUE'.

Used by the symmetry machinery for mirror symmetry operations.

References core::chemical::INVERTED_VIRTUAL_RESIDUE, and properties_.

Referenced by core::conformation::symmetry::calculate_inverting_virtuals(), core::pose::symmetry::make_symmetric_pose(), and core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues().

bool core::chemical::ResidueType::is_l_aa ( ) const
bool core::chemical::ResidueType::is_l_rna ( ) const

is this an l-RNA?

References core::chemical::L_RNA, and properties_.

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

bool core::chemical::ResidueType::is_ligand ( ) const

is ligand?

References core::chemical::LIGAND, and properties_.

Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::enzdes::EnzdesBaseProtocol::catalytic_res(), protocols::enzdes::enzutil::catalytic_res(), protocols::enzdes::LigDSasaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::flxbb::constraints_sheet(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), core::pack::rotamers::SingleLigandRotamerLibraryCreator::create(), protocols::enzdes::EnzdesBaseProtocol::design_targets(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::get_ligand_seqpos(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), core::conformation::Residue::is_ligand(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::toolbox::match_enzdes_util::EnzdesCstCache::ordered_constrained_positions(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::Energies::update_neighbor_links(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_lipid ( ) const
bool core::chemical::ResidueType::is_lower_terminus ( ) const

is lower terminus?

References core::chemical::LOWER_TERMINUS, and properties_.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_lower_terminus(), is_terminus(), core::pose::make_pose_from_sequence(), core::conformation::Residue::orient_onto_residue_peptoid(), core::conformation::Residue::place(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_membrane ( ) const
bool core::chemical::ResidueType::is_metal ( ) const
bool core::chemical::ResidueType::is_metalbinding ( ) const

Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.), false otherwise.

The METALBINDING property is specified in the params file under PROPERTIES.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::METALBINDING, and properties_.

Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_metalbinding(), and perform_checks().

bool core::chemical::ResidueType::is_methylated_cterminus ( ) const

is methylated c terminus

References core::chemical::METHYLATED_CTERMINUS, and properties_.

bool core::chemical::ResidueType::is_NA ( ) const
bool core::chemical::ResidueType::is_oligourea ( ) const
bool core::chemical::ResidueType::is_peptoid ( ) const
bool core::chemical::ResidueType::is_PNA ( ) const

is PNA?

References core::chemical::PNA, and properties_.

bool core::chemical::ResidueType::is_polar ( ) const
bool core::chemical::ResidueType::is_polymer ( ) const

is polymer?

References core::chemical::POLYMER, and properties_.

Referenced by protocols::simple_moves::MissingDensityToJumpMover::apply(), core::select::residue_selector::BinSelector::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), core::chemical::gasteiger::assign_gasteiger_atom_types(), atom_depends_on_lower_polymeric_connection(), atom_depends_on_polymeric_connection(), atom_depends_on_upper_polymeric_connection(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::ligand_docking::constrain_ligand_torsions(), core::chemical::rna::default_jump_atom(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::loops::find_non_protein_chunks(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose(), core::conformation::get_root_residue_root_atomno(), protocols::loophash::get_rt_over_leap_fast(), core::conformation::Residue::has_lower_connect(), has_polymer_dependent_groups(), core::conformation::Residue::has_upper_connect(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_residue_level_screeners(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_screeners(), protocols::toolbox::rigid_body::initialize_stub(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_polymer_bonded(), protocols::stepwise::modeler::is_protein(), core::pose::make_pose_from_sequence(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::conformation::Residue::place(), core::io::serialization::read_binary(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::pose::rna::update_map(), update_polymer_dependent_groups(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_protein ( ) const

is protein?

References properties_, and core::chemical::PROTEIN.

Referenced by add_actcoord_atom(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::hybridization::add_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_zaxis(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_terminus_variants_at_protein_rna_boundaries(), atom_index(), autodetermine_chi_bonds(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::toolbox::CA_superimpose(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::stepwise::modeler::protein::contains_protein(), protocols::cyclic_peptide::SymmetricCycpepAlign::count_protein_residues(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::calc_taskop_movers::ConsensusDesignMover::create_sequence_profile_constraints(), core::chemical::rna::default_jump_atom(), 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::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_trim_to_single_repeat(), protocols::loops::extract_secondary_structure_chunks(), protocols::stepwise::modeler::protein::figure_out_protein_modeling_info(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::rna::movers::find_nearby_res(), protocols::loops::find_non_protein_chunks(), core::scoring::cryst::fix_bfactorsMissing(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fix_phi_psi_offsets(), protocols::stepwise::modeler::fix_protein_jump_atom(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::stepwise::modeler::protein::get_bridge_res(), protocols::match::BfactorMPM::get_ca_bfactors(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::scoring::elec::FA_ElecEnergy::get_countpair_representative_atom(), core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_stepwise_jump_atom(), core::pose::rna::get_suite_torsion_info(), core::sequence::ABEGOManager::get_symbols(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_phi_psi_offsets(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), protocols::toolbox::rigid_body::initialize_stub(), protocols::stepwise::modeler::is_protein(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), protocols::stepwise::modeler::protein::just_protein(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), 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::stepwise::modeler::output_movemap(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::hybridization::BackboneTorsionSampler::perturb(), 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::pose_metric_calculators::HPatchCalculator::recompute(), protocols::pose_metric_calculators::SurfaceCalculator::recompute(), protocols::pose_metric_calculators::ChargeCalculator::recompute(), protocols::pose_metric_calculators::PackstatCalculator::recompute(), protocols::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(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::save_phi_psi_offsets(), protocols::cyclic_peptide::SymmetricCycpepAlign::select_protein_residues(), core::pose::set_ss_from_phipsi(), protocols::simple_moves::CyclizationMover::setup_connections(), core::import_pose::setup_fold_trees(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), core::pose::transfer_phi_psi(), core::pose::rna::update_map(), protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(), and protocols::stepwise::modeler::virtualize_side_chains().

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