Rosetta 3.4
Public Member Functions
core::chemical::ResidueType Class Reference

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

#include <ResidueType.hh>

Inheritance diagram for core::chemical::ResidueType:
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Collaboration diagram for core::chemical::ResidueType:
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List of all members.

Public Member Functions

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

Detailed Description

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

Basically a slice of aaproperties pack!

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

Properties:

Questions:


Constructor & Destructor Documentation

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

destructor

References core::chemical::tr().

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

constructor

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

Referenced by clone().


Member Function Documentation

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

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

References core::chemical::aa_from_name().

Referenced by protocols::simple_moves::MinimalRotamer::aa(), core::conformation::Residue::aa(), protocols::loops::add_loop(), protocols::motifs::add_motif_bb_constraints(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_moves::GreedyOptMutationMover::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), protocols::motifs::backbone_stub_match(), core::io::pdb::build_pose_as_is1(), core::scoring::methods::CartesianBondedEnergy::eval_atom_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), core::scoring::methods::get_parallel_h_for_arg(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::scoring::dna::get_y_axis_atoms(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::constraints::is_aromatic(), core::conformation::Residue::is_similar_aa(), core::conformation::Residue::is_similar_rotamer(), core::scoring::methods::BondLengthDatabase::lookup(), core::scoring::methods::BondAngleDatabase::lookup(), core::scoring::methods::TorsionDatabase::lookup(), core::chemical::Selector_AA::operator[](), core::scoring::constraints::parse_NMR_name(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::toolbox::pose_metric_calculators::ChargeCalculator::recompute(), core::scoring::constraints::requires_CB_mapping(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::residue_type_has_waters(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::constraints_additional::SequenceCouplingConstraint::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().

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

our traditional residue type, if any

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

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

Size core::chemical::ResidueType::abase2 ( Size const  atomno) const [inline]

get index of an atom's second base atom

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

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

indices of atoms as Hbond acceptors

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

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

indices of atoms as Hbond acceptors

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

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

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

add an atom to the list for calculating actcoord center

References atom_index(), is_protein(), and core::chemical::tr().

void core::chemical::ResidueType::add_adduct ( Adduct adduct_in) [inline]
void core::chemical::ResidueType::add_atom ( std::string const &  atom_name,
std::string const &  atom_type_name,
std::string const &  mm_atom_type_name,
Real const  charge 
)

add an atom into this residue

Note:
this does not set xyz coordiates for the added atom

References atom_name(), core::chemical::strip_whitespace(), and core::chemical::tr().

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

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

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

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

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

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

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

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

References has().

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

add a chi angle defined by four atoms

References has().

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

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

add a rotamer bin for a given chi

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

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 has().

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

add an orbital onto a residue based upon atom

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

References orbital_name(), 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 has(), and has_orbital().

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

add properties

add a property to this residue update boolean property member data accordingly

References core::chemical::tr().

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

Size core::chemical::ResidueType::add_residue_connection ( std::string const &  atom_name,
std::string const &  connect_atom_type = "VIRT" 
)

add a ResidueConnection Doesnt set the ideal geometry -- maybe it should?

References atom_index().

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

void core::chemical::ResidueType::add_variant_type ( VariantType const &  variant_type) [inline]

add one more variant type to this ResidueType

References has_variant_type().

AtomIndices const& core::chemical::ResidueType::all_bb_atoms ( ) const [inline]
AtomIndices const& core::chemical::ResidueType::all_sc_atoms ( ) const [inline]
void core::chemical::ResidueType::assign_internal_coordinates ( )
void core::chemical::ResidueType::assign_neighbor_atom ( )
Size core::chemical::ResidueType::atom_base ( Size const  atomno) const [inline]
bool core::chemical::ResidueType::atom_forms_residue_connection ( Size const  atomid) [inline]

Does an atom form any inter-residue chemical bonds?

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

get atom index by name

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

Referenced by add_actcoord_atom(), core::coarse::Translator::add_atom(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::add_gap_constraints_to_pose(), add_residue_connection(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::antibody2::Ab_GraftOneCDR_Mover::apply(), protocols::antibody::GraftOneMover::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::PrependMainchainAtom::apply(), protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata(), core::conformation::Residue::atom_index(), core::io::pdb::build_pose_as_is1(), calculate_icoor(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), delete_atom(), protocols::topology_broker::fix_mainchain_connect(), protocols::loops::fix_with_coord_cst(), protocols::comparative_modeling::hybridize::InsertChunkMover::get_local_sequence_mapping(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::ICoorAtomID::ICoorAtomID(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), core::pose::named_atom_id_to_atom_id(), nbr_atom(), core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(), core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(), core::scoring::constraints::parse_NMR_name(), 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(), core::scoring::constraints::requires_CB_mapping(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), core::pack::task::operation::util::select_coord_for_residue(), set_atom_type(), set_atomic_charge(), set_backbone_heavyatom(), set_lower_connect_atom(), set_mm_atom_type(), set_upper_connect_atom(), set_xyz(), protocols::rna::setup_base_pair_constraints(), and core::scoring::constraints::SiteConstraint::setup_csts().

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

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

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

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

get atom name by index

Referenced by core::coarse::Translator::add_atom(), add_atom(), assign_internal_coordinates(), core::conformation::Residue::atom_name(), protocols::swa::rna::atom_square_deviation(), protocols::swa::rna::base_atoms_square_deviation(), core::io::pdb::build_pose_as_is1(), debug_dump_icoor(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::scoring::methods::BondLengthDatabase::lookup(), core::scoring::methods::BondAngleDatabase::lookup(), core::scoring::methods::TorsionDatabase::lookup(), core::pose::MiniPose::MiniPose(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), protocols::swa::rna::print_atom_info(), protocols::swa::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::swa::rna::Print_torsion_info(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::mm::score_atom_centrally(), protocols::comparative_modeling::hybridize::InsertChunkMover::set_bb_xyz_aligned(), protocols::swa::rna::setup_suite_atom_id_map(), core::scoring::methods::setup_water_builders_for_residue_type(), protocols::comparative_modeling::hybridize::InsertChunkMover::steal_torsion_and_bonds_from_template(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), and core::chemical::write_topology_file().

AtomType const & core::chemical::ResidueType::atom_type ( Size const  atomno) const
int core::chemical::ResidueType::atom_type_index ( Size const  atmno) const

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

Referenced by protocols::match::bump_grid_to_enclose_pose(), and core::conformation::Residue::Residue().

AtomTypeSet const& core::chemical::ResidueType::atom_type_set ( ) const [inline]

access by reference the atomset for which this residue is constructed

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

AtomTypeSetCAP core::chemical::ResidueType::atom_type_set_ptr ( ) const [inline]
Real core::chemical::ResidueType::atomic_charge ( Size const  atm) const [inline]
utility::vector1< AtomIndices > const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( ) const [inline]
AtomIndices const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( Size  chi) const [inline]

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

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]

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.

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

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.

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

AtomIndices const& core::chemical::ResidueType::attached_H_begin ( ) const [inline]

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

Size core::chemical::ResidueType::attached_H_begin ( Size const  atom) const [inline]
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

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.

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

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

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

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

indices of the bonded neighbors for an atom

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

void core::chemical::ResidueType::debug_dump_icoor ( )

Dump out atomnames and icoor values.

References atom_name(), name3(), natoms(), core::chemical::tr(), and xyz().

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

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

References atom_index(), and has().

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

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

delete properties

delete a property to this residue update boolean property member data accordingly

References core::chemical::tr().

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

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.

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

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

access by reference the atomset for which this residue is constructed

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

recalculate derived data, potentially reordering atom-indices

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

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

index of the first sidehchain hydrogen

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

sdf::MolData core::chemical::ResidueType::get_mol_data ( ) const [inline]
Size core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot ( Size  n_rot) [inline]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

return indices of aromatic Hydrogens

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?

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

bool core::chemical::ResidueType::has_atom_name ( std::string const &  name) const
bool core::chemical::ResidueType::has_orbital ( std::string const &  orbital_name) const [inline]

is this orbital present in this residue?

Referenced by add_orbital_bond().

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

does this residue have sidechain orbitals?

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

bool core::chemical::ResidueType::has_variant_type ( VariantType const &  variant_type) const [inline]
bool core::chemical::ResidueType::heavyatom_has_polar_hydrogens ( Size  ind) const [inline]
bool core::chemical::ResidueType::heavyatom_is_an_acceptor ( Size  ind) const [inline]
AtomIndices const& core::chemical::ResidueType::Hpol_index ( ) const [inline]

return indices of polar Hydrogens

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

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

indices of non-polar hydrogens as potential carbon Hbond donors

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

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

indices of polar hydrogens as Hbond donors

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

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

is actylated n terminus

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

is an adduct-modified residue?

bool core::chemical::ResidueType::is_aromatic ( ) const [inline]
bool core::chemical::ResidueType::is_charged ( ) const [inline]
bool core::chemical::ResidueType::is_coarse ( ) const [inline]
bool core::chemical::ResidueType::is_DNA ( ) const [inline]
bool core::chemical::ResidueType::is_ligand ( ) const [inline]
bool core::chemical::ResidueType::is_lower_terminus ( ) const [inline]
bool core::chemical::ResidueType::is_methylated_cterminus ( ) const [inline]

is methylated c terminus

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

is protein?

Referenced by add_actcoord_atom(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), atom_index(), protocols::toolbox::CA_superimpose(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::methods::dfire::DFIRE_Energy::defines_residue_pair_energy(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), protocols::comparative_modeling::hybridize::discontinued_lower(), protocols::comparative_modeling::hybridize::discontinued_upper(), protocols::loops::extract_secondary_structure_chunks(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::surface_docking::FullatomRelaxMover::FinalizeMovers(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), protocols::loops::native_loop_core_CA_rmsd(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::motifs::LigandMotifSearch::position_vector_setup(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::pose_metric_calculators::SurfaceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::PackstatCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::HPatchCalculator::recompute(), protocols::toolbox::pose_metric_calculators::ChargeCalculator::recompute(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::pose::set_ss_from_phipsi(), core::pose::transfer_phi_psi(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_proton_chi ( Size const  chino) const [inline]
bool core::chemical::ResidueType::is_RNA ( ) const [inline]
bool core::chemical::ResidueType::is_surface ( ) const [inline]
bool core::chemical::ResidueType::is_terminus ( ) const [inline]
bool core::chemical::ResidueType::is_upper_terminus ( ) const [inline]
bool core::chemical::ResidueType::is_virtual ( Size const &  atomno) const

Check if atom is virtual.

References atom_type().

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

Check if residue is 'VIRTUAL_RESIDUE'.

References has_variant_type().

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

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

Read access to the last_controlling_chi_ array.

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

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

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

ResidueConnection const& core::chemical::ResidueType::lower_connect ( ) const [inline]
Size core::chemical::ResidueType::lower_connect_atom ( ) const [inline]

index number of the atom which connects to the lower connection

Referenced by core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::lower_connect_atom(), and core::chemical::ICoorAtomID::xyz().

Size core::chemical::ResidueType::lower_connect_id ( ) const [inline]
Size core::chemical::ResidueType::mainchain_atom ( Size const  atm) const [inline]
AtomIndices const& core::chemical::ResidueType::mainchain_atoms ( ) const [inline]
std::string const& core::chemical::ResidueType::mm_atom_name ( Size const  index) const [inline]
MMAtomType const & core::chemical::ResidueType::mm_atom_type ( Size const  atomno) const

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

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

int core::chemical::ResidueType::mm_atom_type_index ( Size const  atomno) const
core::Real& core::chemical::ResidueType::molecular_weight ( ) [inline]

get the molecular weight of this residue

Size core::chemical::ResidueType::n_hbond_acceptors ( ) const [inline]
Size core::chemical::ResidueType::n_hbond_donors ( ) const [inline]

number of hbond_donors

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

number of orbitals

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

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

get our (unique) residue name

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::abinitio::DomainAssembly::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::AddBond::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddChi::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::DeleteAtom::apply(), core::chemical::Patch::apply(), core::chemical::apply_adducts_to_residue(), core::io::pdb::build_pose_as_is1(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::import_pose::atom_tree_diffs::dump_reference_pose(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::conformation::Residue::fill_missing_atoms(), core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), protocols::loops::get_tenA_neighbor_residues(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::pack::dunbrack::load_unboundrot(), core::pose::make_pose_from_sequence(), protocols::rotamer_recovery::RRProtocol::measure_rotamer_recovery(), core::conformation::Residue::name(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::coarse::CoarseEtable::print_residue_info(), core::pose::remove_virtual_residues(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::loops::select_loop_residues(), core::import_pose::set_reasonable_fold_tree(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), core::scoring::methods::setup_water_builders_for_residue_type(), core::util::switch_to_residue_type_set(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), core::io::serialization::write_binary(), core::chemical::ResidueDatabaseIO::write_residuetype_to_database(), and core::chemical::write_topology_file().

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

set our (unique) residue name

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

set our 1letter code

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

set our 3letter code

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

get our 3letter code

Referenced by protocols::loops::add_loop(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), protocols::dna::WatsonCrickRotamerCouplings::apply(), protocols::comparative_modeling::StealSideChainsMover::apply(), core::pack::task::operation::OptCysHG::apply(), core::chemical::SetIO_String::apply(), atom_index(), core::scoring::automorphic_rmsd(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), debug_dump_icoor(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::frac_atoms_within(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), core::conformation::Residue::name3(), core::pack::task::operation::ResidueName3Is::operator()(), core::chemical::Selector_NAME3::operator[](), orbital_index(), core::scoring::constraints::parse_NMR_name(), protocols::dna::DnaChains::print(), protocols::viewer::print_node(), protocols::match::output::print_node(), core::conformation::print_node(), report_adducts(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::conformation::setup_corresponding_atoms(), core::scoring::hbonds::HBond::show(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_residue_type_set(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().

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

number of atoms

Referenced by core::conformation::annotated_atom_graph_from_conformation(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frame(), protocols::comparative_modeling::hybridize::InsertChunkMover::apply_transform(), core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::apply_transform_Rx_plus_v(), core::conformation::atom_graph_from_conformation(), core::scoring::automorphic_rmsd(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::io::pdb::build_pose_as_is1(), protocols::toolbox::CA_superimpose(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::toolbox::AllowInsert::calculate_atom_id_domain_map(), protocols::toolbox::AllowInsert::calculate_atom_id_map(), protocols::comparative_modeling::hybridize::InsertChunkMover::check_overlap(), core::pose::copy_dofs(), debug_dump_icoor(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::io::silent::BinaryRNASilentStruct::fill_pose(), protocols::ligand_docking::frac_atoms_within(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::get_residue_path_distances(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::pose::initialize_atomid_map(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::natoms(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::conformation::symmetry::recenter(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), protocols::fibril::reorient_extended_fibril(), core::conformation::Residue::Residue(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), protocols::swa::rotate(), core::conformation::Residue::select_orient_atoms(), protocols::comparative_modeling::hybridize::InsertChunkMover::set_bb_xyz_aligned(), core::scoring::methods::setup_water_builders_for_residue_type(), core::scoring::superimpose_pose(), protocols::swa::translate(), core::chemical::write_topology_file(), and core::fragment::xform_pose().

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

get nbr_atom used to define residue-level neighbors

Referenced by assign_neighbor_atom().

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

set nbr_radius_ used to define residue-level neighbors

Referenced by core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), and core::chemical::write_topology_file().

Real core::chemical::ResidueType::nbr_radius ( ) const [inline]

get nbr_radius_ used to define residue-level neighbors

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

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

Referenced by core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), and core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy().

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

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

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

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

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

indicates how many heavyatom bonded neighbors an atom has

References number_bonded_hydrogens().

Size core::chemical::ResidueType::number_bonded_hydrogens ( Size const  atomno) const [inline]
orbitals::ICoorOrbitalData const& core::chemical::ResidueType::orbital_icoor_data ( Size const  orbital_index) const [inline]

References orbital_index().

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

get orbital index by name

References name3().

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

std::string const& core::chemical::ResidueType::orbital_name ( Size const  index) const [inline]

orbital name by index

Referenced by add_orbital(), and core::conformation::Residue::orbital_name().

orbitals::OrbitalType const & core::chemical::ResidueType::orbital_type ( int const  orbital_index) const
utility::vector1< int > const& core::chemical::ResidueType::path_distance ( Size  atom) const [inline]

shortest path distance for an atom to all other residue atoms

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

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

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

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

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

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

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

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

this might return 0, so please check for that

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

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

print chemical-bond path distances to standard out

References core::chemical::tr().

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

acess specified properties

get all specified properties for this residue type

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

translate proton_chi to global chi

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

redefine a chi angle based on four atoms

References has().

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

void core::chemical::ResidueType::report_adducts ( )
void core::chemical::ResidueType::require_final ( ) const [inline]

an assertion funtion to ensure an ResidueType has been finalized

bool core::chemical::ResidueType::requires_actcoord ( ) const [inline]

require actcoord?

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

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

set the residue type set of origin.

core::chemical::rna::RNA_ResidueType const& core::chemical::ResidueType::RNA_type ( ) const [inline]
void core::chemical::ResidueType::set_adduct_flag ( bool  adduct_in) [inline]
void core::chemical::ResidueType::set_atom_base ( std::string const &  atom_name1,
std::string const &  atom_name2 
)

sets atom_base[ atom1 ] = atom2

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

References has().

Referenced by set_icoor().

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

set atom type

References atom_index().

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

void core::chemical::ResidueType::set_atomic_charge ( std::string const &  atm,
Real const  charge 
) [inline]

set atom charge

References atom_index().

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

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

set an atom as backbone heavy atom

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

References atom_index().

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

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

set AtomICoor for an atom

set AtomICoor for an atom

will update the xyz coords as well if desired, useful inside a patching operation where new atoms are being added.

References core::chemical::AtomICoor::build(), core::chemical::ICoorAtomID::CONNECT, has(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ICoorAtomID::POLYMER_LOWER, core::chemical::ICoorAtomID::POLYMER_UPPER, set_atom_base(), and set_xyz().

void core::chemical::ResidueType::set_icoor ( std::string const &  atm,
Real const  phi,
Real const  theta,
Real const  d,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3,
bool const  update_xyz = false 
)
void core::chemical::ResidueType::set_lower_connect_atom ( std::string const &  atm_name)

set the atom which connects to the lower connection

References atom_index(), and core::chemical::tr().

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

void core::chemical::ResidueType::set_mainchain_atoms ( AtomIndices const &  mainchain) [inline]
void core::chemical::ResidueType::set_mm_atom_type ( std::string const &  atom_name,
std::string const &  mm_atom_type_name 
)

set mm atom type

References atom_index().

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

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

set the MolData object

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

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

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

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

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

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

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

Sets the path for the NCAA rotlib for the ResidueType.

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

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

set OrbitalICoor for an orbital

References orbital_index().

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

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

void core::chemical::ResidueType::set_RotamerLibraryName ( std::string const &  filename)
void core::chemical::ResidueType::set_upper_connect_atom ( std::string const &  atm_name)

set the atom which connects to the upper connection

References atom_index(), and core::chemical::tr().

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

void core::chemical::ResidueType::set_use_ncaa_rotlib ( bool  flag) [inline]

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

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

void core::chemical::ResidueType::set_xyz ( std::string const &  atm,
Vector const &  xyz_in 
) [inline]
void core::chemical::ResidueType::set_xyz ( Size  index,
Vector const &  xyz_in 
) [inline]
void core::chemical::ResidueType::show_all_atom_names ( std::ostream &  out) const

References core::sequence::end.

Referenced by atom_index().

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

update actcoord

update actcoord average geometrical center of the set of actcoord_atoms_

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

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

ResidueConnection const& core::chemical::ResidueType::upper_connect ( ) const [inline]
Size core::chemical::ResidueType::upper_connect_atom ( ) const [inline]

index number of the atom which connects to the upper connection

Referenced by core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ICoorAtomID::xyz().

Size core::chemical::ResidueType::upper_connect_id ( ) const [inline]
utility::vector1< VariantType > const& core::chemical::ResidueType::variant_types ( ) const [inline]
bool core::chemical::ResidueType::variants_match ( ResidueType const &  other) const

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

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

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

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

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

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

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

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

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

Vector const& core::chemical::ResidueType::xyz ( Size const  atm) const [inline]

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