core::chemical::orbitals Namespace Reference

Classes
class	AssignOrbitals
class	ICoorOrbitalData
class	OrbitalType
class	OrbitalTypeMapper
class	OrbitalTypeSet

Typedefs
typedef utility::pointer::shared_ptr< OrbitalType >	OrbitalTypeOP
typedef utility::pointer::weak_ptr< OrbitalTypeSet >	OrbitalTypeSetAP
typedef utility::pointer::weak_ptr< OrbitalTypeSet const >	OrbitalTypeSetCAP
typedef utility::pointer::shared_ptr< OrbitalTypeSet >	OrbitalTypeSetOP
typedef utility::pointer::shared_ptr< OrbitalTypeSet const >	OrbitalTypeSetCOP

Enumerations
enum	orbital_type_enum {   C_pi_sp2 =1 , N_pi_sp2 , N_p_sp2 , O_pi_sp2 ,   O_p_sp2 , O_p_sp3 , S_p_sp3 , O_pi_sp2_bb ,   O_p_sp2_bb , num_orbital_types = O_p_sp2_bb }

Functions
static basic::Tracer	TR ("core::chemical::orbitals::AssignOrbitals")
std::string	strip_whitespace (std::string const &name)
static basic::Tracer	TR ("core.chemical.orbitals")

Typedef Documentation

OrbitalTypeOP

typedef utility::pointer::shared_ptr< OrbitalType > core::chemical::orbitals::OrbitalTypeOP

OrbitalTypeSetAP

typedef utility::pointer::weak_ptr< OrbitalTypeSet > core::chemical::orbitals::OrbitalTypeSetAP

OrbitalTypeSetCAP

typedef utility::pointer::weak_ptr< OrbitalTypeSet const > core::chemical::orbitals::OrbitalTypeSetCAP

OrbitalTypeSetCOP

typedef utility::pointer::shared_ptr< OrbitalTypeSet const > core::chemical::orbitals::OrbitalTypeSetCOP

OrbitalTypeSetOP

typedef utility::pointer::shared_ptr< OrbitalTypeSet > core::chemical::orbitals::OrbitalTypeSetOP

Enumeration Type Documentation

orbital_type_enum

enum core::chemical::orbitals::orbital_type_enum

Enumerator
C_pi_sp2
N_pi_sp2
N_p_sp2
O_pi_sp2
O_p_sp2
O_p_sp3
S_p_sp3
O_pi_sp2_bb
O_p_sp2_bb
num_orbital_types

Function Documentation

strip_whitespace()

std::string core::chemical::orbitals::strip_whitespace ( std::string const &  name )

inline

Referenced by core::util::add_covalent_linkage_helper(), protocols::simple_moves::SimpleThreadingMover::apply(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::io::pose_from_sfr::bonding_distance_threshold(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), core::io::mmcif::create_sfr_from_cif_file(), core::io::pdb::create_sfr_from_pdb_records(), core::pack::interaction_graph::generate_pose_from_packer_description(), core::pack::interaction_graph::generate_rotamers_from_packer_solution_description(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names(), core::io::silent::SilentFileData::get_sequence(), core::sequence::get_sequence_object(), core::chemical::heavy_atom_names_match(), protocols::drug_design::RandomFragmentLigand::keep_atom(), protocols::drug_design::ReactionFragment::keep_atom(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), core::chemical::ResidueTypeFinder::matches_any_atom_name(), core::io::pose_from_sfr::GeometricRenameVerticiesEquivalent::operator()(), core::scoring::constraints::parse_NMR_name_general(), core::io::rna::RDAT::read_rdat_file(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::io::pose_from_sfr::remap_names_on_geometry(), core::chemical::orbitals::AssignOrbitals::set_orbital_type_and_bond(), and core::io::HeaderInformation::store_title().

TR() [1/2]

static basic::Tracer core::chemical::orbitals::TR ( "core.chemical.orbitals"  )

static

TR() [2/2]

static basic::Tracer core::chemical::orbitals::TR ( "core::chemical::orbitals::AssignOrbitals"  )

static

Referenced by core::chemical::orbitals::AssignOrbitals::assign_only_pi_orbitals_to_atom(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), and core::chemical::orbitals::OrbitalTypeSet::read_file().