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core::scoring::rna::chemical_shift Namespace Reference

Classes

class  ChemicalShiftData
 
class  RNA_ChemicalShiftEnergy
 
class  RNA_ChemicalShiftEnergyCreator
 
class  RNA_ChemicalShiftPotential
 
class  RNA_CS_parameters
 
class  RNA_CS_residue_parameters
 

Typedefs

typedef
utility::pointer::shared_ptr
< RNA_ChemicalShiftPotential
RNA_ChemicalShiftPotentialOP
 
typedef
utility::pointer::shared_ptr
< RNA_ChemicalShiftPotential
const > 
RNA_ChemicalShiftPotentialCOP
 

Enumerations

enum  atomitem {
  oshi = 1, xdir, ydir, zdir,
  csca, suga, rcl1, rcl2,
  rcl3, maca, maqx, maqw,
  maqy, maqz, marx, mary,
  marz, chco, chrg, last_atomdesc
}
 

Functions

chemical::AA get_res_aa_from_BASE_name (std::string const &BASE_name, std::string const &text_line)
 
std::string remove_whitespaces (std::string const &in_atom_name)
 
std::string add_whitespaces (std::string const &in_atom_name)
 
bool is_polar_hydrogen (std::string const &input_atom_name)
 
std::string get_rosetta_hatom_name (std::string const &input_atom_name, std::string const &text_line, utility::vector1< std::string > const &flat_proton_entry_list)
 
void print_chemical_shift_data (std::string const &prestring, ChemicalShiftData const &CS_data, bool const print_data_line)
 
core::Size string_to_int (std::string const &input_string)
 
core::Real string_to_real (std::string const &input_string)
 
bool Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
 
utility::vector1
< ChemicalShiftData
filter_chem_shift_data_list (utility::vector1< ChemicalShiftData > const &flat_EXP_chem_shift_data_list, core::Size const seq_num, utility::vector1< std::string > const &proton_entry)
 
Real delta_magnetic_anisotropy (numeric::xyzVector< core::Real > const &CS_data_atom_xyz, numeric::xyzVector< core::Real > const &source_atom_xyz, numeric::xyzMatrix< core::Real > const &base_coordinate_matrix, RNA_CS_residue_parameters const &source_rsd_CS_params, Size const realatomdata_index)
 The magnetic_anisotropy contribution of heavy-base atom at src_xyz to the chemqical_shift at CS_data_atom_xyz. More...
 
numeric::xyzVector< core::Realget_delta_magnetic_anisotropy_deriv (numeric::xyzVector< core::Real > const &CS_data_atom_xyz, numeric::xyzVector< core::Real > const &source_atom_xyz, numeric::xyzMatrix< core::Real > const &base_coordinate_matrix, RNA_CS_residue_parameters const &source_rsd_CS_params, Size const realatomdata_index)
 
Real magnetic_anisotropy_effect (numeric::xyzVector< core::Real > const &atom_xyz, conformation::Residue const &source_rsd, RNA_CS_residue_parameters const &source_rsd_CS_params)
 The magnetic_anisotropy contribution of source_rsd to the chemical_shift at atom_xyz. More...
 
numeric::xyzVector< core::Realring_pos (conformation::Residue const &rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params, Size const ring_ID)
 
static Real dellintk_dm (Real const m)
 
static Real dellinte_dm (Real const m)
 
static Real ellintk (Real const m)
 
static Real ellinte (Real const m)
 
void get_rho_and_z (numeric::xyzVector< core::Real > const &atom_xyz, numeric::xyzVector< core::Real > const &ring_center, numeric::xyzVector< core::Real > const &base_z_axis, Real &rho, Real &z)
 
Real delta_ring_current_term (Real const rho, Real const z, Real const ring_radius, Real const ring_z_offset)
 
void get_ring_current_term_derivatives (Real const rho, Real const z, Real const ring_radius, Real const ring_z_offset, Real &dterm_drho, Real &dterm_dz)
 
Real delta_ring_current (numeric::xyzVector< core::Real > const &atom_xyz, numeric::xyzVector< core::Real > const &molecular_ring_center, numeric::xyzVector< core::Real > const &base_z_axis, RNA_CS_residue_parameters const &source_rsd_CS_params, Size const ring_ID)
 
Real ring_current_effect (numeric::xyzVector< core::Real > const &atom_xyz, conformation::Residue const &source_rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params)
 The ring_current contribution of source_rsd to the chemical_shift at atom_xyz. More...
 
Real ring_current_effect_individual_ring (numeric::xyzVector< core::Real > const &atom_xyz, conformation::Residue const &source_rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params, Size const source_ring_ID)
 
numeric::xyzVector< core::Realget_ring_current_deriv (numeric::xyzVector< core::Real > const &CS_data_atom_xyz, conformation::Residue const &source_rsd, core::Size const source_ring_ID, RNA_CS_residue_parameters const &source_rsd_CS_params)
 
numeric::xyzMatrix< core::Real >
const 
get_rna_base_coordinate_system_from_CS_params (core::conformation::Residue const &rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params)
 
core::Size dround (core::Real var)
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
oshi 
xdir 
ydir 
zdir 
csca 
suga 
rcl1 
rcl2 
rcl3 
maca 
maqx 
maqw 
maqy 
maqz 
marx 
mary 
marz 
chco 
chrg 
last_atomdesc 

Function Documentation

std::string core::scoring::rna::chemical_shift::add_whitespaces ( std::string const &  in_atom_name)
bool core::scoring::rna::chemical_shift::Contain_seq_num ( Size const &  seq_num,
utility::vector1< core::Size > const &  residue_list 
)
static Real core::scoring::rna::chemical_shift::dellinte_dm ( Real const  m)
static
static Real core::scoring::rna::chemical_shift::dellintk_dm ( Real const  m)
static
Real core::scoring::rna::chemical_shift::delta_magnetic_anisotropy ( numeric::xyzVector< core::Real > const &  CS_data_atom_xyz,
numeric::xyzVector< core::Real > const &  source_atom_xyz,
numeric::xyzMatrix< core::Real > const &  base_coordinate_matrix,
RNA_CS_residue_parameters const &  source_rsd_CS_params,
Size const  realatomdata_index 
)
Real core::scoring::rna::chemical_shift::delta_ring_current ( numeric::xyzVector< core::Real > const &  atom_xyz,
numeric::xyzVector< core::Real > const &  molecular_ring_center,
numeric::xyzVector< core::Real > const &  base_z_axis,
RNA_CS_residue_parameters const &  source_rsd_CS_params,
Size const  ring_ID 
)
Real core::scoring::rna::chemical_shift::delta_ring_current_term ( Real const  rho,
Real const  z,
Real const  ring_radius,
Real const  ring_z_offset 
)

References ellinte(), and ellintk().

Referenced by delta_ring_current().

core::Size core::scoring::rna::chemical_shift::dround ( core::Real  var)
inline
static Real core::scoring::rna::chemical_shift::ellinte ( Real const  m)
static
static Real core::scoring::rna::chemical_shift::ellintk ( Real const  m)
static
utility::vector1< ChemicalShiftData > core::scoring::rna::chemical_shift::filter_chem_shift_data_list ( utility::vector1< ChemicalShiftData > const &  flat_EXP_chem_shift_data_list,
core::Size const  seq_num,
utility::vector1< std::string > const &  proton_entry 
)
numeric::xyzVector< core::Real > core::scoring::rna::chemical_shift::get_delta_magnetic_anisotropy_deriv ( numeric::xyzVector< core::Real > const &  CS_data_atom_xyz,
numeric::xyzVector< core::Real > const &  source_atom_xyz,
numeric::xyzMatrix< core::Real > const &  base_coordinate_matrix,
RNA_CS_residue_parameters const &  source_rsd_CS_params,
Size const  realatomdata_index 
)
chemical::AA core::scoring::rna::chemical_shift::get_res_aa_from_BASE_name ( std::string const &  BASE_name,
std::string const &  text_line 
)
void core::scoring::rna::chemical_shift::get_rho_and_z ( numeric::xyzVector< core::Real > const &  atom_xyz,
numeric::xyzVector< core::Real > const &  ring_center,
numeric::xyzVector< core::Real > const &  base_z_axis,
Real &  rho,
Real &  z 
)
numeric::xyzVector< core::Real > core::scoring::rna::chemical_shift::get_ring_current_deriv ( numeric::xyzVector< core::Real > const &  CS_data_atom_xyz,
conformation::Residue const &  source_rsd,
core::Size const  source_ring_ID,
RNA_CS_residue_parameters const &  source_rsd_CS_params 
)
void core::scoring::rna::chemical_shift::get_ring_current_term_derivatives ( Real const  rho,
Real const  z,
Real const  ring_radius,
Real const  ring_z_offset,
Real &  dterm_drho,
Real &  dterm_dz 
)
numeric::xyzMatrix< core::Real > const core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params ( core::conformation::Residue const &  rsd,
RNA_CS_residue_parameters const &  rna_cs_rsd_params 
)
std::string core::scoring::rna::chemical_shift::get_rosetta_hatom_name ( std::string const &  input_atom_name,
std::string const &  text_line,
utility::vector1< std::string > const &  flat_proton_entry_list 
)
bool core::scoring::rna::chemical_shift::is_polar_hydrogen ( std::string const &  input_atom_name)
core::Real core::scoring::rna::chemical_shift::magnetic_anisotropy_effect ( numeric::xyzVector< core::Real > const &  atom_xyz,
conformation::Residue const &  source_rsd,
RNA_CS_residue_parameters const &  source_rsd_CS_params 
)
void core::scoring::rna::chemical_shift::print_chemical_shift_data ( std::string const &  prestring,
ChemicalShiftData const &  CS_data,
bool const  print_data_line 
)
std::string core::scoring::rna::chemical_shift::remove_whitespaces ( std::string const &  in_atom_name)
core::Real core::scoring::rna::chemical_shift::ring_current_effect ( numeric::xyzVector< core::Real > const &  atom_xyz,
conformation::Residue const &  source_rsd,
RNA_CS_residue_parameters const &  rna_cs_rsd_params 
)
Real core::scoring::rna::chemical_shift::ring_current_effect_individual_ring ( numeric::xyzVector< core::Real > const &  atom_xyz,
conformation::Residue const &  source_rsd,
RNA_CS_residue_parameters const &  rna_cs_rsd_params,
Size const  source_ring_ID 
)
numeric::xyzVector< core::Real > core::scoring::rna::chemical_shift::ring_pos ( conformation::Residue const &  rsd,
RNA_CS_residue_parameters const &  rna_cs_rsd_params,
Size const  ring_ID 
)
core::Size core::scoring::rna::chemical_shift::string_to_int ( std::string const &  input_string)
core::Real core::scoring::rna::chemical_shift::string_to_real ( std::string const &  input_string)