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protocols::sparta Namespace Reference

Classes

class  ANN
 
class  ChemicalShiftEvaluator
 
class  ChemicalShiftEvaluatorCreator
 creator for the ChemicalShiftsEvaluatorCreator class More...
 
class  GDB
 
class  PDB
 
struct  PDB_Entry
 
struct  RingData
 
class  Sparta
 

Typedefs

typedef float Vec3 [3]
 
typedef float Mat3 [3][3]
 
typedef boost::unordered_map
< int, PDB_Entry
Mol
 
typedef boost::unordered_map
< int, Mol
Mols
 
typedef utility::vector0
< std::string > 
StringList
 
typedef boost::unordered_map
< float, boost::unordered_map
< float, float > > 
PHIPSI_ERR_SURF
 

Functions

static basic::Tracer tr ("protocols.sparta")
 
std::ostream & operator<< (std::ostream &os, PDB_Entry const &pe)
 
static basic::Tracer tr ("protocols.sparta")
 
void calc_per_residue_scores (Sparta::SpartaLib::AtomNameList &atom_names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab, utility::vector1< float > &per_residue_scores)
 
Real compareRef_fxn (Sparta::SpartaLib::AtomNameList &names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab)
 
float getDiff (float ang1, float ang2)
 
float getAVG (utility::vector0< float > &v1)
 
float getSTD (utility::vector0< float > &v1)
 
float getRMS (utility::vector0< float > &v1, utility::vector0< float > &v2)
 
char * itoa (int n, char *buff, int)
 
char * ftoa (float n, char *buff, char f, int prec)
 
int MKDIR (const char *dirName)
 
bool isDirExists (const string &Dir)
 
std::string simplifyWhiteSpace (const std::string &str)
 
int contains (const std::string &str, const std::string &c)
 
int contains (const string &str, const char &c)
 
bool isDigit (const char &c)
 
bool isSpace (const char &c)
 
StringList split (const char sep, const string &str)
 
StringList split (const string &sep, const string &str)
 
StringList split_WhiteSpace (const string &str)
 
char * section (const string &str, const char &sep, char *buff, int start, int end)
 

Typedef Documentation

typedef float protocols::sparta::Mat3[3][3]
typedef boost::unordered_map<int, PDB_Entry> protocols::sparta::Mol
typedef boost::unordered_map<int, Mol> protocols::sparta::Mols
typedef boost::unordered_map<float, boost::unordered_map<float, float> > protocols::sparta::PHIPSI_ERR_SURF
typedef utility::vector0< std::string > protocols::sparta::StringList
typedef float protocols::sparta::Vec3[3]

Function Documentation

void protocols::sparta::calc_per_residue_scores ( Sparta::SpartaLib::AtomNameList &  atom_names,
GDB &  Pred_Sum,
GDB &  REF_CS_Tab,
GDB &  COMP_Tab,
utility::vector1< float > &  per_residue_scores 
)
core::Real protocols::sparta::compareRef_fxn ( Sparta::SpartaLib::AtomNameList &  names,
GDB &  Pred_Sum,
GDB &  REF_CS_Tab,
GDB &  COMP_Tab 
)
int protocols::sparta::contains ( const std::string &  str,
const std::string &  c 
)
int protocols::sparta::contains ( const string &  str,
const char &  c 
)
char * protocols::sparta::ftoa ( float  n,
char *  buff,
char  f,
int  prec 
)
float protocols::sparta::getAVG ( utility::vector0< float > &  v1)
float protocols::sparta::getDiff ( float  ang1,
float  ang2 
)
float protocols::sparta::getRMS ( utility::vector0< float > &  v1,
utility::vector0< float > &  v2 
)
float protocols::sparta::getSTD ( utility::vector0< float > &  v1)
bool protocols::sparta::isDigit ( const char &  c)
bool protocols::sparta::isDirExists ( const string &  Dir)
bool protocols::sparta::isSpace ( const char &  c)

Referenced by simplifyWhiteSpace().

char * protocols::sparta::itoa ( int  n,
char *  buff,
int   
)
int protocols::sparta::MKDIR ( const char *  dirName)
std::ostream & protocols::sparta::operator<< ( std::ostream &  os,
PDB_Entry const &  pe 
)
char * protocols::sparta::section ( const string &  str,
const char &  sep,
char *  buff,
int  start,
int  end 
)
std::string protocols::sparta::simplifyWhiteSpace ( const std::string &  str)
StringList protocols::sparta::split ( const char  sep,
const string &  str 
)

Referenced by core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(), protocols::jd2::JobOutputter::affixed_numbered_name(), protocols::hybridization::CartesianSampler::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::electron_density::DockIntoDensityMover::apply_multi(), core::scoring::ScoringManager::create_nmer_svm_rank(), protocols::surface_docking::SurfaceVectorLoader::create_surface_params(), protocols::loophash::extract_sample_weights(), protocols::splice::RotLibdb::fill_rotamer_matrix_from_db_file(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file(), core::scoring::epr_deer::DEERIO::get_splitlines(), protocols::splice::RBInMover::init(), core::kinematics::MoveMap::init_from_file(), protocols::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file(), protocols::antibody::clusters::CDRClusterMatcher::load_center_data(), protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight(), protocols::mpi_refinement::MPI_Refine_Master::load_sample_weight(), protocols::kinematic_closure::perturbers::LogFilePerturber::LogFilePerturber(), main(), protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input(), protocols::jobdist::BasicJob::output_tag(), core::chemical::sdf::parse_bond_type_data(), protocols::hotspot_hashing::LSMSearchPattern::parse_lsm_spec(), protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement::parse_my_tag(), protocols::md::MDBase::parse_schfile(), core::import_pose::pose_from_file(), core::scoring::epr_deer::DEERIO::pull_coords(), core::conformation::symmetry::SymDof::read(), protocols::parser::BluePrint::read_blueprint_stream(), protocols::mpi_refinement::Scheduler::read_cmd(), protocols::toolbox::match_enzdes_util::ResInteractions::read_data(), protocols::toolbox::match_enzdes_util::CstResInteractions::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::scoring::methods::SequenceDependentRefEnergy::read_energy_weight_table(), protocols::loophash::BackboneDB::read_homologs(), protocols::loops::LoopsFileIO::read_loop_file_stream(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), core::scoring::methods::NMerRefEnergy::read_nmer_table_list(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), section(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_apolar_res(), protocols::constraint_movers::ConstraintSetMover::set_cst_map_file_contents(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), protocols::relax::FastRelax::set_script_from_lines(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), protocols::moves::StructureRestrictor::setup_relevant_chains(), protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner(), and protocols::sparta::GDB::VARS_str_parser().

StringList protocols::sparta::split ( const string &  sep,
const string &  str 
)
StringList protocols::sparta::split_WhiteSpace ( const string &  str)
static basic::Tracer protocols::sparta::tr ( "protocols.sparta"  )
static
static basic::Tracer protocols::sparta::tr ( "protocols.sparta"  )
static