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basic Namespace Reference

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...

Namespaces

 database
 
 datacache
 
 gpu
 
 mpi
 
 options
 
 random
 
 resource_manager
 
 sampling
 
 svd
 
 thread_manager
 

Classes

class  basic_otstream
 Base class for TracerImpl, TracerProxyImpl and UTracer objects. More...
 
class  ComparingTracer
 
class  DynamicProfileThis
 
class  Emitter
 Lightweight class to ease writting YAML documents (http://yaml.org) More...
 
struct  ExecutionResult
 Struct that hold result code + output of external process. More...
 
class  JsonEmitter
 Lightweight class to ease writting JSON documents, a subset of YAML (http://json.org) More...
 
class  MemTracer
 
class  MemTracerImpl
 
class  MetricValue
 
class  MetricValueBase
 
class  ProfileThis
 
class  PyTracer
 Special PyRosetta friendly Tracer like buffer. Use it to capture Tracer output with set_ios_hook. More...
 
class  Report
 Data class to hold Report information. Use Reporter class for write access. More...
 
class  Reporter
 Proxy class to access Reporter class though OP. Allow null OP on init (all reporter function in this case do nothing) More...
 
class  Tracer
 Class for handling user debug/warnings/errors. Use instance of this class instead of 'std::cout' for all your regular io. Channel argument must be related to the location of the source file. For example if you create Tracer object in src/basic/scoring/myfile.cc, then channel must be something like 'basic.scoring.myfile'. More...
 
class  TracerImpl
 Class for handling user debug/warnings/errors. Use instance of this class instead of 'std::cout' for all your regular io. Channel argument must be related to the location of the source file. For example if you create Tracer object in src/basic/scoring/myfile.cc, then channel must be something like 'src.basic.scoring.myfile'. More...
 
struct  TracerOptions
 data structure to store all system level options for Tracer system. More...
 
class  TracerToFile
 
class  YamlEmitter
 Emitter for more classically formatted YAML. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< Emitter
EmitterOP
 
typedef
utility::pointer::shared_ptr
< Emitter const > 
EmitterCOP
 
typedef
utility::pointer::shared_ptr
< YamlEmitter
YamlEmitterOP
 
typedef
utility::pointer::shared_ptr
< YamlEmitter const > 
YamlEmitterCOP
 
typedef
utility::pointer::shared_ptr
< JsonEmitter
JsonEmitterOP
 
typedef
utility::pointer::shared_ptr
< JsonEmitter const > 
JsonEmitterCOP
 
typedef
utility::pointer::shared_ptr
< MetricValueBase
MetricValueBaseOP
 
typedef
utility::pointer::shared_ptr
< MetricValueBase const > 
MetricValueBaseCOP
 
typedef
utility::pointer::shared_ptr
< Report
ReportOP
 
typedef
utility::pointer::shared_ptr
< Report const > 
ReportCOP
 
typedef int TracerOP
 
typedef int TracerCOP
 
typedef
utility::pointer::shared_ptr
< TracerImpl
TracerImplOP
 
typedef
utility::pointer::shared_ptr
< TracerImpl const > 
TracerImplCOP
 
typedef basic_otstream< char > otstream
 
typedef
utility::pointer::shared_ptr
< otstream
otstreamOP
 
typedef
utility::pointer::shared_ptr
< TracerOptions
TracerOptionsOP
 

Enumerations

enum  ProfTag {
  TEST1 = 1, TEST2, TEST3, TEST4,
  TEST5, ATOM_TREE_UPDATE_INTERNAL_COORDS, ATOM_TREE_UPDATE_XYZ_COORDS, UPDATE_RESIDUE_TORSIONS,
  UPDATE_RESIDUE_COORDINATES, ROTAMER_TRIALS, PACK_ROTAMERS, UPDATE_RESIDUE_NEIGHBORS,
  SETUP_NBLIST, CONSTRAINT_SCORE, CONSTRAINT_SET_COPY, SCORE,
  SCORE_SETUP, SCORE_FINALIZE, SCORE_ONEBODY_ENERGIES, SCORE_NEIGHBOR_ENERGIES,
  SCORE_LONG_RANGE_ENERGIES, SCORE_DOT, SCORE_END_NOTIFY, SCORE_BEGIN_NOTIFY,
  VDW_ENERGY, ENERGY_ENVPAIR_POTENTIAL, SECONDARY_STRUCTURE_ENERGY, SECONDARY_STRUCTURE_SSPAIR_ENERGY,
  SECONDARY_STRUCTURE_HSPAIR_ENERGY, SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY, POSE_COPY, ENERGY_GRAPH_COPY,
  ENERGIES_COPY, CONFORMATION_DETECT_DISULF, CONFORMATION_FIX_DISULF, CONFORMATION_COPY,
  CHEMICAL_MAKE_POSE, CCD_CLOSE, FUNC, DFUNC,
  GET_ENERGIES, SIMANNEALING, INSERT_FRAGS, MC_ACCEPT,
  GB_SETUP_FOR_PACKING, GB_GET_ALL_BORN_RADII, GEN_BORN_ROTAMER_PAIR_ENERGIES, GEN_BORN_ROTAMER_BACKGROUND_ENERGIES,
  MULTIPOLE_SETUP, MULTIPOLE_ENERGIES, FACTS_SETUP_FOR_PACKING, FACTS_GET_ALL_BORN_RADII,
  FACTS_ROTAMER_PAIR_ENERGIES, FACTS_ROTAMER_BACKGROUND_ENERGIES, ABINITIO, STAGE1,
  STAGE2, STAGE3, STAGE4, STAGE5,
  FRAGMENT_MOVER, MINMOVER_APPLY, BACKRUB_MOVER, FIND_SUGAR_AND_SUITE_FRAGS_I,
  FIND_SUGAR_AND_SUITE_FRAGS_II, MAKE_BASE_PAIR_MOVE, MAKE_BASE_STEP_MOVE, RG,
  RG_LOCAL, SEQUENCE_COMPARISON, KDTREE_CONSTRUCT, KDTREE_SEARCH,
  CONSTRUCT_DISTANCE_MATRIX, DALPHABALL, DALPHABALL_DERIV, MPI_FILE_BUF,
  JD2, JD2_OUTPUT, JD2_SILENT_OUTPUTTER, JD2_INIT_MOVER,
  ARCHIVE_SYNC_BATCHES, ARCHIVE_JOBSCOMPLETE, ARCHIVE_BLOCK_FILE, SAVE_ARCHIVE,
  ARCHIVE_CRITICAL_JOBSCOMPLETE, ARCHIVE_GEN_BATCH, ARCHIVE_READ_DECOYS, ARCHIVE_EVAL_DECOYS,
  ARCHIVE_FILL_POSE, ARCHIVE_SCORE_POSE, ARCHIVE_EVALUATORS, MPI_JD2_WAITS_FOR_ARCHIVE,
  MPI_NOTIFY_ARCHIVE, SILENT_READ_TAG_TEST, CA_RMSD_EVALUATION, CA_DME_EVALUATION,
  TRUNCATED_SCORE_EVALUATOR, SAXS, FRAGMENTPICKING_CS_SCORE, FRAGMENTPICKING_PROFILE_SCORE,
  FRAGMENTPICKING_PROFILE_CAHING, FRAGMENTPICKING_SECONDARY_SCORE, FRAGMENTPICKING_READ_VALL, FRAGMENTPICKING,
  FRAGMENTPICKING_CANDIDATES_COLLECTING, FRAGMENTPICKING_ATOMPAIR_SCORE, FRAGMENTPICKING_PHIPSI_SCORE, FRAGMENTPICKING_DIHEDRALCONSTR_SCORE,
  MPICANONICALSAMPLING, MPIPOOLCOMMUNICATION, MPICOMMCREATION, MPIBARRIER,
  MPIBARRIER_BEGIN, MPIBARRIER_END, MPI_GATHER_BARRIER, FARRAY_MANIPULATION,
  MPI_SLAVE_REPORT_NEW_COORDS, MPI_SLAVE_REPORT_SIZES, MPI_SEND_UPDATE, MPI_SYNC_POOL_DIFF,
  MPI_SEND_ACCEPTED, POOL_RMSD_ADD_STRUCTURE, POOL_RMSD_EVALUATE, POOL_RMSD_MASTER_EVALUATE,
  MPI_MASTER_BCAST_COORDS, MPI_MASTER_BCAST_WINNING_RANKS, MPI_MASTER_BCAST_WINNING_STRUCTURES, MPI_MASTER_BCAST_NEW_COMM_SIZE,
  MPI_MASTER_BCAST_NEW_POOL_RANKS, MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD, MPI_POOL_MASTER_THINKS, MPI_POOL_SLAVE_THINKS,
  SIDECHAINMCMOVER, SIMPLEINTGRAPH, SIDECHAINMOVER, INITIALIZE,
  COMM_REDUCE_SIZE, CANONICALMOVER_WRITE_TO_FILE, WRITE_TO_FILE, CHECK_COMM_SIZE,
  APPLY_MOVE, DATA_STORAGE, MASTER_PROCESS_NEW_STRUCTURES, COPY_COORDS,
  APPLY_SC_MOVE, APPLY_BB_MOVE, HIERARCHICAL_EVALUATE, HIERARCHICAL_ADD,
  LOAD_HIERARCHY, HIERARCHY_SEND_COORDS, HIERARCHY_RECV_COORDS, INITIALIZE_HIERARCHY,
  HIERARCHY_SETUP_TO_RECV, WRITE_DECOYS_TO_HIERARCHY, HIERARCHY_GET_NEXT_CANDIDATE, HIERARCHY_FIND_ADDRESS,
  MPIH_EVAL_CHECK_PROGRESS, MPIH_EVAL_COMMUNICATE_NEW, MPIH_EVAL_AGAINST_NBR, MPIH_PREPARE_WRITE_STRUCTURES,
  MPIH_UPDATE_EVAL, MPIH_ADD_FIRST_STRUCTURE, MPIH_WRITE_STRUCT, FINALIZE,
  SORT_POOL, HIERARCHICAL_FIND, HIERARCHICAL_FIND_ADDRESS, HIERARCHICAL_SORT_ADDRESSES,
  HIERARCHICAL_ROUND, HIERARCHICAL_POOL_SIZE, HIERARCHICAL_ADD_ELEM_TO_CACHE, LIB_FULL_PATH,
  NOESY_ASSIGN_TOTAL, NOESY_ASSIGN_INITIAL, NOESY_ASSIGN_DIAGONAL, NOESY_ASSIGN_CHEMSHIFT,
  NOESY_ASSIGN_SYMMETRY, NOESY_ASSIGN_DISTANCE, NOESY_ASSIGN_DECOY_COMP, NOESY_ASSIGN_NETWORK_TOTAL,
  NOESY_ASSIGN_NETWORK, NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN, NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA, NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN,
  NOESY_ASSIGN_NETWORK_COMPUTE_NK, NOESY_ASSIGN_NETWORK_PEAK_COUNT, NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL, NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE,
  NOESY_ASSIGN_UPDATE_PEAK_VOL, NOESY_ASSIGN_CALIBRATE, NOESY_ASSIGN_ELIMINATE, NOESY_ASSIGN_GEN_CST,
  NOESY_ASSIGN_WRITE_CST, NOESY_ASSIGN_MAP2CB, NOESY_ASSIGN_CP_GEN_CST, NOESY_ASSIGN_PA_GEN_CST,
  NOESY_ASSIGN_NMR_STRING, NOESY_ASSIGN_REQUIRES_CB_MAPPING, NOESY_ASSIGN_MAP2CB_NEW, NOESY_ASSIGN_WRITE_ASSIGNMENTS,
  NOESY_ASSIGN_READ_INPUT, NOESY_ASSIGN_DIST_INIT, NOESY_ASSIGN_DIST_PREP_SCORE, NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE,
  NOESY_ASSIGN_DIST_APPLY, NOESY_ASSIGN_DIST_MAKE_POSE, NOESY_ASSIGN_DIST_CST_EVAL, NOESY_ASSIGN_DIST_CST_CAST,
  SILENT_FILL_POSE, SILENT_SET_POSE_COORDS, SILENT_FILL_STRUCT, MEAN_FIELD,
  TOTAL, n_prof_tags = TOTAL
}
 
enum  TracerPriority {
  t_fatal = 0, t_error = 100, t_warning = 200, t_info = 300,
  t_debug = 400, t_trace = 500
}
 Priority levels for T() and Tracer object, modeled on the log4j project and its offspring. Priorities in Tracer are still ints so users can pass other arbitrary integer values (for now). More...
 

Functions

void calc_quadratic (double a, double b, double c, double &n1, double &n2)
 calculates quadratic polynomial solutions More...
 
double subtract_degree_angles (double a, double b)
 subtract angles in degrees, restricting the range of the result More...
 
double subtract_radian_angles (double a, double b)
 subtract angles in radians, restricting the range of the result More...
 
double periodic_range (double a, double x)
 a is restricted to [-x/2,x/2), assuming that a=a+n*x, n=any integer More...
 
double unsigned_periodic_range (double a, double x)
 a is restricted to [0.,x), assuming that a=a+n*x,, n=any integer More...
 
void angle_in_range (double &ang)
 taken from wobble.cc More...
 
ExecutionResult execute (std::string const &message, std::string const &command_line, bool terminate_on_failure=true, bool silent=false)
 excute provided command_line though shell and return exit_code and output More...
 
bool was_init_called ()
 return true if core::init was already called and false otherwise More...
 
void init ()
 set global 'init_was_called' to true More...
 
void interpolate_bilinear_by_value (double const x0y0, double const x1y0, double const x0y1, double const x1y1, double const xd, double const yd, double const binrange, bool const angles, double &val, double &dval_dx, double &dval_dy)
 get bilinear interpolate, given four points of a 2d periodic function More...
 
void interpolate_trilinear_by_value (double const x0y0z0, double const x1y0z0, double const x0y1z0, double const x1y1z0, double const x0y0z1, double const x1y0z1, double const x0y1z1, double const x1y1z1, double const xd, double const yd, double const zd, double const binrange, bool const angles, double &val, double &dval_dx, double &dval_dy, double &dval_dz)
 paraphazed from above for three dimentions Without additional scaling this will only work if the bin sizes in each dimention are equal I think. Otherwise it could be computed as the product of three linear interpolations More...
 
void interpolate_get_angle_bins (double const x, double const binrange, int &xbin, int &xbin_next, double &xd)
 get bin information for a periodic value w/ periodic bins More...
 
void interpolate_bilinear (int const xbin, int const xbin_next, double const xd, int const ybin, int const ybin_next, double const yd, ObjexxFCL::FArray2A< double > xy_func, int const xbin_count, int const ybin_count, double const binrange, bool const angles, double &val, double &dval_dx, double &dval_dy)
 get bilinear interpolate of a 2d periodic function More...
 
void interpolate_trilinear (int const xbin, int const xbin_next, double const xd, int const ybin, int const ybin_next, double const yd, int const zbin, int const zbin_next, double const zd, ObjexxFCL::FArray3A< double > xyz_func, int const xbin_count, int const ybin_count, int const zbin_count, double const binrange, bool const angles, double &val, double &dval_dx, double &dval_dy, double &dval_dz)
 
void interpolate_2d_func_of_angles (double const x, double const y, ObjexxFCL::FArray2A< double > xy_func, double &val, double &dval_dx, double &dval_dy)
 get bilinear interpolate of a 2d function with degree angle arguments More...
 
void get_usage_from_procfilesystem (std::ostream &mem_report)
 
template<class desired_T >
void check_cast (const basic::MetricValueBase *const valptr, const desired_T *const, std::string const &error_msg)
 
template<class desired_T >
void check_cast (const basic::MetricValueBase *const valptr, std::string const &error_msg)
 
template<class desired_T >
bool check_cast (const basic::MetricValueBase *const valptr, const desired_T *const )
 
template<class desired_T >
bool check_cast (const basic::MetricValueBase *const valptr)
 
template<class T >
bool write_metric_value_scalar (std::ostream &os, MetricValue< T > const &metric_value, std::string const &type_name)
 
template<class T >
bool write_metric_value_vector1 (std::ostream &os, MetricValue< vector1< T > > const &metric_value, std::string const &type_name)
 
bool write_metric_value (std::ostream &os, MetricValueBase const &metric_value)
 central write introspection and delegation function More...
 
bool handles_metric_value (MetricValueBase const &metric_value)
 check whether a MetricValue can be written to or read from a stream More...
 
template<class T >
bool read_metric_value_scalar (std::istream &is, MetricValueBase &metric_value)
 
template<class T >
bool read_metric_value_scalar (std::istream &is, MetricValueBaseOP &metric_value)
 
template<class T >
bool read_metric_value_vector1 (std::istream &is, MetricValueBase &metric_value)
 
template<class T >
bool read_metric_value_vector1 (std::istream &is, MetricValueBaseOP &metric_value)
 
template<class MetricValueBase_or_MetricValueBaseOP >
bool read_metric_value_template (std::istream &is, MetricValueBase_or_MetricValueBaseOP &metric_value)
 central read introspection and delegation function More...
 
bool read_metric_value (std::istream &is, MetricValueBase &metric_value)
 read a MetricValue from a stream, returns true if successful More...
 
MetricValueBaseOP read_metric_value (std::istream &is)
 read a MetricValue from a stream, returns NULL if unsuccessful More...
 
clock_t const SHRINK_FACTOR (2)
 
double const clock_factor (((double) SHRINK_FACTOR *100.0)/CLOCKS_PER_SEC)
 
bool show_time_on_cerr (false)
 
void show_time (basic::Tracer &tr, std::string const &msg)
 
void setup_tag2string ()
 
void prof_show ()
 
void prof_reset ()
 
void prof_start_function_body (ProfTag const tag)
 
void prof_stop_function_body (ProfTag const tag)
 
numeric::Size get_pymol_num_unique_ids ()
 
char get_pymol_chain (numeric::Size i)
 
numeric::Size get_pymol_chain_index_1 (char c)
 
static std::string const pymol_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz!@#$&.<>?]|-_\\~=%")
 
TracerError ()
 Predefined Error-level tracer, for use in headers. More...
 
TracerWarning ()
 Predefined Warning tracer, for use in headers. More...
 

Variables

static basic::Tracer TR ("basic.execute")
 
static bool init_was_called = false
 
static basic::Tracer tt ("core.util.prof", basic::t_info, true)
 
utility::vector1< std::string > tag2string
 
utility::vector1< clock_t > start_clock (n_prof_tags, 0)
 
utility::vector1< double > total_clock (n_prof_tags, 0)
 
utility::vector1< intcalls (n_prof_tags, 0)
 
utility::vector1< intbad_calls (n_prof_tags, 0)
 
std::map< std::string, double > dynamic_prof_total
 
std::map< std::string, intdynamic_prof_calls
 
double const clock_factor
 
clock_t const SHRINK_FACTOR
 
bool show_time_on_cerr
 print "TIME_STAMP: Www Mmm dd hh:mm:ss yyyy msg" on tr.Error and on std::cerr (if boolean is true) More...
 
static basic::Tracer TR_Error ("Error", basic::t_error)
 
static basic::Tracer TR_Warning ("Warning", basic::t_warning)
 

Detailed Description

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

Typedef Documentation

typedef utility::pointer::shared_ptr< Emitter const > basic::EmitterCOP
typedef utility::pointer::shared_ptr< Emitter > basic::EmitterOP
typedef utility::pointer::shared_ptr< JsonEmitter const > basic::JsonEmitterCOP
typedef utility::pointer::shared_ptr< JsonEmitter > basic::JsonEmitterOP
typedef utility::pointer::shared_ptr< MetricValueBase const > basic::MetricValueBaseCOP
typedef utility::pointer::shared_ptr< MetricValueBase > basic::MetricValueBaseOP
typedef utility::pointer::shared_ptr< otstream > basic::otstreamOP
typedef utility::pointer::shared_ptr< Report const > basic::ReportCOP
typedef utility::pointer::shared_ptr< Report > basic::ReportOP
typedef utility::pointer::shared_ptr< TracerImpl const > basic::TracerImplCOP
typedef utility::pointer::shared_ptr< TracerImpl > basic::TracerImplOP
typedef utility::pointer::shared_ptr< TracerOptions > basic::TracerOptionsOP
typedef utility::pointer::shared_ptr< YamlEmitter const > basic::YamlEmitterCOP
typedef utility::pointer::shared_ptr< YamlEmitter > basic::YamlEmitterOP

Enumeration Type Documentation

Enumerator
TEST1 
TEST2 
TEST3 
TEST4 
TEST5 
ATOM_TREE_UPDATE_INTERNAL_COORDS 
ATOM_TREE_UPDATE_XYZ_COORDS 
UPDATE_RESIDUE_TORSIONS 
UPDATE_RESIDUE_COORDINATES 
ROTAMER_TRIALS 
PACK_ROTAMERS 
UPDATE_RESIDUE_NEIGHBORS 
SETUP_NBLIST 
CONSTRAINT_SCORE 
CONSTRAINT_SET_COPY 
SCORE 
SCORE_SETUP 
SCORE_FINALIZE 
SCORE_ONEBODY_ENERGIES 
SCORE_NEIGHBOR_ENERGIES 
SCORE_LONG_RANGE_ENERGIES 
SCORE_DOT 
SCORE_END_NOTIFY 
SCORE_BEGIN_NOTIFY 
VDW_ENERGY 
ENERGY_ENVPAIR_POTENTIAL 
SECONDARY_STRUCTURE_ENERGY 
SECONDARY_STRUCTURE_SSPAIR_ENERGY 
SECONDARY_STRUCTURE_HSPAIR_ENERGY 
SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY 
POSE_COPY 
ENERGY_GRAPH_COPY 
ENERGIES_COPY 
CONFORMATION_DETECT_DISULF 
CONFORMATION_FIX_DISULF 
CONFORMATION_COPY 
CHEMICAL_MAKE_POSE 
CCD_CLOSE 
FUNC 
DFUNC 
GET_ENERGIES 
SIMANNEALING 
INSERT_FRAGS 
MC_ACCEPT 
GB_SETUP_FOR_PACKING 
GB_GET_ALL_BORN_RADII 
GEN_BORN_ROTAMER_PAIR_ENERGIES 
GEN_BORN_ROTAMER_BACKGROUND_ENERGIES 
MULTIPOLE_SETUP 
MULTIPOLE_ENERGIES 
FACTS_SETUP_FOR_PACKING 
FACTS_GET_ALL_BORN_RADII 
FACTS_ROTAMER_PAIR_ENERGIES 
FACTS_ROTAMER_BACKGROUND_ENERGIES 
ABINITIO 
STAGE1 
STAGE2 
STAGE3 
STAGE4 
STAGE5 
FRAGMENT_MOVER 
MINMOVER_APPLY 
BACKRUB_MOVER 
FIND_SUGAR_AND_SUITE_FRAGS_I 
FIND_SUGAR_AND_SUITE_FRAGS_II 
MAKE_BASE_PAIR_MOVE 
MAKE_BASE_STEP_MOVE 
RG 
RG_LOCAL 
SEQUENCE_COMPARISON 
KDTREE_CONSTRUCT 
KDTREE_SEARCH 
CONSTRUCT_DISTANCE_MATRIX 
DALPHABALL 
DALPHABALL_DERIV 
MPI_FILE_BUF 
JD2 
JD2_OUTPUT 
JD2_SILENT_OUTPUTTER 
JD2_INIT_MOVER 
ARCHIVE_SYNC_BATCHES 
ARCHIVE_JOBSCOMPLETE 
ARCHIVE_BLOCK_FILE 
SAVE_ARCHIVE 
ARCHIVE_CRITICAL_JOBSCOMPLETE 
ARCHIVE_GEN_BATCH 
ARCHIVE_READ_DECOYS 
ARCHIVE_EVAL_DECOYS 
ARCHIVE_FILL_POSE 
ARCHIVE_SCORE_POSE 
ARCHIVE_EVALUATORS 
MPI_JD2_WAITS_FOR_ARCHIVE 
MPI_NOTIFY_ARCHIVE 
SILENT_READ_TAG_TEST 
CA_RMSD_EVALUATION 
CA_DME_EVALUATION 
TRUNCATED_SCORE_EVALUATOR 
SAXS 
FRAGMENTPICKING_CS_SCORE 
FRAGMENTPICKING_PROFILE_SCORE 
FRAGMENTPICKING_PROFILE_CAHING 
FRAGMENTPICKING_SECONDARY_SCORE 
FRAGMENTPICKING_READ_VALL 
FRAGMENTPICKING 
FRAGMENTPICKING_CANDIDATES_COLLECTING 
FRAGMENTPICKING_ATOMPAIR_SCORE 
FRAGMENTPICKING_PHIPSI_SCORE 
FRAGMENTPICKING_DIHEDRALCONSTR_SCORE 
MPICANONICALSAMPLING 
MPIPOOLCOMMUNICATION 
MPICOMMCREATION 
MPIBARRIER 
MPIBARRIER_BEGIN 
MPIBARRIER_END 
MPI_GATHER_BARRIER 
FARRAY_MANIPULATION 
MPI_SLAVE_REPORT_NEW_COORDS 
MPI_SLAVE_REPORT_SIZES 
MPI_SEND_UPDATE 
MPI_SYNC_POOL_DIFF 
MPI_SEND_ACCEPTED 
POOL_RMSD_ADD_STRUCTURE 
POOL_RMSD_EVALUATE 
POOL_RMSD_MASTER_EVALUATE 
MPI_MASTER_BCAST_COORDS 
MPI_MASTER_BCAST_WINNING_RANKS 
MPI_MASTER_BCAST_WINNING_STRUCTURES 
MPI_MASTER_BCAST_NEW_COMM_SIZE 
MPI_MASTER_BCAST_NEW_POOL_RANKS 
MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD 
MPI_POOL_MASTER_THINKS 
MPI_POOL_SLAVE_THINKS 
SIDECHAINMCMOVER 
SIMPLEINTGRAPH 
SIDECHAINMOVER 
INITIALIZE 
COMM_REDUCE_SIZE 
CANONICALMOVER_WRITE_TO_FILE 
WRITE_TO_FILE 
CHECK_COMM_SIZE 
APPLY_MOVE 
DATA_STORAGE 
MASTER_PROCESS_NEW_STRUCTURES 
COPY_COORDS 
APPLY_SC_MOVE 
APPLY_BB_MOVE 
HIERARCHICAL_EVALUATE 
HIERARCHICAL_ADD 
LOAD_HIERARCHY 
HIERARCHY_SEND_COORDS 
HIERARCHY_RECV_COORDS 
INITIALIZE_HIERARCHY 
HIERARCHY_SETUP_TO_RECV 
WRITE_DECOYS_TO_HIERARCHY 
HIERARCHY_GET_NEXT_CANDIDATE 
HIERARCHY_FIND_ADDRESS 
MPIH_EVAL_CHECK_PROGRESS 
MPIH_EVAL_COMMUNICATE_NEW 
MPIH_EVAL_AGAINST_NBR 
MPIH_PREPARE_WRITE_STRUCTURES 
MPIH_UPDATE_EVAL 
MPIH_ADD_FIRST_STRUCTURE 
MPIH_WRITE_STRUCT 
FINALIZE 
SORT_POOL 
HIERARCHICAL_FIND 
HIERARCHICAL_FIND_ADDRESS 
HIERARCHICAL_SORT_ADDRESSES 
HIERARCHICAL_ROUND 
HIERARCHICAL_POOL_SIZE 
HIERARCHICAL_ADD_ELEM_TO_CACHE 
LIB_FULL_PATH 
NOESY_ASSIGN_TOTAL 
NOESY_ASSIGN_INITIAL 
NOESY_ASSIGN_DIAGONAL 
NOESY_ASSIGN_CHEMSHIFT 
NOESY_ASSIGN_SYMMETRY 
NOESY_ASSIGN_DISTANCE 
NOESY_ASSIGN_DECOY_COMP 
NOESY_ASSIGN_NETWORK_TOTAL 
NOESY_ASSIGN_NETWORK 
NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN 
NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA 
NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN 
NOESY_ASSIGN_NETWORK_COMPUTE_NK 
NOESY_ASSIGN_NETWORK_PEAK_COUNT 
NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL 
NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE 
NOESY_ASSIGN_UPDATE_PEAK_VOL 
NOESY_ASSIGN_CALIBRATE 
NOESY_ASSIGN_ELIMINATE 
NOESY_ASSIGN_GEN_CST 
NOESY_ASSIGN_WRITE_CST 
NOESY_ASSIGN_MAP2CB 
NOESY_ASSIGN_CP_GEN_CST 
NOESY_ASSIGN_PA_GEN_CST 
NOESY_ASSIGN_NMR_STRING 
NOESY_ASSIGN_REQUIRES_CB_MAPPING 
NOESY_ASSIGN_MAP2CB_NEW 
NOESY_ASSIGN_WRITE_ASSIGNMENTS 
NOESY_ASSIGN_READ_INPUT 
NOESY_ASSIGN_DIST_INIT 
NOESY_ASSIGN_DIST_PREP_SCORE 
NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE 
NOESY_ASSIGN_DIST_APPLY 
NOESY_ASSIGN_DIST_MAKE_POSE 
NOESY_ASSIGN_DIST_CST_EVAL 
NOESY_ASSIGN_DIST_CST_CAST 
SILENT_FILL_POSE 
SILENT_SET_POSE_COORDS 
SILENT_FILL_STRUCT 
MEAN_FIELD 
TOTAL 
n_prof_tags 

Priority levels for T() and Tracer object, modeled on the log4j project and its offspring. Priorities in Tracer are still ints so users can pass other arbitrary integer values (for now).

Enumerator
t_fatal 
t_error 
t_warning 
t_info 
t_debug 
t_trace 

Function Documentation

void basic::angle_in_range ( double &  ang)

taken from wobble.cc

References debug_assert, and ObjexxFCL::mod().

Referenced by interpolate_bilinear_by_value().

void basic::calc_quadratic ( double  a,
double  b,
double  c,
double &  n1,
double &  n2 
)

calculates quadratic polynomial solutions

solves for solutions of x in the polynomial: a*x^2+b*x+c=0

Parameters
[in]a- in - x^2 term
[in]b- in - x term
[in]c- in - constant term
[out]n1- out - one solution
[out]n2- out - another solution
Remarks
courtesy of Jerry Tsai
References:
Author
ctsa 8=19-03

References basic::options::OptionKeys::score::fiber_diffraction::a, and basic::options::OptionKeys::score::fiber_diffraction::b.

template<class desired_T >
void basic::check_cast ( const basic::MetricValueBase *const  valptr,
const desired_T *  const,
std::string const &  error_msg 
)

References Error(), and utility_exit.

template<class desired_T >
void basic::check_cast ( const basic::MetricValueBase *const  valptr,
std::string const &  error_msg 
)

References Error(), and utility_exit.

template<class desired_T >
bool basic::check_cast ( const basic::MetricValueBase *const  valptr,
const desired_T *  const 
)
template<class desired_T >
bool basic::check_cast ( const basic::MetricValueBase *const  valptr)
double const basic::clock_factor ( ((double) SHRINK_FACTOR *100.0)/  CLOCKS_PER_SEC)
Tracer & basic::Error ( )

Predefined Error-level tracer, for use in headers.

References TR_Error.

Referenced by check_cast(), main(), and APDBCMover::read_in_insert_loop_info().

ExecutionResult basic::execute ( std::string const &  message,
std::string const &  command_line,
bool  terminate_on_failure,
bool  silent 
)

excute provided command_line though shell and return exit_code and output

References basic::ExecutionResult::output, basic::ExecutionResult::result, TR, and utility_exit_with_message.

char basic::get_pymol_chain ( numeric::Size  i)

References pymol_chains().

numeric::Size basic::get_pymol_chain_index_1 ( char  c)

References pymol_chains().

numeric::Size basic::get_pymol_num_unique_ids ( )

References pymol_chains().

void basic::get_usage_from_procfilesystem ( std::ostream &  mem_report)
bool basic::handles_metric_value ( MetricValueBase const &  metric_value)

check whether a MetricValue can be written to or read from a stream

References test.T008_Serialization::oss, and write_metric_value().

void basic::init ( )
void basic::interpolate_2d_func_of_angles ( double const  x,
double const  y,
ObjexxFCL::FArray2A< double xy_func,
double val,
double dval_dx,
double dval_dy 
)
inline

get bilinear interpolate of a 2d function with degree angle arguments

Value and derivatives of bilinear interpolation on a 2d function with degree angle arguments represented by a 2d array with binned degree angle indices. (see Num. Recipes v2, sec 3.6, "Interpolation in two or more dimensions")

The derivatives are of the bilinear interpolation only. This is not the same value as a numerical derivative of function values. The derivatives here are discontinuous every time you cross over a bin boundary in either dimension

Parameters
[in]x- in - function argument value in 1st dim to find interpolate for
[in]y- in - " 2nd dim "
[in]xy_func- in - 2d array with binned angle value indicies; represents known values of 2d function being interpolated.
[out]val- out - bilinear interpolated value
[out]dval_dx- out - derivative of interpolated value w.r.t. 1st dim angle
[out]dval_dy- out - " 2nd dim "
Remarks
!!! assumes 10 degree bins in both dimensions of xy_func
References:
Author
ctsa 8-19-03

References ObjexxFCL::FArray2A< typename >::dimension(), interpolate_bilinear(), and interpolate_get_angle_bins().

void basic::interpolate_bilinear ( int const  xbin,
int const  xbin_next,
double const  xd,
int const  ybin,
int const  ybin_next,
double const  yd,
ObjexxFCL::FArray2A< double xy_func,
int const  xbin_count,
int const  ybin_count,
double const  binrange,
bool const  angles,
double val,
double dval_dx,
double dval_dy 
)
inline

get bilinear interpolate of a 2d periodic function

Value and derivatives of bilinear interpolation on a 2d binned periodic function, represented as a 2d array. (see Num. Recipes v2, sec 3.6, "Interpolation in two or more dimensions")

Note that it is automatically assumed that the arguments are periodic, that is f(a,b),a,b=periodic value; the value of the function can be treated as periodic ( fixed to a periodicity of 360.) as well when the input parameter angle is set to true

The derivatives are of the bilinear interpolation only. This is not the same value as a numerical derivative of function values. The derivatives here are discontinuous every time you cross over a bin boundary in either dimension

Parameters
[in]xbin- in - low bin in 1st dim
[in]xbin_next- in - high bin in 1st dim
[in]xd- in - error between low and real val in 1st dim
[in]ybin- in - " 2nd dim "
[in]ybin_next- in - " 2nd dim "
[in]yd- in - " 2nd dim "
[in]xy_func- in - 2d-array specifying the 2d binned function values, assumed to be periodic in each dimension
[in]xbin_count- in - number of bins in the 1st dim of the periodic function
[in]ybin_count- in - " 2nd dim "
[in]binrange- in - range of bin in angles ( for both dimensions )
[in]angles- in - if true, treat the the values of xy_func as as having a periodicity of 360. ( note that the bin ranges are already assumed periodic )
[out]val- out - bilinear interpolated value of xy_func
[out]dval_dx- out - derivative of interpolation w.r.t 1st dim
[out]dval_dy- out - " 2nd dim "
Remarks
References:
Author
ctsa 8-19-03

References ObjexxFCL::FArray2A< typename >::dimension(), and interpolate_bilinear_by_value().

Referenced by interpolate_2d_func_of_angles().

void basic::interpolate_bilinear_by_value ( double const  x0y0,
double const  x1y0,
double const  x0y1,
double const  x1y1,
double const  xd,
double const  yd,
double const  binrange,
bool const  angles,
double val,
double dval_dx,
double dval_dy 
)

get bilinear interpolate, given four points of a 2d periodic function

Value and derivatives of bilinear interpolation between four specified input values, which are the function values corresponding to four points which bracket the interpolated point in 2-dimensions. (see diagram below) (see Num. Recipes v2, sec 3.6, "Interpolation in two or more dimensions")

Note that it is automatically assumed that the arguments are periodic, that is f(a,b),a,b=periodic value; the value of the function can be treated as periodic ( fixed to a periodicity of 360.) as well when the input parameter angle is set to true

The derivatives are of the bilinear interpolation only. This is not the same value as a numerical derivative of function values. The derivatives here are discontinuous every time you cross over a bin boundary in either dimension

  • bilinear interpolation:

    x0y1 +-------—+ x1y1 | | 1-yd | (x,y) |

    • - + | yd | . | | . | x0y0 +—|---—+ x1y0 xd 1-xd
Parameters
[in]x0y0- in - input bracketing function value (see diagram)
[in]x1y0- in - " "
[in]x0y1- in - " "
[in]x1y1- in - " "
[in]xd- in - error value in the 1st dim between lower lst dim bracket value 'x0' and point to be interpolated, 'x'
[in]yd- in - " 2nd dim "
[in]binrange- in - range of bin in angles ( for both dimensions )
[in]angles- in - if true, treat the the values of xy_func as as having a periodicity of 360. ( note that the bin ranges are already assumed periodic )
[out]val- out - biliinear interpolated value
[out]dval_dx- out - derivative of 'val' in the 1st ('x') dim
[out]dval_dy- out - " 2nd dim "
Remarks
References:
Author
ctsa 8-19-03

References angle_in_range(), demo.D060_Folding::f, and subtract_degree_angles().

Referenced by interpolate_bilinear().

void basic::interpolate_get_angle_bins ( double const  x,
double const  binrange,
int xbin,
int xbin_next,
double xd 
)
inline

get bin information for a periodic value w/ periodic bins

for 'x', an angle in degrees, and angular bins of width 'binrange' aligned to start bin 1 at a value of 0. degrees, find the two bins, whose average bin values 'x' falls between, and report the error between the lower average bin value and the real value of 'x'

Parameters
[in]x- in - angle in degrees
[in]binrange- in - degrees per bin
[out]xbin- out - anglular bin whose average value is the lower of the two average bin values bracketing 'x'
[out]xbin_next- out - anglular bin whose average value is the lower of the two average bin values bracketing 'x'
[out]xd- out - error between the average value of bin 'xbin' and 'x'
Remarks
References:
Author

References ObjexxFCL::mod().

Referenced by interpolate_2d_func_of_angles().

void basic::interpolate_trilinear ( int const  xbin,
int const  xbin_next,
double const  xd,
int const  ybin,
int const  ybin_next,
double const  yd,
int const  zbin,
int const  zbin_next,
double const  zd,
ObjexxFCL::FArray3A< double xyz_func,
int const  xbin_count,
int const  ybin_count,
int const  zbin_count,
double const  binrange,
bool const  angles,
double val,
double dval_dx,
double dval_dy,
double dval_dz 
)
inline
void basic::interpolate_trilinear_by_value ( double const  x0y0z0,
double const  x1y0z0,
double const  x0y1z0,
double const  x1y1z0,
double const  x0y0z1,
double const  x1y0z1,
double const  x0y1z1,
double const  x1y1z1,
double const  xd,
double const  yd,
double const  zd,
double const  binrange,
bool const  angles,
double val,
double dval_dx,
double dval_dy,
double dval_dz 
)

paraphazed from above for three dimentions Without additional scaling this will only work if the bin sizes in each dimention are equal I think. Otherwise it could be computed as the product of three linear interpolations

Perform linear interpolation between x0y0z0 and x1y0z0 to find y0z0 Preform linear interpolation between x0y0z1 and x1y0z1 to find y0z1 Preform linear interpolation between x0y1z1 and x1y1z1 to find y1z1 Preform linear interpolation between x0y1z0 and x1y1z0 to find y1z0 Preform linear interpolation between y0z0 and y1z0 to find z0 Preform linear interpolation between y0z1 and y1z1 to find z1 Preform linear interpolation between z0 and z1 to find val

References demo.D060_Folding::f.

Referenced by interpolate_trilinear().

double basic::periodic_range ( double  a,
double  x 
)

a is restricted to [-x/2,x/2), assuming that a=a+n*x, n=any integer

Parameters
[in]a- in - input value with periodicity x
[in]x- in - periodicity of a
Returns
a restricted to [-x/2,x/2)
Remarks
References:
Author
ctsa 8-19-03

References ObjexxFCL::mod(), and numeric::crick_equations::x().

Referenced by subtract_degree_angles(), and subtract_radian_angles().

void basic::prof_reset ( )
void basic::prof_show ( )
void basic::prof_start_function_body ( ProfTag const  tag)
inline
void basic::prof_stop_function_body ( ProfTag const  tag)
inline
static std::string const basic::pymol_chains ( )
static
bool basic::read_metric_value ( std::istream &  is,
MetricValueBase &  metric_value 
)

read a MetricValue from a stream, returns true if successful

References read_metric_value_template().

MetricValueBaseOP basic::read_metric_value ( std::istream &  is)

read a MetricValue from a stream, returns NULL if unsuccessful

References read_metric_value_template().

template<class T >
bool basic::read_metric_value_scalar ( std::istream &  is,
MetricValueBase &  metric_value 
)

References value.

template<class T >
bool basic::read_metric_value_scalar ( std::istream &  is,
MetricValueBaseOP &  metric_value 
)
template<class MetricValueBase_or_MetricValueBaseOP >
bool basic::read_metric_value_template ( std::istream &  is,
MetricValueBase_or_MetricValueBaseOP &  metric_value 
)

central read introspection and delegation function

Referenced by read_metric_value().

template<class T >
bool basic::read_metric_value_vector1 ( std::istream &  is,
MetricValueBase &  metric_value 
)
template<class T >
bool basic::read_metric_value_vector1 ( std::istream &  is,
MetricValueBaseOP &  metric_value 
)
void basic::setup_tag2string ( )

References ABINITIO, APPLY_BB_MOVE, APPLY_MOVE, APPLY_SC_MOVE, ARCHIVE_BLOCK_FILE, ARCHIVE_CRITICAL_JOBSCOMPLETE, ARCHIVE_EVAL_DECOYS, ARCHIVE_EVALUATORS, ARCHIVE_FILL_POSE, ARCHIVE_GEN_BATCH, ARCHIVE_JOBSCOMPLETE, ARCHIVE_READ_DECOYS, ARCHIVE_SCORE_POSE, ARCHIVE_SYNC_BATCHES, ATOM_TREE_UPDATE_INTERNAL_COORDS, ATOM_TREE_UPDATE_XYZ_COORDS, BACKRUB_MOVER, CA_RMSD_EVALUATION, CANONICALMOVER_WRITE_TO_FILE, CCD_CLOSE, CHECK_COMM_SIZE, CHEMICAL_MAKE_POSE, COMM_REDUCE_SIZE, CONFORMATION_COPY, CONFORMATION_DETECT_DISULF, CONFORMATION_FIX_DISULF, CONSTRAINT_SCORE, CONSTRAINT_SET_COPY, CONSTRUCT_DISTANCE_MATRIX, COPY_COORDS, DATA_STORAGE, DFUNC, ENERGIES_COPY, ENERGY_ENVPAIR_POTENTIAL, ENERGY_GRAPH_COPY, FACTS_GET_ALL_BORN_RADII, FACTS_ROTAMER_BACKGROUND_ENERGIES, FACTS_ROTAMER_PAIR_ENERGIES, FACTS_SETUP_FOR_PACKING, FARRAY_MANIPULATION, FINALIZE, FIND_SUGAR_AND_SUITE_FRAGS_I, FIND_SUGAR_AND_SUITE_FRAGS_II, FRAGMENT_MOVER, FRAGMENTPICKING, FRAGMENTPICKING_ATOMPAIR_SCORE, FRAGMENTPICKING_CANDIDATES_COLLECTING, FRAGMENTPICKING_CS_SCORE, FRAGMENTPICKING_DIHEDRALCONSTR_SCORE, FRAGMENTPICKING_PHIPSI_SCORE, FRAGMENTPICKING_PROFILE_CAHING, FRAGMENTPICKING_PROFILE_SCORE, FRAGMENTPICKING_READ_VALL, FRAGMENTPICKING_SECONDARY_SCORE, FUNC, GB_GET_ALL_BORN_RADII, GB_SETUP_FOR_PACKING, GEN_BORN_ROTAMER_BACKGROUND_ENERGIES, GEN_BORN_ROTAMER_PAIR_ENERGIES, GET_ENERGIES, HIERARCHICAL_ADD, HIERARCHICAL_ADD_ELEM_TO_CACHE, HIERARCHICAL_EVALUATE, HIERARCHICAL_FIND, HIERARCHICAL_FIND_ADDRESS, HIERARCHICAL_POOL_SIZE, HIERARCHICAL_ROUND, HIERARCHICAL_SORT_ADDRESSES, HIERARCHY_FIND_ADDRESS, HIERARCHY_GET_NEXT_CANDIDATE, HIERARCHY_RECV_COORDS, HIERARCHY_SEND_COORDS, HIERARCHY_SETUP_TO_RECV, INITIALIZE, INITIALIZE_HIERARCHY, INSERT_FRAGS, JD2, JD2_INIT_MOVER, JD2_OUTPUT, JD2_SILENT_OUTPUTTER, KDTREE_CONSTRUCT, KDTREE_SEARCH, LIB_FULL_PATH, LOAD_HIERARCHY, MAKE_BASE_PAIR_MOVE, MAKE_BASE_STEP_MOVE, MASTER_PROCESS_NEW_STRUCTURES, MC_ACCEPT, MEAN_FIELD, MINMOVER_APPLY, MPI_FILE_BUF, MPI_GATHER_BARRIER, MPI_JD2_WAITS_FOR_ARCHIVE, MPI_MASTER_BCAST_COORDS, MPI_MASTER_BCAST_NEW_COMM_SIZE, MPI_MASTER_BCAST_NEW_POOL_RANKS, MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD, MPI_MASTER_BCAST_WINNING_RANKS, MPI_MASTER_BCAST_WINNING_STRUCTURES, MPI_NOTIFY_ARCHIVE, MPI_POOL_MASTER_THINKS, MPI_POOL_SLAVE_THINKS, MPI_SEND_ACCEPTED, MPI_SEND_UPDATE, MPI_SLAVE_REPORT_NEW_COORDS, MPI_SLAVE_REPORT_SIZES, MPI_SYNC_POOL_DIFF, MPIBARRIER, MPIBARRIER_BEGIN, MPIBARRIER_END, MPICANONICALSAMPLING, MPICOMMCREATION, MPIH_ADD_FIRST_STRUCTURE, MPIH_EVAL_AGAINST_NBR, MPIH_EVAL_CHECK_PROGRESS, MPIH_EVAL_COMMUNICATE_NEW, MPIH_PREPARE_WRITE_STRUCTURES, MPIH_UPDATE_EVAL, MPIH_WRITE_STRUCT, MPIPOOLCOMMUNICATION, MULTIPOLE_ENERGIES, MULTIPOLE_SETUP, n_prof_tags, NOESY_ASSIGN_CALIBRATE, NOESY_ASSIGN_CHEMSHIFT, NOESY_ASSIGN_CP_GEN_CST, NOESY_ASSIGN_DECOY_COMP, NOESY_ASSIGN_DIAGONAL, NOESY_ASSIGN_DIST_APPLY, NOESY_ASSIGN_DIST_CST_CAST, NOESY_ASSIGN_DIST_CST_EVAL, NOESY_ASSIGN_DIST_INIT, NOESY_ASSIGN_DIST_MAKE_POSE, NOESY_ASSIGN_DIST_PREP_SCORE, NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE, NOESY_ASSIGN_DISTANCE, NOESY_ASSIGN_ELIMINATE, NOESY_ASSIGN_GEN_CST, NOESY_ASSIGN_INITIAL, NOESY_ASSIGN_MAP2CB, NOESY_ASSIGN_MAP2CB_NEW, NOESY_ASSIGN_NETWORK, NOESY_ASSIGN_NETWORK_COMPUTE_NK, NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA, NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN, NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE, NOESY_ASSIGN_NETWORK_PEAK_COUNT, NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL, NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN, NOESY_ASSIGN_NETWORK_TOTAL, NOESY_ASSIGN_NMR_STRING, NOESY_ASSIGN_PA_GEN_CST, NOESY_ASSIGN_READ_INPUT, NOESY_ASSIGN_REQUIRES_CB_MAPPING, NOESY_ASSIGN_SYMMETRY, NOESY_ASSIGN_TOTAL, NOESY_ASSIGN_UPDATE_PEAK_VOL, NOESY_ASSIGN_WRITE_ASSIGNMENTS, NOESY_ASSIGN_WRITE_CST, PACK_ROTAMERS, POOL_RMSD_ADD_STRUCTURE, POOL_RMSD_EVALUATE, POOL_RMSD_MASTER_EVALUATE, POSE_COPY, RG, RG_LOCAL, ROTAMER_TRIALS, SAVE_ARCHIVE, SAXS, SCORE, SCORE_BEGIN_NOTIFY, SCORE_DOT, SCORE_END_NOTIFY, SCORE_FINALIZE, SCORE_LONG_RANGE_ENERGIES, SCORE_NEIGHBOR_ENERGIES, SCORE_ONEBODY_ENERGIES, SCORE_SETUP, SECONDARY_STRUCTURE_ENERGY, SECONDARY_STRUCTURE_HSPAIR_ENERGY, SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY, SECONDARY_STRUCTURE_SSPAIR_ENERGY, SEQUENCE_COMPARISON, SETUP_NBLIST, SIDECHAINMCMOVER, SIDECHAINMOVER, SILENT_FILL_POSE, SILENT_FILL_STRUCT, SILENT_READ_TAG_TEST, SILENT_SET_POSE_COORDS, SIMANNEALING, SIMPLEINTGRAPH, SORT_POOL, STAGE1, STAGE2, STAGE3, STAGE4, STAGE5, ObjexxFCL::string_of(), tag2string, TEST1, TEST2, TEST3, TEST4, TOTAL, TRUNCATED_SCORE_EVALUATOR, UPDATE_RESIDUE_COORDINATES, UPDATE_RESIDUE_NEIGHBORS, UPDATE_RESIDUE_TORSIONS, VDW_ENERGY, WRITE_DECOYS_TO_HIERARCHY, and WRITE_TO_FILE.

Referenced by prof_show().

void basic::show_time ( basic::Tracer tr,
std::string const &  msg 
)
bool basic::show_time_on_cerr ( false  )

Referenced by show_time().

clock_t const basic::SHRINK_FACTOR ( )
double basic::subtract_degree_angles ( double  a,
double  b 
)

subtract angles in degrees, restricting the range of the result

given angles a and b in degrees, get a-b restricted to [-180.,180.), assuming that a-b=a-b+n*360, n=any integer

Parameters
[in]a- in - angle in degrees
[in]b- in - angle in degrees
Returns
angle a-b in degrees, restricted to the specified range
Remarks
References:
Author
ctsa 8-19-03

References periodic_range().

Referenced by interpolate_bilinear_by_value().

double basic::subtract_radian_angles ( double  a,
double  b 
)

subtract angles in radians, restricting the range of the result

given angles a and b in degrees, get a-b restricted to [-pi,pi), assuming that a-b=a-b+n*2*pi, n=any integer

Parameters
[in]a- in - angle in radians
[in]b- in - angle in radians
Returns
angle a-b in degrees, restricted to the specified range
Remarks
References:
Author
ctsa 8-19-03

References demo.D060_Folding::f, periodic_range(), and numeric::constants::f::pi_2.

double basic::unsigned_periodic_range ( double  a,
double  x 
)

a is restricted to [0.,x), assuming that a=a+n*x,, n=any integer

Parameters
[in]a- in - input value with periodicity x
[in]x- in - periodicity of a
Returns
a restricted to [0.,x)
Remarks
References:
Author
ctsa 8-19-03

References ObjexxFCL::mod().

Tracer & basic::Warning ( )

Predefined Warning tracer, for use in headers.

References TR_Warning.

Referenced by basic::Emitter::assert_in(), main(), and supercharge::set_surface().

bool basic::was_init_called ( )

return true if core::init was already called and false otherwise

References init_was_called.

bool basic::write_metric_value ( std::ostream &  os,
MetricValueBase const &  metric_value 
)

central write introspection and delegation function

write a MetricValue to a stream, returns true if successful

This function currently supports some of the most often used MetricValues. The type is always encoded in the output so that an object of the same class can be generated during reading. The supported types and their formats is as follows:

double double <num> int Int <num> std::size_t std::size_t <num> bool Bool <0 or 1> utility::vector1<double> Real[ <num1> <num2> ... ] utility::vector1<int> Int[ <num1> <num2> ... ] utility::vector1<size_t> size_t[ <num1> <num2> ... ] utility::vector1<bool> Bool[ <bool1> <bool2> ... ]

References write_metric_value_scalar(), and write_metric_value_vector1().

Referenced by handles_metric_value().

template<class T >
bool basic::write_metric_value_scalar ( std::ostream &  os,
MetricValue< T > const &  metric_value,
std::string const &  type_name 
)
template<class T >
bool basic::write_metric_value_vector1 ( std::ostream &  os,
MetricValue< vector1< T > > const &  metric_value,
std::string const &  type_name 
)

Referenced by write_metric_value().

Variable Documentation

utility::vector1< int > basic::bad_calls
utility::vector1< int > basic::calls
double const basic::clock_factor

Referenced by prof_stop_function_body().

std::map<std::string, int> basic::dynamic_prof_calls
std::map<std::string, double> basic::dynamic_prof_total
bool basic::init_was_called = false
static

Global variable to check if core::init was ever called. Used to detect situations when user forgot to call init and display helpful message instead of silently crashing. We put it here instead of core/init/init.cc so code from all libraries level have access to it

Referenced by init(), and was_init_called().

bool basic::show_time_on_cerr

print "TIME_STAMP: Www Mmm dd hh:mm:ss yyyy msg" on tr.Error and on std::cerr (if boolean is true)

clock_t const basic::SHRINK_FACTOR
utility::vector1< clock_t > basic::start_clock
utility::vector1< std::string > basic::tag2string

Referenced by prof_show(), and setup_tag2string().

utility::vector1< double > basic::total_clock
basic::Tracer basic::TR("basic.execute")
static
basic::Tracer basic::TR_Error("Error", basic::t_error)
static

Referenced by Error().

basic::Tracer basic::TR_Warning("Warning", basic::t_warning)
static

Referenced by Warning().

basic::Tracer basic::tt("core.util.prof", basic::t_info, true)
static

Referenced by prof_show().