 |
Rosetta
3.7
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Pages
|
Rosetta
3.7
|
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 | |
| resource_manager | |
| sampling | |
| svd | |
Classes | |
| class | basic_otstream |
| Base class for Tracer, TracerProxy 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 | 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 'src.basic.scoring.myfile'. More... | |
| class | TracerManager |
| Simple singleton class to hold the all_tracers_ array, which otherwise suffers from funky double-construction problems when declared as a static data member of Tracer. 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 basic_otstream< char > | otstream |
| typedef utility::pointer::shared_ptr < otstream > | otstreamOP |
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... | |
| static THREAD_LOCAL basic::Tracer | TR ("basic.execute") |
| 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!@#$&.<>?]{}|-_\\~=%") |
| Tracer & | T (std::string const &channel, TracerPriority priority=t_info) |
| T is special function for assign tracer property on the static object. More... | |
| Tracer & | Error (TracerPriority priority=t_error) |
| Predefined Error tracer. More... | |
| Tracer & | Warning (TracerPriority priority=t_warning) |
| Predefined Warning tracer. More... | |
Variables | |
| static bool | init_was_called = false |
| MemTracer | mem_tr |
| 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< int > | calls (n_prof_tags, 0) |
| utility::vector1< int > | bad_calls (n_prof_tags, 0) |
| std::map< std::string, double > | dynamic_prof_total |
| std::map< std::string, int > | dynamic_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... | |
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 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< YamlEmitter const > basic::YamlEmitterCOP |
| typedef utility::pointer::shared_ptr< YamlEmitter > basic::YamlEmitterOP |
| enum basic::ProfTag |
| void basic::angle_in_range | ( | double & | ang | ) |
| 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
| [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 |
References basic::options::OptionKeys::score::fiber_diffraction::a, and basic::options::OptionKeys::score::fiber_diffraction::b.
| void basic::check_cast | ( | const basic::MetricValueBase *const | valptr, |
| const desired_T * | const, | ||
| std::string const & | error_msg | ||
| ) |
References Error(), and utility_exit.
| void basic::check_cast | ( | const basic::MetricValueBase *const | valptr, |
| std::string const & | error_msg | ||
| ) |
References Error(), and utility_exit.
| bool basic::check_cast | ( | const basic::MetricValueBase *const | valptr, |
| const desired_T * | const | ||
| ) |
| bool basic::check_cast | ( | const basic::MetricValueBase *const | valptr | ) |
| double const basic::clock_factor | ( | ((double) SHRINK_FACTOR *100.0)/ | CLOCKS_PER_SEC | ) |
Referenced by basic::DynamicProfileThis::~DynamicProfileThis().
|
inline |
Predefined Error tracer.
References T().
Referenced by check_cast(), BuildPackagedBindings::copy_tree_contents(), 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 write_metric_value().
| void basic::init | ( | ) |
set global 'init_was_called' to true
References init_was_called.
Referenced by toolbox.load_ligand::add_cid_to_database(), utility::io::mpi_stream::basic_mpi_ostreambase< Elem, Tr, ElemA, ByteT, ByteAT >::basic_mpi_ostreambase(), zlib_stream::basic_zip_istreambase< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_istreambase(), zlib_stream::basic_zip_ostreambase< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_ostreambase(), PerformanceBenchmark::execute(), ObjexxFCL::Fstring::Fstring(), instantiate_numeric_functions(), instantiate_real_numeric_containers(), main(), prof_show(), fmt::SystemError::SystemError(), wrap_std_list(), wrap_std_set(), wrap_std_vector(), and wrap_vector1().
|
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
| [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 " |
!!! assumes 10 degree bins in both dimensions of xy_func
References ObjexxFCL::FArray2A< typename >::dimension(), interpolate_bilinear(), and interpolate_get_angle_bins().
|
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
| [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 " |
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) |
| [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 " |
References angle_in_range(), demo.D060_Folding::f, and subtract_degree_angles().
Referenced by interpolate_bilinear().
|
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'
| [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' |
References ObjexxFCL::mod().
Referenced by interpolate_2d_func_of_angles().
|
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
| [in] | a | - in - input value with periodicity x |
| [in] | x | - in - periodicity of a |
References ObjexxFCL::mod(), and x().
Referenced by subtract_degree_angles(), and subtract_radian_angles().
| void basic::prof_reset | ( | ) |
References bad_calls, calls, n_prof_tags, option, options, PROF_START, basic::options::OptionKeys::run::profile, start_clock, TOTAL, and total_clock.
Referenced by main(), and sequence_tolerance_main().
| void basic::prof_show | ( | ) |
References ObjexxFCL::format::A(), bad_calls, calls, ObjexxFCL::format::F(), ObjexxFCL::format::I(), init(), n_prof_tags, option, options, PROF_START, PROF_STOP, basic::options::OptionKeys::run::profile, setup_tag2string(), basic::options::OptionKeys::in::file::t, t_info, tag, tag2string, TOTAL, and total_clock.
Referenced by main(), run(), and sequence_tolerance_main().
|
inline |
References calls, basic::options::option, options, basic::options::OptionKeys::run::profile, SHRINK_FACTOR, start_clock, and tag.
|
inline |
|
static |
Referenced by get_pymol_chain(), get_pymol_chain_index_1(), and get_pymol_num_unique_ids().
| 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().
| bool basic::read_metric_value_scalar | ( | std::istream & | is, |
| MetricValueBase & | metric_value | ||
| ) |
References basic::MetricValue< T >::set(), T(), and value.
| bool basic::read_metric_value_scalar | ( | std::istream & | is, |
| MetricValueBaseOP & | metric_value | ||
| ) |
| 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().
| bool basic::read_metric_value_vector1 | ( | std::istream & | is, |
| MetricValueBase & | metric_value | ||
| ) |
References basic::MetricValue< T >::set(), T(), and value.
| 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, 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 | ||
| ) |
References utility::io::oc::cerr, basic::Tracer::channel(), basic::Tracer::Error, and show_time_on_cerr().
| bool basic::show_time_on_cerr | ( | false | ) |
Referenced by show_time().
| clock_t const basic::SHRINK_FACTOR | ( | 2 | ) |
| 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
| [in] | a | - in - angle in degrees |
| [in] | b | - in - angle in degrees |
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
| [in] | a | - in - angle in radians |
| [in] | b | - in - angle in radians |
References demo.D060_Folding::f, periodic_range(), and numeric::constants::f::pi_2.
| Tracer & basic::T | ( | std::string const & | channel, |
| TracerPriority | priority | ||
| ) |
T is special function for assign tracer property on the static object.
Return reference to static Tracer object (after setting it channel and priority).
References basic::Tracer::begining_of_the_line_, basic::Tracer::calculate_visibility(), basic::Tracer::channel_, basic::Tracer::priority_, and basic::options::OptionKeys::in::file::t.
Referenced by Error(), read_metric_value_scalar(), read_metric_value_vector1(), basic::resource_manager::show_option_vector_map(), basic::options::start_files(), and Warning().
|
static |
Referenced by execute().
| double basic::unsigned_periodic_range | ( | double | a, |
| double | x | ||
| ) |
a is restricted to [0.,x), assuming that a=a+n*x,, n=any integer
| [in] | a | - in - input value with periodicity x |
| [in] | x | - in - periodicity of a |
References ObjexxFCL::mod().
|
inline |
Predefined Warning tracer.
References T().
Referenced by basic::Emitter::assert_in(), basic::database::full_name(), 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().
| bool basic::write_metric_value_scalar | ( | std::ostream & | os, |
| MetricValue< T > const & | metric_value, | ||
| std::string const & | type_name | ||
| ) |
References basic::MetricValue< T >::value().
Referenced by write_metric_value().
| bool basic::write_metric_value_vector1 | ( | std::ostream & | os, |
| MetricValue< vector1< T > > const & | metric_value, | ||
| std::string const & | type_name | ||
| ) |
References basic::options::OptionKeys::mp::mutate_relax::iter.
Referenced by write_metric_value().
| utility::vector1< int > basic::bad_calls |
Referenced by prof_reset(), prof_show(), and prof_stop_function_body().
| utility::vector1< int > basic::calls |
Referenced by prof_reset(), prof_show(), prof_start_function_body(), and prof_stop_function_body().
| 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 |
|
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().
| MemTracer basic::mem_tr |
| 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 |
Referenced by prof_start_function_body(), and prof_stop_function_body().
| utility::vector1< clock_t > basic::start_clock |
Referenced by prof_reset(), prof_start_function_body(), and prof_stop_function_body().
| utility::vector1< std::string > basic::tag2string |
Referenced by prof_show(), and setup_tag2string().
| utility::vector1< double > basic::total_clock |
Referenced by prof_reset(), prof_show(), and prof_stop_function_body().
1.8.7