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rosetta.basic._basic_ module

Module variables

var ABINITIO

var APPLY_BB_MOVE

var APPLY_MOVE

var APPLY_SC_MOVE

var ARCHIVE_BLOCK_FILE

var ARCHIVE_CRITICAL_JOBSCOMPLETE

var ARCHIVE_EVALUATORS

var ARCHIVE_EVAL_DECOYS

var ARCHIVE_FILL_POSE

var ARCHIVE_GEN_BATCH

var ARCHIVE_JOBSCOMPLETE

var ARCHIVE_READ_DECOYS

var ARCHIVE_SCORE_POSE

var ARCHIVE_SYNC_BATCHES

var ATOM_TREE_UPDATE_INTERNAL_COORDS

var ATOM_TREE_UPDATE_XYZ_COORDS

var BACKRUB_MOVER

var CANONICALMOVER_WRITE_TO_FILE

var CA_DME_EVALUATION

var CA_RMSD_EVALUATION

var CCD_CLOSE

var CHECK_COMM_SIZE

var CHEMICAL_MAKE_POSE

var COMM_REDUCE_SIZE

var CONFORMATION_COPY

var CONFORMATION_DETECT_DISULF

var CONFORMATION_FIX_DISULF

var CONSTRAINT_SCORE

var CONSTRAINT_SET_COPY

var CONSTRUCT_DISTANCE_MATRIX

var COPY_COORDS

var DALPHABALL

var DALPHABALL_DERIV

var DATA_STORAGE

var DFUNC

var ENERGIES_COPY

var ENERGY_ENVPAIR_POTENTIAL

var ENERGY_GRAPH_COPY

var FACTS_GET_ALL_BORN_RADII

var FACTS_ROTAMER_BACKGROUND_ENERGIES

var FACTS_ROTAMER_PAIR_ENERGIES

var FACTS_SETUP_FOR_PACKING

var FARRAY_MANIPULATION

var FINALIZE

var FIND_SUGAR_AND_SUITE_FRAGS_I

var FIND_SUGAR_AND_SUITE_FRAGS_II

var FRAGMENTPICKING

var FRAGMENTPICKING_ATOMPAIR_SCORE

var FRAGMENTPICKING_CANDIDATES_COLLECTING

var FRAGMENTPICKING_CS_SCORE

var FRAGMENTPICKING_DIHEDRALCONSTR_SCORE

var FRAGMENTPICKING_PHIPSI_SCORE

var FRAGMENTPICKING_PROFILE_CAHING

var FRAGMENTPICKING_PROFILE_SCORE

var FRAGMENTPICKING_READ_VALL

var FRAGMENTPICKING_SECONDARY_SCORE

var FRAGMENT_MOVER

var FUNC

var GB_GET_ALL_BORN_RADII

var GB_SETUP_FOR_PACKING

var GEN_BORN_ROTAMER_BACKGROUND_ENERGIES

var GEN_BORN_ROTAMER_PAIR_ENERGIES

var GET_ENERGIES

var HIERARCHICAL_ADD

var HIERARCHICAL_ADD_ELEM_TO_CACHE

var HIERARCHICAL_EVALUATE

var HIERARCHICAL_FIND

var HIERARCHICAL_FIND_ADDRESS

var HIERARCHICAL_POOL_SIZE

var HIERARCHICAL_ROUND

var HIERARCHICAL_SORT_ADDRESSES

var HIERARCHY_FIND_ADDRESS

var HIERARCHY_GET_NEXT_CANDIDATE

var HIERARCHY_RECV_COORDS

var HIERARCHY_SEND_COORDS

var HIERARCHY_SETUP_TO_RECV

var INITIALIZE

var INITIALIZE_HIERARCHY

var INSERT_FRAGS

var JD2

var JD2_INIT_MOVER

var JD2_OUTPUT

var JD2_SILENT_OUTPUTTER

var KDTREE_CONSTRUCT

var LIB_FULL_PATH

var LOAD_HIERARCHY

var MAKE_BASE_PAIR_MOVE

var MAKE_BASE_STEP_MOVE

var MASTER_PROCESS_NEW_STRUCTURES

var MC_ACCEPT

var MINMOVER_APPLY

var MPIBARRIER

var MPIBARRIER_BEGIN

var MPIBARRIER_END

var MPICANONICALSAMPLING

var MPICOMMCREATION

var MPIH_ADD_FIRST_STRUCTURE

var MPIH_EVAL_AGAINST_NBR

var MPIH_EVAL_CHECK_PROGRESS

var MPIH_EVAL_COMMUNICATE_NEW

var MPIH_PREPARE_WRITE_STRUCTURES

var MPIH_UPDATE_EVAL

var MPIH_WRITE_STRUCT

var MPIPOOLCOMMUNICATION

var MPI_FILE_BUF

var MPI_GATHER_BARRIER

var MPI_JD2_WAITS_FOR_ARCHIVE

var MPI_MASTER_BCAST_COORDS

var MPI_MASTER_BCAST_NEW_COMM_SIZE

var MPI_MASTER_BCAST_NEW_POOL_RANKS

var MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD

var MPI_MASTER_BCAST_WINNING_RANKS

var MPI_MASTER_BCAST_WINNING_STRUCTURES

var MPI_NOTIFY_ARCHIVE

var MPI_POOL_MASTER_THINKS

var MPI_POOL_SLAVE_THINKS

var MPI_SEND_ACCEPTED

var MPI_SEND_UPDATE

var MPI_SLAVE_REPORT_NEW_COORDS

var MPI_SLAVE_REPORT_SIZES

var MPI_SYNC_POOL_DIFF

var NOESY_ASSIGN_CALIBRATE

var NOESY_ASSIGN_CHEMSHIFT

var NOESY_ASSIGN_CP_GEN_CST

var NOESY_ASSIGN_DECOY_COMP

var NOESY_ASSIGN_DIAGONAL

var NOESY_ASSIGN_DISTANCE

var NOESY_ASSIGN_DIST_APPLY

var NOESY_ASSIGN_DIST_CST_CAST

var NOESY_ASSIGN_DIST_CST_EVAL

var NOESY_ASSIGN_DIST_INIT

var NOESY_ASSIGN_DIST_MAKE_POSE

var NOESY_ASSIGN_DIST_PREP_SCORE

var NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE

var NOESY_ASSIGN_ELIMINATE

var NOESY_ASSIGN_GEN_CST

var NOESY_ASSIGN_INITIAL

var NOESY_ASSIGN_MAP2CB

var NOESY_ASSIGN_MAP2CB_NEW

var NOESY_ASSIGN_NETWORK

var NOESY_ASSIGN_NETWORK_COMPUTE_NK

var NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA

var NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN

var NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE

var NOESY_ASSIGN_NETWORK_PEAK_COUNT

var NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL

var NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN

var NOESY_ASSIGN_NETWORK_TOTAL

var NOESY_ASSIGN_NMR_STRING

var NOESY_ASSIGN_PA_GEN_CST

var NOESY_ASSIGN_READ_INPUT

var NOESY_ASSIGN_REQUIRES_CB_MAPPING

var NOESY_ASSIGN_SYMMETRY

var NOESY_ASSIGN_TOTAL

var NOESY_ASSIGN_UPDATE_PEAK_VOL

var NOESY_ASSIGN_WRITE_ASSIGNMENTS

var NOESY_ASSIGN_WRITE_CST

var PACK_ROTAMERS

var POOL_RMSD_ADD_STRUCTURE

var POOL_RMSD_EVALUATE

var POOL_RMSD_MASTER_EVALUATE

var POSE_COPY

var RG

var RG_LOCAL

var ROTAMER_TRIALS

var SAVE_ARCHIVE

var SAXS

var SCORE

var SCORE_BEGIN_NOTIFY

var SCORE_DOT

var SCORE_END_NOTIFY

var SCORE_FINALIZE

var SCORE_LONG_RANGE_ENERGIES

var SCORE_NEIGHBOR_ENERGIES

var SCORE_ONEBODY_ENERGIES

var SCORE_SETUP

var SECONDARY_STRUCTURE_ENERGY

var SECONDARY_STRUCTURE_HSPAIR_ENERGY

var SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY

var SECONDARY_STRUCTURE_SSPAIR_ENERGY

var SEQUENCE_COMPARISON

var SETUP_NBLIST

var SIDECHAINMCMOVER

var SIDECHAINMOVER

var SILENT_FILL_POSE

var SILENT_FILL_STRUCT

var SILENT_READ_TAG_TEST

var SILENT_SET_POSE_COORDS

var SIMANNEALING

var SIMPLEINTGRAPH

var SORT_POOL

var STAGE1

var STAGE2

var STAGE3

var STAGE4

var STAGE5

var TEST1

var TEST2

var TEST3

var TEST4

var TEST5

var TOTAL

var TRUNCATED_SCORE_EVALUATOR

var UPDATE_RESIDUE_COORDINATES

var UPDATE_RESIDUE_NEIGHBORS

var UPDATE_RESIDUE_TORSIONS

var VDW_ENERGY

var WRITE_DECOYS_TO_HIERARCHY

var WRITE_TO_FILE

var n_prof_tags

var t_debug

var t_error

var t_fatal

var t_info

var t_trace

var t_warning

Functions

def Error(

...)

Error([ (TracerPriority)priority=rosetta.basic.basic.TracerPriority.t_error]) -> Tracer : Predefined Error tracer.

C++ signature : basic::Tracer {lvalue} Error([ basic::TracerPriority=rosetta.basic.basic.TracerPriority.t_error])

def T(

...)

T( (str) [, (TracerPriority)=rosetta.basic.basic.TracerPriority.t_info]) -> Tracer : T is special function for assign tracer property on the static object.

C++ signature : basic::Tracer {lvalue} T(std::string [,basic::TracerPriority=rosetta.basic.basic.TracerPriority.t_info])

def Warning(

...)

Warning([ (TracerPriority)priority=rosetta.basic.basic.TracerPriority.t_warning]) -> Tracer : Predefined Warning tracer.

C++ signature : basic::Tracer {lvalue} Warning([ basic::TracerPriority=rosetta.basic.basic.TracerPriority.t_warning])

def angle_in_range(

...)

angle_in_range( (float)ang) -> None : taken from wobble.cc

C++ signature : void angle_in_range(double {lvalue})

def calc_quadratic(

...)

calc_quadratic( (float)a, (float)b, (float)c, (float)n1, (float)n2) -> None : basic/basic.hh:29

C++ signature : void calc_quadratic(double,double,double,double {lvalue},double {lvalue})

def get_boolean_option(

...)

get_boolean_option( (str)arg1) -> bool :

C++ signature : bool get_boolean_option(std::string)

def get_boolean_vector_option(

...)

get_boolean_vector_option( (str)arg1) -> vector1_bool :

C++ signature : utility::vector1 > get_boolean_vector_option(std::string)

def get_file_option(

...)

get_file_option( (str)arg1) -> str :

C++ signature : std::string get_file_option(std::string)

def get_file_vector_option(

...)

get_file_vector_option( (str)arg1) -> vector1_string :

C++ signature : utility::vector1 > get_file_vector_option(std::string)

def get_integer_option(

...)

get_integer_option( (str)arg1) -> int :

C++ signature : int get_integer_option(std::string)

def get_integer_vector_option(

...)

get_integer_vector_option( (str)arg1) -> vector1_int :

C++ signature : utility::vector1 > get_integer_vector_option(std::string)

def get_pymol_chain(

...)

get_pymol_chain( (int)i) -> str : basic/pymol_chains.hh:28

C++ signature : char get_pymol_chain(unsigned long)

def get_pymol_chain_index_1(

...)

get_pymol_chain_index_1( (str)c) -> int : basic/pymol_chains.hh:30

C++ signature : unsigned long get_pymol_chain_index_1(char)

def get_pymol_num_unique_ids(

...)

get_pymol_num_unique_ids() -> int : basic/pymol_chains.hh:26

C++ signature : unsigned long get_pymol_num_unique_ids()

def get_real_option(

...)

get_real_option( (str)arg1) -> float :

C++ signature :
    double get_real_option(std::string)

get_real_option( (str)arg1) -> vector1_Real :

C++ signature :
    utility::vector1<double, std::allocator<double> > get_real_option(std::string)

def get_string_option(

...)

get_string_option( (str)arg1) -> str :

C++ signature : std::string get_string_option(std::string)

def get_string_vector_option(

...)

get_string_vector_option( (str)arg1) -> vector1_string :

C++ signature : utility::vector1 > get_string_vector_option(std::string)

def get_usage_from_procfilesystem(

...)

get_usage_from_procfilesystem( (OStream)mem_report) -> None : basic/MemTracer.hh:49

C++ signature : void get_usage_from_procfilesystem(std::ostream {lvalue})

def handles_metric_value(

...)

handles_metric_value( (MetricValueBase)metric_value) -> bool : check whether a MetricValue can be written to or read from a stream

C++ signature : bool handles_metric_value(basic::MetricValueBase)

def init(

...)

init() -> None : set global 'init_was_called' to true

C++ signature : void init()

def interpolate_2d_func_of_angles(

...)

interpolate_2d_func_of_angles( (float)x, (float)y, (object)xy_func, (float)val, (float)dval_dx, (float)dval_dy) -> None : /////////////////////////////////////////////////////////////////////////////

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 "

@remarks

 !!! assumes 10 degree bins in both dimensions of xy_func

@references

ctsa 8-19-03

//////////////////////////////////////////////////////////////////////////////

C++ signature : void interpolate_2d_func_of_angles(double,double,ObjexxFCL::FArray2A,double {lvalue},double {lvalue},double {lvalue})

def interpolate_bilinear(

...)

interpolate_bilinear( (int)xbin, (int)xbin_next, (float)xd, (int)ybin, (int)ybin_next, (float)yd, (object)xy_func, (int)xbin_count, (int)ybin_count, (float)binrange, (bool)angles, (float)val, (float)dval_dx, (float)dval_dy) -> None : /////////////////////////////////////////////////////////////////////////////

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 "

@remarks

@references

ctsa 8-19-03

//////////////////////////////////////////////////////////////////////////////

C++ signature : void interpolate_bilinear(int,int,double,int,int,double,ObjexxFCL::FArray2A,int,int,double,bool,double {lvalue},double {lvalue},double {lvalue})

def interpolate_bilinear_by_value(

...)

interpolate_bilinear_by_value( (float)x0y0, (float)x1y0, (float)x0y1, (float)x1y1, (float)xd, (float)yd, (float)binrange, (bool)angles, (float)val, (float)dval_dx, (float)dval_dy) -> None : basic/interpolate.hh:112

C++ signature : void interpolate_bilinear_by_value(double,double,double,double,double,double,double,bool,double {lvalue},double {lvalue},double {lvalue})

def interpolate_get_angle_bins(

...)

interpolate_get_angle_bins( (float)x, (float)binrange, (int)xbin, (int)xbin_next, (float)xd) -> None : /////////////////////////////////////////////////////////////////////////////

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'

@remarks

@references

//////////////////////////////////////////////////////////////////////////////

C++ signature : void interpolate_get_angle_bins(double,double,int {lvalue},int {lvalue},double {lvalue})

def interpolate_trilinear(

...)

interpolate_trilinear( (int)xbin, (int)xbin_next, (float)xd, (int)ybin, (int)ybin_next, (float)yd, (int)zbin, (int)zbin_next, (float)zd, (object)xyz_func, (int)xbin_count, (int)ybin_count, (int)zbin_count, (float)binrange, (bool)angles, (float)val, (float)dval_dx, (float)dval_dy, (float)dval_dz) -> None : basic/interpolate.hh:351

C++ signature : void interpolate_trilinear(int,int,double,int,int,double,int,int,double,ObjexxFCL::FArray3A,int,int,int,double,bool,double {lvalue},double {lvalue},double {lvalue},double {lvalue})

def interpolate_trilinear_by_value(

...)

interpolate_trilinear_by_value( (float)x0y0z0, (float)x1y0z0, (float)x0y1z0, (float)x1y1z0, (float)x0y0z1, (float)x1y0z1, (float)x0y1z1, (float)x1y1z1, (float)xd, (float)yd, (float)zd, (float)binrange, (bool)angles, (float)val, (float)dval_dx, (float)dval_dy, (float)dval_dz) -> None : basic/interpolate.hh:156

C++ signature : void interpolate_trilinear_by_value(double,double,double,double,double,double,double,double,double,double,double,double,bool,double {lvalue},double {lvalue},double {lvalue},double {lvalue})

def periodic_range(

...)

periodic_range( (float)a, (float)x) -> float : basic/basic.hh:50

C++ signature : double periodic_range(double,double)

def prof_reset(

...)

prof_reset() -> None : basic/prof.hh:473

C++ signature : void prof_reset()

def prof_show(

...)

prof_show() -> None : basic/prof.hh:475

C++ signature : void prof_show()

def prof_start_function_body(

...)

prof_start_function_body( (ProfTag)tag) -> None : basic/prof.hh:437

C++ signature : void prof_start_function_body(basic::ProfTag)

def prof_stop_function_body(

...)

prof_stop_function_body( (ProfTag)tag) -> None : basic/prof.hh:453

C++ signature : void prof_stop_function_body(basic::ProfTag)

def read_metric_value(

...)

read_metric_value( (std_istream)is) -> MetricValueBase : read a MetricValue from a stream, returns NULL if unsuccessful

C++ signature :
    boost::shared_ptr<basic::MetricValueBase> read_metric_value(std::istream {lvalue})

read_metric_value( (std_istream)is, (MetricValueBase)metric_value) -> bool : read a MetricValue from a stream, returns true if successful

C++ signature :
    bool read_metric_value(std::istream {lvalue},basic::MetricValueBase {lvalue})

def set_boolean_option(

...)

set_boolean_option( (str)arg1, (bool)arg2) -> None :

C++ signature : void set_boolean_option(std::string,bool)

def set_boolean_vector_option(

...)

set_boolean_vector_option( (str)arg1, (vector1_bool)arg2) -> None :

C++ signature : void set_boolean_vector_option(std::string,utility::vector1 >)

def set_file_option(

...)

set_file_option( (str)arg1, (str)arg2) -> None :

C++ signature : void set_file_option(std::string,std::string)

def set_file_vector_option(

...)

set_file_vector_option( (str)arg1, (vector1_string)arg2) -> None :

C++ signature : void set_file_vector_option(std::string,utility::vector1 >)

def set_integer_option(

...)

set_integer_option( (str)arg1, (int)arg2) -> None :

C++ signature : void set_integer_option(std::string,int)

def set_integer_vector_option(

...)

set_integer_vector_option( (str)arg1, (vector1_int)arg2) -> None :

C++ signature : void set_integer_vector_option(std::string,utility::vector1 >)

def set_real_option(

...)

set_real_option( (str)arg1, (float)arg2) -> None :

C++ signature :
    void set_real_option(std::string,double)

set_real_option( (str)arg1, (vector1_Real)arg2) -> None :

C++ signature :
    void set_real_option(std::string,utility::vector1<double, std::allocator<double> >)

def set_string_option(

...)

set_string_option( (str)arg1, (str)arg2) -> None :

C++ signature : void set_string_option(std::string,std::string)

def set_string_vector_option(

...)

set_string_vector_option( (str)arg1, (vector1_string)arg2) -> None :

C++ signature : void set_string_vector_option(std::string,utility::vector1 >)

def show_time(

...)

show_time( (Tracer)tr, (str)msg) -> None : basic/prof.hh:500

C++ signature : void show_time(basic::Tracer {lvalue},std::string)

def subtract_degree_angles(

...)

subtract_degree_angles( (float)a, (float)b) -> float : basic/basic.hh:36

C++ signature : double subtract_degree_angles(double,double)

def subtract_radian_angles(

...)

subtract_radian_angles( (float)a, (float)b) -> float : basic/basic.hh:43

C++ signature : double subtract_radian_angles(double,double)

def unsigned_periodic_range(

...)

unsigned_periodic_range( (float)a, (float)x) -> float : a is restricted to [0.,x), assuming that a=a+n*x,, n=any integer

C++ signature : double unsigned_periodic_range(double,double)

def was_init_called(

...)

was_init_called() -> bool : return true if core::init was already called and false otherwise

C++ signature : bool was_init_called()

def write_metric_value(

...)

write_metric_value( (OStream)os, (MetricValueBase)metric_value) -> bool : 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 int Int std::size_t std::size_t bool Bool <0 or 1> utility::vector1 Real[ ... ] utility::vector1 Int[ ... ] utility::vector1 size_t[ ... ] utility::vector1 Bool[ ... ]

C++ signature : bool write_metric_value(std::ostream {lvalue},basic::MetricValueBase)

Classes

class ComparingTracer

basic/ComparingTracer.hh:42

Ancestors (in MRO)

Methods

def __init__(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.__init__

init( (object)arg1, (str)file_name) -> None : basic/ComparingTracer.hh:44

C++ signature : void init(_object*,std::string)

def is_flushed(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.is_flushed

is_flushed( (basic_otstream_T_char_std_char_traits_T_char_T__T)arg1) -> bool : Return true if inner string buffer is empty.

C++ signature : bool is_flushed(basic::basic_otstream > {lvalue})

class ComparingTracerAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (ComparingTracerAP)arg1) -> ComparingTracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class ComparingTracerCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (ComparingTracerCAP)arg1) -> ComparingTracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class DynamicProfileThis

basic/prof.hh:489

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1, (str)prof_tag) -> None : basic/prof.hh:491

C++ signature :
    void __init__(_object*,std::string)

init( (object)arg1, (DynamicProfileThis)) -> None : basic/prof.hh:489

C++ signature :
    void __init__(_object*,basic::DynamicProfileThis)

class DynamicProfileThisAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (DynamicProfileThisAP)arg1) -> DynamicProfileThis :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class DynamicProfileThisCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (DynamicProfileThisCAP)arg1) -> DynamicProfileThis :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class Emitter

Lightweight class to ease writting YAML documents (http://yaml.org) YAML is a structured data format, a more human-readable alternative to XML. I use the terms "map" and "list" here, but you may also see "mapping" and "sequence". The former is a series of key : value pairs, while the latter is a simple series of items. This class is not entirely able to enforce the generation of valid YAML -- you can still e.g. write a key : value pair in the middle of a list. It will print a warning message but will otherwise try to continue on. YAML documents have optional explicit start/end markers; if the emitter supports them, they will be auto-generated when the class is initialized and when you're finished and you call end(). Whitespace is YAML documents is semi-significant. By default, this class will try to pretty-print, showing the depth of nesting through indentation. When starting a new list or map, you can request that it not be indented (i.e., be printed all on one line), but all lists and maps nested inside it will also be printed without linebreaks, regardless of the requested indentation. YAML refers to these two styles as "block" and "flow", respectively.

Ancestors (in MRO)

  • Emitter
  • Boost.Python.instance
  • __builtin__.object

Methods

def depth(

...)

depth( (Emitter)arg1) -> int : Number of closing brackets/braces required to end document (non-negative)

C++ signature : int depth(basic::Emitter {lvalue})

def end(

...)

end( (Emitter)arg1 [, (int)desired_depth=0]) -> None : By default, closes all open maps/lists, ending the document.

C++ signature : void end(basic::Emitter {lvalue} [,unsigned long=0])

def end_list(

...)

end_list( (Emitter)arg1) -> None : Counterpart to start_list() -- writes closing bracket.

C++ signature : void end_list(basic::Emitter {lvalue})

def end_map(

...)

end_map( (Emitter)arg1) -> None : Counterpart to start_map() -- writes closing brace.

C++ signature : void end_map(basic::Emitter {lvalue})

def flush(

...)

flush( (Emitter)arg1) -> None : Flush the underlying output stream.

C++ signature : void flush(basic::Emitter {lvalue})

def set_indent(

...)

set_indent( (Emitter)arg1, (int)num_spaces) -> None : Number of spaces used for indenting. Default is one.

C++ signature : void set_indent(basic::Emitter {lvalue},int)

def start_doc(

...)

start_doc( (Emitter)arg1) -> None : Start a new document, ending the previous one first if necessary. A no-op for some types of output (e.g. JSON) that don't allow multiple documents.

C++ signature :
    void start_doc(basic::Emitter {lvalue})

start_doc( (Emitter)arg1) -> None :

C++ signature :
    void start_doc(boost::shared_ptr<basic::Emitter> {lvalue})

def start_list(

...)

start_list( (Emitter)arg1 [, (bool)indent=True]) -> None : Write method for use inside lists / arrays

C++ signature :
    void start_list(basic::Emitter {lvalue} [,bool=True])

start_list( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_list(basic::Emitter {lvalue},std::string [,bool=True])

start_list( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_list(basic::Emitter {lvalue},char const* [,bool=True])

def start_map(

...)

start_map( (Emitter)arg1 [, (bool)indent=True]) -> None : Write method for use inside lists / arrays

C++ signature :
    void start_map(basic::Emitter {lvalue} [,bool=True])

start_map( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_map(basic::Emitter {lvalue},std::string [,bool=True])

start_map( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_map(basic::Emitter {lvalue},char const* [,bool=True])

class EmitterAP

Ancestors (in MRO)

  • EmitterAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EmitterAP)arg1) -> Emitter :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class EmitterCAP

Ancestors (in MRO)

  • EmitterCAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (EmitterCAP)arg1) -> Emitter :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class JsonEmitter

/////////////////////////////////////////////////////////////////////////// Lightweight class to ease writting JSON documents, a subset of YAML (http://json.org) Using this class is not recommended -- use YamlEmitter instead.

JSON is JavaScript Object Notation, the format for object and array literals in the JavaScript language. It also looks a great deal like nested Python dicts and lists, except for the special JSON values true, false, and null. (Python uses True, False, and None instead. Otherwise, JSON can be embedded directly into Python scripts.)

JSON is legal subset of YAML, but leaves out much of YAML's complexity and advanced features. At the present time, there appears to be more library support for JSON than for YAML, especially for reading and parsing. (Both are fairly easy to write, as demonstrated here.)

The topmost level of every valid JSON document consists of exactly one map, which is automatically started for you when the class is initialized. When you're finished you should call end(), and then probably flush().

Whitespace is JSON documents is not significant. By default, this class will try to pretty-print, showing the depth of nesting through indentation. When starting a new list or map, you can request that it not be indented (i.e., be printed all on one line), but all lists and maps nested inside it will also be printed without linebreaks, regardless of the requested indentation.

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1, (OStream)out) -> None : basic/Emitter.hh:356

C++ signature : void init(_object*,std::ostream {lvalue})

def depth(

...)

Inheritance: Emitter.depth

depth( (Emitter)arg1) -> int : Number of closing brackets/braces required to end document (non-negative)

C++ signature : int depth(basic::Emitter {lvalue})

def end(

...)

Inheritance: Emitter.end

end( (Emitter)arg1 [, (int)desired_depth=0]) -> None : By default, closes all open maps/lists, ending the document.

C++ signature : void end(basic::Emitter {lvalue} [,unsigned long=0])

def end_list(

...)

Inheritance: Emitter.end_list

end_list( (Emitter)arg1) -> None : Counterpart to start_list() -- writes closing bracket.

C++ signature : void end_list(basic::Emitter {lvalue})

def end_map(

...)

Inheritance: Emitter.end_map

end_map( (Emitter)arg1) -> None : Counterpart to start_map() -- writes closing brace.

C++ signature : void end_map(basic::Emitter {lvalue})

def flush(

...)

Inheritance: Emitter.flush

flush( (Emitter)arg1) -> None : Flush the underlying output stream.

C++ signature : void flush(basic::Emitter {lvalue})

def set_indent(

...)

Inheritance: Emitter.set_indent

set_indent( (Emitter)arg1, (int)num_spaces) -> None : Number of spaces used for indenting. Default is one.

C++ signature : void set_indent(basic::Emitter {lvalue},int)

def start_doc(

...)

Inheritance: Emitter.start_doc

start_doc( (JsonEmitter)arg1) -> None : JSON doesn't support multiple documents, so this just calls end(1) to return you to the top (least-nested) level.

C++ signature : void start_doc(basic::JsonEmitter {lvalue})

def start_list(

...)

Inheritance: Emitter.start_list

start_list( (Emitter)arg1 [, (bool)indent=True]) -> None : Write method for use inside lists / arrays

C++ signature :
    void start_list(basic::Emitter {lvalue} [,bool=True])

start_list( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_list(basic::Emitter {lvalue},std::string [,bool=True])

start_list( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_list(basic::Emitter {lvalue},char const* [,bool=True])

def start_map(

...)

Inheritance: Emitter.start_map

start_map( (Emitter)arg1 [, (bool)indent=True]) -> None : Write method for use inside lists / arrays

C++ signature :
    void start_map(basic::Emitter {lvalue} [,bool=True])

start_map( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_map(basic::Emitter {lvalue},std::string [,bool=True])

start_map( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_map(basic::Emitter {lvalue},char const* [,bool=True])

class JsonEmitterAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (JsonEmitterAP)arg1) -> JsonEmitter :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class JsonEmitterCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (JsonEmitterCAP)arg1) -> JsonEmitter :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class MemTracer

basic/MemTracer.hh:51

Ancestors (in MRO)

Methods

def __init__(

...)

Inheritance: Tracer.__init__

init( (object)arg1 [, (TracerPriority)priority=rosetta.basic.basic.TracerPriority.t_info [, (bool)muted_by_default=True]]) -> None : basic/MemTracer.hh:55

C++ signature : void init(object* [,basic::TracerPriority=rosetta.basic._basic.TracerPriority.t_info [,bool=True]])

def channel(

...)

Inheritance: Tracer.channel

channel( (Tracer)arg1) -> str : basic/Tracer.hh:189

C++ signature : std::string channel(basic::Tracer {lvalue})

def flush_all_channels(

...)

Inheritance: Tracer.flush_all_channels

flush_all_channels( (Tracer)arg1) -> None : flush tracer buffer and flush buffers of all sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace

C++ signature : void flush_all_channels(basic::Tracer {lvalue})

def init(

...)

Inheritance: Tracer.init

init( (Tracer)arg1, (Tracer)tr) -> None : re-init using data from another tracer object.

C++ signature : void init(basic::Tracer {lvalue},basic::Tracer)

def is_flushed(

...)

Inheritance: Tracer.is_flushed

is_flushed( (basic_otstream_T_char_std_char_traits_T_char_T__T)arg1) -> bool : Return true if inner string buffer is empty.

C++ signature : bool is_flushed(basic::basic_otstream > {lvalue})

def priority(

...)

Inheritance: Tracer.priority

priority( (Tracer)arg1) -> int : get/set tracer priority level.

C++ signature :
    int priority(basic::Tracer {lvalue})

priority( (Tracer)arg1, (int)priority) -> None : basic/Tracer.hh:187

C++ signature :
    void priority(basic::Tracer {lvalue},int)

def visible(

...)

Inheritance: Tracer.visible

visible( (Tracer)arg1) -> bool : Is this tracer currently visible?.

C++ signature :
    bool visible(basic::Tracer {lvalue})

visible( (Tracer)arg1, (int)priority) -> bool : is this tracer visible, if it used the given priority value?

C++ signature :
    bool visible(basic::Tracer {lvalue},int)

class MemTracerAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (MemTracerAP)arg1) -> MemTracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class MemTracerCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (MemTracerCAP)arg1) -> MemTracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class MetricValueBase

basic/MetricValue.hh:43

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def clone(

...)

clone( (MetricValueBase)arg1) -> MetricValueBase : basic/MetricValue.hh:48

C++ signature :
    boost::shared_ptr<basic::MetricValueBase> clone(basic::MetricValueBase {lvalue})

clone( (MetricValueBase)arg1) -> MetricValueBase :

C++ signature :
    boost::shared_ptr<basic::MetricValueBase> clone(MetricValueBase_exposer_callback {lvalue})

class MetricValueBaseAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (MetricValueBaseAP)arg1) -> MetricValueBase :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class MetricValueBaseCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (MetricValueBaseCAP)arg1) -> MetricValueBase :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class ProfTag

not intended for profiling inside tight loops the clock() routine currently being used has fairly crappy resolution and it will introduce some small overhead with the function calls and the if-check even if not using -profile on the command line you can wrap it around large-ish chunks of code, like fullatom_energy or rotamer_trials... A simple setup for timing code fragments. Probably not optimal timing functions -- I'm open to suggestions. looks like (see eg fullatom_energy or scorefxn) PROF_START( prof::TAG ); PROF_STOP( prof::TAG ); where TAG is in the enum "Prof_tag" below (feel free to add new ones) also add to tag2string if you want friendly output. PROF_STOP checks the time and increments the total time assigned to TAG 2. later on, in your simulation code you can do: prof_reset(); -- miscellaneous simulation -- prof_show(); The final call to prof::show() will display the time usage measured by all the PROF_* calls between reset() and show()

Ancestors (in MRO)

  • ProfTag
  • Boost.Python.enum
  • __builtin__.int
  • __builtin__.object

Class variables

var ABINITIO

var APPLY_BB_MOVE

var APPLY_MOVE

var APPLY_SC_MOVE

var ARCHIVE_BLOCK_FILE

var ARCHIVE_CRITICAL_JOBSCOMPLETE

var ARCHIVE_EVALUATORS

var ARCHIVE_EVAL_DECOYS

var ARCHIVE_FILL_POSE

var ARCHIVE_GEN_BATCH

var ARCHIVE_JOBSCOMPLETE

var ARCHIVE_READ_DECOYS

var ARCHIVE_SCORE_POSE

var ARCHIVE_SYNC_BATCHES

var ATOM_TREE_UPDATE_INTERNAL_COORDS

var ATOM_TREE_UPDATE_XYZ_COORDS

var BACKRUB_MOVER

var CANONICALMOVER_WRITE_TO_FILE

var CA_DME_EVALUATION

var CA_RMSD_EVALUATION

var CCD_CLOSE

var CHECK_COMM_SIZE

var CHEMICAL_MAKE_POSE

var COMM_REDUCE_SIZE

var CONFORMATION_COPY

var CONFORMATION_DETECT_DISULF

var CONFORMATION_FIX_DISULF

var CONSTRAINT_SCORE

var CONSTRAINT_SET_COPY

var CONSTRUCT_DISTANCE_MATRIX

var COPY_COORDS

var DALPHABALL

var DALPHABALL_DERIV

var DATA_STORAGE

var DFUNC

var ENERGIES_COPY

var ENERGY_ENVPAIR_POTENTIAL

var ENERGY_GRAPH_COPY

var FACTS_GET_ALL_BORN_RADII

var FACTS_ROTAMER_BACKGROUND_ENERGIES

var FACTS_ROTAMER_PAIR_ENERGIES

var FACTS_SETUP_FOR_PACKING

var FARRAY_MANIPULATION

var FINALIZE

var FIND_SUGAR_AND_SUITE_FRAGS_I

var FIND_SUGAR_AND_SUITE_FRAGS_II

var FRAGMENTPICKING

var FRAGMENTPICKING_ATOMPAIR_SCORE

var FRAGMENTPICKING_CANDIDATES_COLLECTING

var FRAGMENTPICKING_CS_SCORE

var FRAGMENTPICKING_DIHEDRALCONSTR_SCORE

var FRAGMENTPICKING_PHIPSI_SCORE

var FRAGMENTPICKING_PROFILE_CAHING

var FRAGMENTPICKING_PROFILE_SCORE

var FRAGMENTPICKING_READ_VALL

var FRAGMENTPICKING_SECONDARY_SCORE

var FRAGMENT_MOVER

var FUNC

var GB_GET_ALL_BORN_RADII

var GB_SETUP_FOR_PACKING

var GEN_BORN_ROTAMER_BACKGROUND_ENERGIES

var GEN_BORN_ROTAMER_PAIR_ENERGIES

var GET_ENERGIES

var HIERARCHICAL_ADD

var HIERARCHICAL_ADD_ELEM_TO_CACHE

var HIERARCHICAL_EVALUATE

var HIERARCHICAL_FIND

var HIERARCHICAL_FIND_ADDRESS

var HIERARCHICAL_POOL_SIZE

var HIERARCHICAL_ROUND

var HIERARCHICAL_SORT_ADDRESSES

var HIERARCHY_FIND_ADDRESS

var HIERARCHY_GET_NEXT_CANDIDATE

var HIERARCHY_RECV_COORDS

var HIERARCHY_SEND_COORDS

var HIERARCHY_SETUP_TO_RECV

var INITIALIZE

var INITIALIZE_HIERARCHY

var INSERT_FRAGS

var JD2

var JD2_INIT_MOVER

var JD2_OUTPUT

var JD2_SILENT_OUTPUTTER

var KDTREE_CONSTRUCT

var LIB_FULL_PATH

var LOAD_HIERARCHY

var MAKE_BASE_PAIR_MOVE

var MAKE_BASE_STEP_MOVE

var MASTER_PROCESS_NEW_STRUCTURES

var MC_ACCEPT

var MINMOVER_APPLY

var MPIBARRIER

var MPIBARRIER_BEGIN

var MPIBARRIER_END

var MPICANONICALSAMPLING

var MPICOMMCREATION

var MPIH_ADD_FIRST_STRUCTURE

var MPIH_EVAL_AGAINST_NBR

var MPIH_EVAL_CHECK_PROGRESS

var MPIH_EVAL_COMMUNICATE_NEW

var MPIH_PREPARE_WRITE_STRUCTURES

var MPIH_UPDATE_EVAL

var MPIH_WRITE_STRUCT

var MPIPOOLCOMMUNICATION

var MPI_FILE_BUF

var MPI_GATHER_BARRIER

var MPI_JD2_WAITS_FOR_ARCHIVE

var MPI_MASTER_BCAST_COORDS

var MPI_MASTER_BCAST_NEW_COMM_SIZE

var MPI_MASTER_BCAST_NEW_POOL_RANKS

var MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD

var MPI_MASTER_BCAST_WINNING_RANKS

var MPI_MASTER_BCAST_WINNING_STRUCTURES

var MPI_NOTIFY_ARCHIVE

var MPI_POOL_MASTER_THINKS

var MPI_POOL_SLAVE_THINKS

var MPI_SEND_ACCEPTED

var MPI_SEND_UPDATE

var MPI_SLAVE_REPORT_NEW_COORDS

var MPI_SLAVE_REPORT_SIZES

var MPI_SYNC_POOL_DIFF

var NOESY_ASSIGN_CALIBRATE

var NOESY_ASSIGN_CHEMSHIFT

var NOESY_ASSIGN_CP_GEN_CST

var NOESY_ASSIGN_DECOY_COMP

var NOESY_ASSIGN_DIAGONAL

var NOESY_ASSIGN_DISTANCE

var NOESY_ASSIGN_DIST_APPLY

var NOESY_ASSIGN_DIST_CST_CAST

var NOESY_ASSIGN_DIST_CST_EVAL

var NOESY_ASSIGN_DIST_INIT

var NOESY_ASSIGN_DIST_MAKE_POSE

var NOESY_ASSIGN_DIST_PREP_SCORE

var NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE

var NOESY_ASSIGN_ELIMINATE

var NOESY_ASSIGN_GEN_CST

var NOESY_ASSIGN_INITIAL

var NOESY_ASSIGN_MAP2CB

var NOESY_ASSIGN_MAP2CB_NEW

var NOESY_ASSIGN_NETWORK

var NOESY_ASSIGN_NETWORK_COMPUTE_NK

var NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA

var NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN

var NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE

var NOESY_ASSIGN_NETWORK_PEAK_COUNT

var NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL

var NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN

var NOESY_ASSIGN_NETWORK_TOTAL

var NOESY_ASSIGN_NMR_STRING

var NOESY_ASSIGN_PA_GEN_CST

var NOESY_ASSIGN_READ_INPUT

var NOESY_ASSIGN_REQUIRES_CB_MAPPING

var NOESY_ASSIGN_SYMMETRY

var NOESY_ASSIGN_TOTAL

var NOESY_ASSIGN_UPDATE_PEAK_VOL

var NOESY_ASSIGN_WRITE_ASSIGNMENTS

var NOESY_ASSIGN_WRITE_CST

var PACK_ROTAMERS

var POOL_RMSD_ADD_STRUCTURE

var POOL_RMSD_EVALUATE

var POOL_RMSD_MASTER_EVALUATE

var POSE_COPY

var RG

var RG_LOCAL

var ROTAMER_TRIALS

var SAVE_ARCHIVE

var SAXS

var SCORE

var SCORE_BEGIN_NOTIFY

var SCORE_DOT

var SCORE_END_NOTIFY

var SCORE_FINALIZE

var SCORE_LONG_RANGE_ENERGIES

var SCORE_NEIGHBOR_ENERGIES

var SCORE_ONEBODY_ENERGIES

var SCORE_SETUP

var SECONDARY_STRUCTURE_ENERGY

var SECONDARY_STRUCTURE_HSPAIR_ENERGY

var SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY

var SECONDARY_STRUCTURE_SSPAIR_ENERGY

var SEQUENCE_COMPARISON

var SETUP_NBLIST

var SIDECHAINMCMOVER

var SIDECHAINMOVER

var SILENT_FILL_POSE

var SILENT_FILL_STRUCT

var SILENT_READ_TAG_TEST

var SILENT_SET_POSE_COORDS

var SIMANNEALING

var SIMPLEINTGRAPH

var SORT_POOL

var STAGE1

var STAGE2

var STAGE3

var STAGE4

var STAGE5

var TEST1

var TEST2

var TEST3

var TEST4

var TEST5

var TOTAL

var TRUNCATED_SCORE_EVALUATOR

var UPDATE_RESIDUE_COORDINATES

var UPDATE_RESIDUE_NEIGHBORS

var UPDATE_RESIDUE_TORSIONS

var VDW_ENERGY

var WRITE_DECOYS_TO_HIERARCHY

var WRITE_TO_FILE

var denominator

var imag

var n_prof_tags

var name

var names

var numerator

var real

var values

class ProfileThis

basic/prof.hh:477

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1, (ProfTag)tag) -> None : basic/prof.hh:479

C++ signature :
    void __init__(_object*,basic::ProfTag)

init( (object)arg1, (ProfileThis)) -> None : basic/prof.hh:477

C++ signature :
    void __init__(_object*,basic::ProfileThis)

class ProfileThisAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (ProfileThisAP)arg1) -> ProfileThis :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class ProfileThisCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (ProfileThisCAP)arg1) -> ProfileThis :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class PyTracer

Special PyRosetta friendly Tracer like buffer. Use it to capture Tracer output with set_ios_hook

Ancestors (in MRO)

Methods

def __init__(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.__init__

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def buf(

...)

buf( (PyTracer)arg1) -> str : basic/Tracer.hh:388

C++ signature :
    std::string buf(basic::PyTracer {lvalue})

buf( (PyTracer)arg1, (str)b) -> None : basic/Tracer.hh:389

C++ signature :
    void buf(basic::PyTracer {lvalue},std::string)

def is_flushed(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.is_flushed

is_flushed( (basic_otstream_T_char_std_char_traits_T_char_T__T)arg1) -> bool : Return true if inner string buffer is empty.

C++ signature : bool is_flushed(basic::basic_otstream > {lvalue})

def output_callback(

...)

output_callback( (PyTracer)arg1, (str)) -> None : basic/Tracer.hh:391

C++ signature :
    void output_callback(basic::PyTracer {lvalue},std::string)

output_callback( (PyTracer)arg1, (str)) -> None :

C++ signature :
    void output_callback(PyTracer_exposer_callback {lvalue},std::string)

class PyTracerAP

Ancestors (in MRO)

  • PyTracerAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (PyTracerAP)arg1) -> PyTracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class PyTracerCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (PyTracerCAP)arg1) -> PyTracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

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'

Ancestors (in MRO)

Methods

def __init__(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.__init__

init( (object)arg1 [, (str)channel='' [, (TracerPriority)priority=rosetta.basic.basic.TracerPriority.t_info [, (bool)muted_by_default=False]]]) -> None : Create Tracer object with given channel and priority

C++ signature : void init(object* [,std::string='' [,basic::TracerPriority=rosetta.basic._basic.TracerPriority.t_info [,bool=False]]])

def channel(

...)

channel( (Tracer)arg1) -> str : basic/Tracer.hh:189

C++ signature : std::string channel(basic::Tracer {lvalue})

def flush_all_channels(

...)

flush_all_channels( (Tracer)arg1) -> None : flush tracer buffer and flush buffers of all sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace

C++ signature : void flush_all_channels(basic::Tracer {lvalue})

def init(

...)

init( (Tracer)arg1, (Tracer)tr) -> None : re-init using data from another tracer object.

C++ signature : void init(basic::Tracer {lvalue},basic::Tracer)

def is_flushed(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.is_flushed

is_flushed( (basic_otstream_T_char_std_char_traits_T_char_T__T)arg1) -> bool : Return true if inner string buffer is empty.

C++ signature : bool is_flushed(basic::basic_otstream > {lvalue})

def priority(

...)

priority( (Tracer)arg1) -> int : get/set tracer priority level.

C++ signature :
    int priority(basic::Tracer {lvalue})

priority( (Tracer)arg1, (int)priority) -> None : basic/Tracer.hh:187

C++ signature :
    void priority(basic::Tracer {lvalue},int)

def visible(

...)

visible( (Tracer)arg1) -> bool : Is this tracer currently visible?.

C++ signature :
    bool visible(basic::Tracer {lvalue})

visible( (Tracer)arg1, (int)priority) -> bool : is this tracer visible, if it used the given priority value?

C++ signature :
    bool visible(basic::Tracer {lvalue},int)

class TracerAP

Ancestors (in MRO)

  • TracerAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerAP)arg1) -> Tracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class TracerCAP

Ancestors (in MRO)

  • TracerCAP
  • Boost.Python.instance
  • __builtin__.object

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerCAP)arg1) -> Tracer :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

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.

Ancestors (in MRO)

Methods

def all_tracers(

...)

all_tracers( (TracerManager)arg1) -> object : basic/Tracer.hh:361

C++ signature : std::vector > {lvalue} all_tracers(basic::TracerManager {lvalue})

class TracerManagerAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerManagerAP)arg1) -> TracerManager :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class TracerManagerCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerManagerCAP)arg1) -> TracerManager :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class TracerOptions

data structure to store all system level options for Tracer system.

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

class TracerOptionsAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerOptionsAP)arg1) -> TracerOptions :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class TracerOptionsCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerOptionsCAP)arg1) -> TracerOptions :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class TracerPriority

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).

Ancestors (in MRO)

Class variables

var denominator

var imag

var name

var names

var numerator

var real

var t_debug

var t_error

var t_fatal

var t_info

var t_trace

var t_warning

var values

class TracerToFile

basic/TracerToFile.hh:43

Ancestors (in MRO)

Methods

def __init__(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.__init__

init( (object)arg1, (str)file_name) -> None : basic/TracerToFile.hh:45

C++ signature : void init(_object*,std::string)

def is_flushed(

...)

Inheritance: basic_otstream_T_char_std_char_traits_T_char_T__T.is_flushed

is_flushed( (basic_otstream_T_char_std_char_traits_T_char_T__T)arg1) -> bool : Return true if inner string buffer is empty.

C++ signature : bool is_flushed(basic::basic_otstream > {lvalue})

class TracerToFileAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerToFileAP)arg1) -> TracerToFile :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class TracerToFileCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (TracerToFileCAP)arg1) -> TracerToFile :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class YamlEmitter

/////////////////////////////////////////////////////////////////////////// Emitter for more classically formatted YAML

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1, (OStream)out) -> None : basic/Emitter.hh:232

C++ signature : void init(_object*,std::ostream {lvalue})

def depth(

...)

Inheritance: Emitter.depth

depth( (Emitter)arg1) -> int : Number of closing brackets/braces required to end document (non-negative)

C++ signature : int depth(basic::Emitter {lvalue})

def end(

...)

Inheritance: Emitter.end

end( (Emitter)arg1 [, (int)desired_depth=0]) -> None : By default, closes all open maps/lists, ending the document.

C++ signature : void end(basic::Emitter {lvalue} [,unsigned long=0])

def end_list(

...)

Inheritance: Emitter.end_list

end_list( (Emitter)arg1) -> None : Counterpart to start_list() -- writes closing bracket.

C++ signature : void end_list(basic::Emitter {lvalue})

def end_map(

...)

Inheritance: Emitter.end_map

end_map( (Emitter)arg1) -> None : Counterpart to start_map() -- writes closing brace.

C++ signature : void end_map(basic::Emitter {lvalue})

def flush(

...)

Inheritance: Emitter.flush

flush( (Emitter)arg1) -> None : Flush the underlying output stream.

C++ signature : void flush(basic::Emitter {lvalue})

def set_indent(

...)

Inheritance: Emitter.set_indent

set_indent( (Emitter)arg1, (int)num_spaces) -> None : Number of spaces used for indenting. Default is one.

C++ signature : void set_indent(basic::Emitter {lvalue},int)

def start_doc(

...)

Inheritance: Emitter.start_doc

start_doc( (YamlEmitter)arg1) -> None : Start a new YAML document, ending the previous one first if necessary

C++ signature : void start_doc(basic::YamlEmitter {lvalue})

def start_list(

...)

Inheritance: Emitter.start_list

start_list( (Emitter)arg1 [, (bool)indent=True]) -> None : Write method for use inside lists / arrays

C++ signature :
    void start_list(basic::Emitter {lvalue} [,bool=True])

start_list( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_list(basic::Emitter {lvalue},std::string [,bool=True])

start_list( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_list(basic::Emitter {lvalue},char const* [,bool=True])

def start_map(

...)

Inheritance: Emitter.start_map

start_map( (Emitter)arg1 [, (bool)indent=True]) -> None : Write method for use inside lists / arrays

C++ signature :
    void start_map(basic::Emitter {lvalue} [,bool=True])

start_map( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_map(basic::Emitter {lvalue},std::string [,bool=True])

start_map( (Emitter)arg1, (str)label [, (bool)indent=True]) -> None : Write method for use inside maps / dicts / objects

C++ signature :
    void start_map(basic::Emitter {lvalue},char const* [,bool=True])

class YamlEmitterAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (YamlEmitterAP)arg1) -> YamlEmitter :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class YamlEmitterCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (YamlEmitterCAP)arg1) -> YamlEmitter :

C++ signature : boost::shared_ptr get(boost::weak_ptr)

class basic_otstream_T_char_std_char_traits_T_char_T__T

Base class for Tracer, TracerProxy and UTracer objects.

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def is_flushed(

...)

is_flushed( (basic_otstream_T_char_std_char_traits_T_char_T__T)arg1) -> bool : Return true if inner string buffer is empty.

C++ signature : bool is_flushed(basic::basic_otstream > {lvalue})

class basic_otstream_T_char_std_char_traits_T_char_T__TAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (basic_otstream_T_char_std_char_traits_T_char_TTAP)arg1) -> basic_otstream_T_char_std_char_traits_T_char_TT :

C++ signature : boost::shared_ptr > > get(boost::weak_ptr > >)

class basic_otstream_T_char_std_char_traits_T_char_T__TCAP

Ancestors (in MRO)

Methods

def __init__(

...)

init( (object)arg1) -> None :

C++ signature : void init(_object*)

def get(

...)

get( (basic_otstream_T_char_std_char_traits_T_char_TTCAP)arg1) -> basic_otstream_T_char_std_char_traits_T_char_TT :

C++ signature : boost::shared_ptr > const> get(boost::weak_ptr > const>)