sd Namespace Reference

Functions
def	syntax

Variables
list	non_numerical_cols
	showfilename = False
	Analyse options. More...
	multifilemode = False
	summode = False
	normalize_sums = False
	normalize_all = False
	offset_sums = False
	offset_all = False
	columnbreak = False
list	columns = []
list	files = []
list	sums = []
string	next_sum_type = ""
	column_name = arg
	sum_type = next_sum_type
list	final_data = []
list	lines = []
	now iterate through files and print columns etc. More...
tuple	file = gzip.open(filename,"r")
	gzipped More...
	donetitles = False
list	names = []
tuple	token = string.split(l)
	SCORE LINE. More...
	Error = False
	SCORE LINE HEADERS. More...
	brokenline = False
	if it does not then ignore this line - we assume it's corrupted More...
	is_nonnumtag = False
	Check columns for correctness. More...
tuple	t = float( token[i] )
	print n,i,token[i] if we're here, the tag is considered a numeric one and thus must pass the float conversion test More...
tuple	newdataline = dict()
	Ignore broken lines! More...
list	combined_data = []
	record the filename as "data" More...
int	sum = 0
	sumactive = False
list	new_combined_data_line = []
tuple	range_data = dict()
tuple	perc_high = dict()
tuple	perc_low = dict()
tuple	value = float(i)

Function Documentation

def sd.syntax

(

)

Variable Documentation

sd.brokenline = False

if it does not then ignore this line - we assume it's corrupted

sd.column_name = arg

sd.columnbreak = False

list sd.columns = []

Referenced by numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.extract_eigenvectors().

list sd.combined_data = []

record the filename as "data"

extract the data itself and append that array to the overall data stack

sd.donetitles = False

sd.Error = False

SCORE LINE HEADERS.

special column

look for names if names match remember index

Referenced by BuildPackagedBindings.copy_tree_contents(), main(), and APDBCMover.read_in_insert_loop_info().

tuple sd.file = gzip.open(filename,"r")

gzipped

plain text

Referenced by add_rosetta_options_0(), BuildBindings.buildModule_All(), BuildBindings.buildModule_One(), BuildBindings.buildModule_UsingCppParser(), BuildBindings.BuildRosettaOnWindows(), ca_to_allatom_main(), BuildBindings.calculate_source_modification_date(), BuildPackagedBindings.ModuleBuilder.compileBindings(), BuildBindings.ModuleBuilder.compileBindings(), tools.CppParser.generate_monolith_main(), BuildBindings.ModuleBuilder.generate_monolith_main(), BuildPackagedBindings.ModuleBuilder.generateBindings(), BuildBindings.ModuleBuilder.generateBindings(), BuildBindings.get_all_rosetta_objs(), utility::io.get_lines_from_file_data(), BuildBindings.getAllRosettaSourceFiles(), exclude.isFileInScons(), BuildBindings.ModuleBuilder.link_monolith_main(), BuildPackagedBindings.ModuleBuilder.linkBindings(), BuildBindings.ModuleBuilder.linkBindings(), predict_ddG.main(), mp_ddG.main(), BuildBindings.main(), TestBindings.main(), main(), make_templates.makeFile(), BuildPackagedBindings.prepareMiniLibs(), BuildBindings.prepareMiniLibs(), predict_ddG.print_ddG_breakdown(), mp_ddG.print_ddG_breakdown(), predict_ddG.print_score_labels_to_file(), mp_ddG.print_score_labels_to_file(), TestBindings.run_test(), BuildBindings.split_obj_file_in_to_chunks(), basic::options.start_files(), stepwise_monte_carlo(), BuildBindings.windows_buildOneNamespace(), and options_class.writeToFile().

list sd.files = []

Referenced by main(), and basic::options.start_file().

list sd.final_data = []

sd.is_nonnumtag = False

Check columns for correctness.

Allow only special columns to have non-numerical values ( see array at the top of this code file) Figure out if the tag is an official non-numeric one

tuple sd.lines = []

now iterate through files and print columns etc.

gzipped

. gzip/bzip support

sd.multifilemode = False

list sd.names = []

Referenced by basic::options.start_files().

list sd.new_combined_data_line = []

tuple sd.newdataline = dict()

Ignore broken lines!

Ok, if we're here, the line is clean and we can go ahead to extract the data

string sd.next_sum_type = ""

list sd.non_numerical_cols

Initial value:

= [
"aln_id",
"user_tag",
"description",
"usid",
"husid",
"__file__"
]

sd.normalize_all = False

sd.normalize_sums = False

sd.offset_all = False

sd.offset_sums = False

tuple sd.perc_high = dict()

tuple sd.perc_low = dict()

tuple sd.range_data = dict()

sd.showfilename = False

Analyse options.

int sd.sum = 0

sd.sum_type = next_sum_type

sd.sumactive = False

sd.summode = False

list sd.sums = []

tuple sd.t = float( token[i] )

print n,i,token[i] if we're here, the tag is considered a numeric one and thus must pass the float conversion test

Referenced by src._extendfunc(), add_rosetta_options_0(), ObjexxFCL::FArray< T >.attach(), ObjexxFCL::format.bite(), ObjexxFCL::CArray< typename >.CArray(), ObjexxFCL::CArrayP< typename >.CArrayP(), utility::options::OptionCollection.cleaned(), ObjexxFCL::FArray1D< double >.dimension(), ObjexxFCL::KeyFArray1D< typename >.dimension(), ObjexxFCL::FArray2D< double >.dimension(), ObjexxFCL::KeyFArray2D< typename >.dimension(), ObjexxFCL::FArray3D< typename >.dimension(), ObjexxFCL::KeyFArray3D< typename >.dimension(), ObjexxFCL::FArray4D< typename >.dimension(), ObjexxFCL::KeyFArray4D< typename >.dimension(), ObjexxFCL::FArray5D< typename >.dimension(), ObjexxFCL::KeyFArray5D< typename >.dimension(), ObjexxFCL::FArray6D< typename >.dimension(), ObjexxFCL::KeyFArray6D< typename >.dimension(), numeric::crick_equations.dz_ddz1(), ObjexxFCL::format.E(), ObjexxFCL.equali(), numeric::model_quality.erfcc(), numeric::statistics.erfcx_y100(), basic::sampling::orientations::Quaternion.euler(), PerformanceBenchmark.execute(), ObjexxFCL::format.F(), ObjexxFCL::FArray1D< double >.FArray1D(), ObjexxFCL::FArray2D< double >.FArray2D(), ObjexxFCL::FArray3D< typename >.FArray3D(), ObjexxFCL::FArray4D< typename >.FArray4D(), ObjexxFCL::FArray5D< typename >.FArray5D(), ObjexxFCL::FArray6D< typename >.FArray6D(), ObjexxFCL.fixed_Fstring_of(), ObjexxFCL.fixed_string_of(), utility.from_string(), ObjexxFCL.Fstring_of(), ObjexxFCL.Fstring_of< std::string >(), ObjexxFCL.general_Fstring_of(), ObjexxFCL.general_string_of(), numeric.hsv_to_rgb(), ObjexxFCL::format.I(), ObjexxFCL::FArray1D< double >.initializer(), ObjexxFCL::KeyFArray1D< typename >.initializer(), ObjexxFCL::FArray2D< double >.initializer(), ObjexxFCL::KeyFArray2D< typename >.initializer(), ObjexxFCL::FArray3D< typename >.initializer(), ObjexxFCL::KeyFArray3D< typename >.initializer(), ObjexxFCL::FArray4D< typename >.initializer(), ObjexxFCL::KeyFArray4D< typename >.initializer(), ObjexxFCL::FArray5D< typename >.initializer(), ObjexxFCL::KeyFArray5D< typename >.initializer(), ObjexxFCL::FArray6D< typename >.initializer(), ObjexxFCL::KeyFArray6D< typename >.initializer(), instantiate_numeric_functions(), ObjexxFCL::Fstring.is_type(), ObjexxFCL.is_type(), ObjexxFCL::FArray< T >.is_uniform(), map_wrapper< Key, Val >.items(), numeric.jacobi_rotation(), ObjexxFCL::KeyFArray1D< typename >.KeyFArray1D(), ObjexxFCL::KeyFArray2D< typename >.KeyFArray2D(), ObjexxFCL::KeyFArray3D< typename >.KeyFArray3D(), ObjexxFCL::KeyFArray4D< typename >.KeyFArray4D(), ObjexxFCL::KeyFArray5D< typename >.KeyFArray5D(), ObjexxFCL::KeyFArray6D< typename >.KeyFArray6D(), map_wrapper< Key, Val >.keys(), numeric::fourier.kf_bfly2(), numeric::fourier.kf_bfly_generic(), ObjexxFCL.lead_zero_Fstring_of(), ObjexxFCL.lead_zero_string_of(), ObjexxFCL.left_Fstring_of(), ObjexxFCL.left_string_of(), ObjexxFCL::format.LJ(), ObjexxFCL.lowercased(), main(), numeric::model_quality.maxsub(), utility::options::OptionCollection.merged(), multiclass_probability(), basic::sampling::orientations::Quaternion.Normalize(), ObjexxFCL.operator!=(), utility::json_spirit::Value_impl< Config >::Variant_converter_visitor.operator()(), ObjexxFCL.operator*(), numeric::sphericalVector< typename >.operator*=(), numeric::xyzTriple< typename >.operator*=(), numeric::xyzVector< T >.operator*=(), ObjexxFCL::CArray< typename >.operator*=(), ObjexxFCL::FArray< T >.operator*=(), ObjexxFCL::CArrayP< typename >.operator*=(), numeric::xyzMatrix< T >.operator*=(), ObjexxFCL.operator+(), numeric::sphericalVector< typename >.operator+=(), numeric::xyzTriple< typename >.operator+=(), numeric::xyzVector< T >.operator+=(), ObjexxFCL::CArray< typename >.operator+=(), ObjexxFCL::FArray< T >.operator+=(), ObjexxFCL::CArrayP< typename >.operator+=(), numeric::xyzMatrix< T >.operator+=(), ObjexxFCL.operator-(), numeric::sphericalVector< typename >.operator-=(), numeric::xyzTriple< typename >.operator-=(), numeric::xyzVector< T >.operator-=(), ObjexxFCL::CArray< typename >.operator-=(), ObjexxFCL::FArray< T >.operator-=(), ObjexxFCL::CArrayP< typename >.operator-=(), numeric::xyzMatrix< T >.operator-=(), ObjexxFCL.operator/(), ObjexxFCL::CArray< typename >.operator/=(), ObjexxFCL::FArray< T >.operator/=(), ObjexxFCL::CArrayP< typename >.operator/=(), numeric.operator<<(), utility::io::ocstream.operator<<(), utility::io::orstream.operator<<(), utility::io::ozstream.operator<<(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.operator<<(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >.operator<<(), ObjexxFCL::CArray< typename >.operator=(), numeric::sphericalVector< typename >.operator=(), numeric::xyzTriple< typename >.operator=(), numeric::xyzVector< T >.operator=(), ObjexxFCL::CArrayP< typename >.operator=(), numeric::xyzMatrix< T >.operator=(), ObjexxFCL.operator>(), ObjexxFCL.operator>=(), numeric.operator>>(), utility::io::icstream.operator>>(), utility::io::irstream.operator>>(), utility::io::izstream.operator>>(), powi(), basic.prof_show(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), basic::YamlEmitter.quote_string(), basic::JsonEmitter.quote_string(), numeric::linear_algebra.qzhes(), numeric::linear_algebra.qzit(), numeric::linear_algebra.qzval(), numeric::linear_algebra.qzvec(), numeric.read_row(), ObjexxFCL::FArray1D< double >.redimension(), ObjexxFCL::KeyFArray1D< typename >.redimension(), ObjexxFCL::FArray2D< double >.redimension(), ObjexxFCL::KeyFArray2D< typename >.redimension(), ObjexxFCL::FArray3D< typename >.redimension(), ObjexxFCL::KeyFArray3D< typename >.redimension(), ObjexxFCL::FArray4D< typename >.redimension(), ObjexxFCL::KeyFArray4D< typename >.redimension(), ObjexxFCL::FArray5D< typename >.redimension(), ObjexxFCL::KeyFArray5D< typename >.redimension(), ObjexxFCL::FArray6D< typename >.redimension(), ObjexxFCL::KeyFArray6D< typename >.redimension(), ObjexxFCL.right_Fstring_of(), ObjexxFCL.right_string_of(), ObjexxFCL::format.RJ(), numeric::model_quality.rmsfitca2(), numeric::model_quality.rmsfitca3(), ObjexxFCL.rvalue_cast(), ObjexxFCL.scientific_Fstring_of(), ObjexxFCL.scientific_string_of(), Solver.select_working_set(), Solver_NU.select_working_set(), sequence_tolerance_main(), src.Set(), sigmoid_train(), numeric::xyzTriple< typename >.square(), numeric::xyzVector< T >.square(), ObjexxFCL::format.SS(), ObjexxFCL.string_of(), utility.string_split(), ObjexxFCL::format.SW(), swap(), numeric::Quaternion< T >.swap(), basic.T(), numeric::kinematic_closure.test_point_value2(), basic::gpu::Timer.Timer(), utility::lua::LuaObject.to(), utility.to_string(), numeric::geometry::BoundingBox< Vector >.translate(), ObjexxFCL::Fstring.type_of(), ObjexxFCL.type_of(), ObjexxFCL.uppercased(), map_wrapper< Key, Val >.values(), src.Vector1(), and numeric::statistics.w_im_y100().

tuple sd.token = string.split(l)

SCORE LINE.

tuple sd.value = float(i)