Rosetta 3.3
Functions | Variables
sd Namespace Reference

Functions

def syntax

Variables

list non_numerical_cols
 showfilename = False
 Analyse options.
 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.
tuple file = gzip.open(filename,"r")
 gzipped
 donetitles = False
list names = []
tuple token = string.split(l)
 SCORE LINE.
 Error = False
 SCORE LINE HEADERS.
 brokenline = False
 if it does not then ignore this line - we assume it's corrupted
 is_nonnumtag = False
 Check columns for correctness.
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
tuple newdataline = dict()
 Ignore broken lines!
list combined_data = []
 record the filename as "data"
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::columnbreak = False
list sd::columns = []
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 main(), and APDBCMover::read_in_insert_loop_info().

tuple sd::file = gzip.open(filename,"r")
list sd::files = []

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

list sd::final_data = []

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

list sd::names = []
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 = ""
Initial value:
00001 [
00002 "aln_id",
00003 "user_tag",
00004 "description",
00005 "usid",
00006 "husid",
00007 "__file__"
00008 ]
sd::offset_all = False
sd::offset_sums = False
tuple sd::perc_high = dict()
tuple sd::perc_low = dict()
tuple sd::range_data = dict()

Analyse options.

int sd::sum = 0
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 numeric::add(), ObjexxFCL::FArray< double >::attach(), ObjexxFCL::fmt::bite(), ObjexxFCL::CArray< T >::CArray(), ObjexxFCL::CArrayP< T >::CArrayP(), utility::options::OptionCollection::cleaned(), ObjexxFCL::KeyFArray6D< T >::dimension(), ObjexxFCL::KeyFArray5D< T >::dimension(), ObjexxFCL::KeyFArray4D< T >::dimension(), ObjexxFCL::KeyFArray3D< T >::dimension(), ObjexxFCL::KeyFArray2D< T >::dimension(), ObjexxFCL::KeyFArray1D< T >::dimension(), ObjexxFCL::FArray6D< T >::dimension(), ObjexxFCL::FArray5D< T >::dimension(), ObjexxFCL::FArray4D< T >::dimension(), ObjexxFCL::FArray3D< T >::dimension(), ObjexxFCL::FArray2D< double >::dimension(), ObjexxFCL::FArray1D< double >::dimension(), ObjexxFCL::fmt::E(), ObjexxFCL::equali(), numeric::model_quality::erfcc(), numeric::statistics::errfc(), Benchmark::execute(), ObjexxFCL::fmt::F(), ObjexxFCL::FArray1D< double >::FArray1D(), ObjexxFCL::FArray2D< double >::FArray2D(), ObjexxFCL::FArray3D< T >::FArray3D(), ObjexxFCL::FArray4D< T >::FArray4D(), ObjexxFCL::FArray5D< T >::FArray5D(), ObjexxFCL::FArray6D< T >::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(), utility::tag::Tag::getOption(), ObjexxFCL::fmt::I(), ObjexxFCL::KeyFArray6D< T >::initializer(), ObjexxFCL::KeyFArray5D< T >::initializer(), ObjexxFCL::KeyFArray4D< T >::initializer(), ObjexxFCL::KeyFArray3D< T >::initializer(), ObjexxFCL::KeyFArray2D< T >::initializer(), ObjexxFCL::KeyFArray1D< T >::initializer(), ObjexxFCL::FArray6D< T >::initializer(), ObjexxFCL::FArray5D< T >::initializer(), ObjexxFCL::FArray4D< T >::initializer(), ObjexxFCL::FArray3D< T >::initializer(), ObjexxFCL::FArray2D< double >::initializer(), ObjexxFCL::FArray1D< double >::initializer(), instantiate_numeric_funs(), ObjexxFCL::is_type(), ObjexxFCL::Fstring::is_type(), ObjexxFCL::FArray< double >::is_uniform(), numeric::jacobi(), numeric::jacobi_rotation(), ObjexxFCL::KeyFArray1D< T >::KeyFArray1D(), ObjexxFCL::KeyFArray2D< T >::KeyFArray2D(), ObjexxFCL::KeyFArray3D< T >::KeyFArray3D(), ObjexxFCL::KeyFArray4D< T >::KeyFArray4D(), ObjexxFCL::KeyFArray5D< T >::KeyFArray5D(), ObjexxFCL::KeyFArray6D< T >::KeyFArray6D(), 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::fmt::LJ(), ObjexxFCL::lowercased(), main(), numeric::model_quality::maxsub(), utility::options::OptionCollection::merged(), numeric::multiply(), ObjexxFCL::operator!=(), numeric::operator!=(), ObjexxFCL::operator*(), ObjexxFCL::FArray< double >::operator*=(), ObjexxFCL::CArrayP< T >::operator*=(), ObjexxFCL::CArray< T >::operator*=(), numeric::xyzVector< T >::operator*=(), numeric::xyzTriple< T >::operator*=(), numeric::xyzMatrix< T >::operator*=(), numeric::sphericalVector< T >::operator*=(), ObjexxFCL::operator+(), ObjexxFCL::FArray< double >::operator+=(), ObjexxFCL::CArrayP< T >::operator+=(), ObjexxFCL::CArray< T >::operator+=(), numeric::xyzVector< T >::operator+=(), numeric::xyzTriple< T >::operator+=(), numeric::xyzMatrix< T >::operator+=(), numeric::sphericalVector< T >::operator+=(), ObjexxFCL::operator-(), ObjexxFCL::FArray< double >::operator-=(), ObjexxFCL::CArrayP< T >::operator-=(), ObjexxFCL::CArray< T >::operator-=(), numeric::xyzVector< T >::operator-=(), numeric::xyzTriple< T >::operator-=(), numeric::xyzMatrix< T >::operator-=(), numeric::sphericalVector< T >::operator-=(), ObjexxFCL::operator/(), ObjexxFCL::FArray< double >::operator/=(), ObjexxFCL::CArrayP< T >::operator/=(), ObjexxFCL::CArray< T >::operator/=(), numeric::operator<(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::operator<<(), utility::io::ozstream::operator<<(), utility::io::orstream::operator<<(), utility::io::ocstream::operator<<(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::operator<<(), numeric::operator<<(), numeric::operator<=(), ObjexxFCL::CArrayP< T >::operator=(), ObjexxFCL::CArray< T >::operator=(), numeric::xyzVector< T >::operator=(), numeric::xyzTriple< T >::operator=(), numeric::xyzMatrix< T >::operator=(), numeric::sphericalVector< T >::operator=(), numeric::operator==(), ObjexxFCL::operator>(), numeric::operator>(), ObjexxFCL::operator>=(), numeric::operator>=(), utility::io::izstream::operator>>(), utility::io::irstream::operator>>(), utility::io::icstream::operator>>(), numeric::operator>>(), basic::prof_show(), basic::JsonEmitter::quote_string(), basic::YamlEmitter::quote_string(), numeric::read_row(), ObjexxFCL::KeyFArray6D< T >::redimension(), ObjexxFCL::KeyFArray5D< T >::redimension(), ObjexxFCL::KeyFArray4D< T >::redimension(), ObjexxFCL::KeyFArray3D< T >::redimension(), ObjexxFCL::KeyFArray2D< T >::redimension(), ObjexxFCL::KeyFArray1D< T >::redimension(), ObjexxFCL::FArray6D< T >::redimension(), ObjexxFCL::FArray5D< T >::redimension(), ObjexxFCL::FArray4D< T >::redimension(), ObjexxFCL::FArray3D< T >::redimension(), ObjexxFCL::FArray2D< double >::redimension(), ObjexxFCL::FArray1D< double >::redimension(), ObjexxFCL::right_Fstring_of(), ObjexxFCL::right_string_of(), ObjexxFCL::fmt::RJ(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), ObjexxFCL::rvalue_cast(), ObjexxFCL::scientific_Fstring_of(), ObjexxFCL::scientific_string_of(), sequence_tolerance_main(), ObjexxFCL::fmt::SS(), ObjexxFCL::string_of(), numeric::subtract(), ObjexxFCL::fmt::SW(), numeric::Quaternion< T >::swap(), basic::T(), utility::to_string(), numeric::geometry::BoundingBox< T >::translate(), ObjexxFCL::type_of(), ObjexxFCL::Fstring::type_of(), and ObjexxFCL::uppercased().

tuple sd::token = string.split(l)

SCORE LINE.

tuple sd::value = float(i)
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