Author: bugman
Date: Sun Nov 4 13:51:00 2007
New Revision: 3401
URL: http://svn.gna.org/viewcvs/relax?rev=3401&view=rev
Log:
Removed dud user functions from 'residue' which remained from the copy of
'sequence'.
Modified:
1.3/prompt/residue.py
Modified: 1.3/prompt/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/residue.py?rev=3401&r1=3400&r2=3401&view=diff
==============================================================================
--- 1.3/prompt/residue.py (original)
+++ 1.3/prompt/residue.py Sun Nov 4 13:51:00 2007
@@ -221,170 +221,6 @@
self.__relax__.generic.sequence.display(run=run)
- def read(self, run=None, file=None, dir=None, num_col=0, name_col=1,
sep=None):
- """Function for reading sequence data.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
-
- file: The name of the file containing the sequence data.
-
- dir: The directory where the file is located.
-
- num_col: The residue number column (the default is 0, ie the first
column).
-
- name_col: The residue name column (the default is 1).
-
- sep: The column separator (the default is white space).
-
-
- Description
- ~~~~~~~~~~~
-
- If no directory is given, the file will be assumed to be in the
current working directory.
-
-
- Examples
- ~~~~~~~~
-
- The following commands will read the sequence data out of a file
called 'seq' where the
- residue numbers and names are in the first and second columns
respectively and assign it to
- the run 'm1'.
-
- relax> sequence.read('m1', 'seq')
- relax> sequence.read('m1', 'seq', num_col=0, name_col=1)
- relax> sequence.read(run='m1', file='seq', num_col=0, name_col=1,
sep=None)
-
-
- The following commands will read the sequence out of the file
'noe.out' which also contains
- the NOE values.
-
- relax> sequence.read('m1', 'noe.out')
- relax> sequence.read('m1', 'noe.out', num_col=0, name_col=1)
- relax> sequence.read(run='m1', file='noe.out', num_col=0, name_col=1)
-
-
- The following commands will read the sequence out of the file
'noe.600.out' where the
- residue numbers are in the second column, the names are in the sixth
column and the columns
- are separated by commas and assign it to the run 'm5'.
-
- relax> sequence.read('m5', 'noe.600.out', num_col=1, name_col=5,
sep=',')
- relax> sequence.read(run='m5', file='noe.600.out', num_col=1,
name_col=5, sep=',')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.read("
- text = text + "run=" + `run`
- text = text + ", file=" + `file`
- text = text + ", dir=" + `dir`
- text = text + ", num_col=" + `num_col`
- text = text + ", name_col=" + `name_col`
- text = text + ", sep=" + `sep` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # The file name.
- if type(file) != str:
- raise RelaxStrError, ('file name', file)
-
- # Directory.
- if dir != None and type(dir) != str:
- raise RelaxNoneStrError, ('directory name', dir)
-
- # Number column.
- if type(num_col) != int:
- raise RelaxIntError, ('residue number column', num_col)
-
- # Name column.
- if type(name_col) != int:
- raise RelaxIntError, ('residue name column', name_col)
-
- # Column separator.
- if sep != None and type(sep) != str:
- raise RelaxNoneStrError, ('column separator', sep)
-
- # Execute the functional code.
- self.__relax__.generic.sequence.read(run=run, file=file, dir=dir,
num_col=num_col, name_col=name_col, sep=sep)
-
-
- def sort(self, run=None):
- """Function for numerically sorting the sequence by residue number.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.sort("
- text = text + "run=" + `run` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # Execute the functional code.
- self.__relax__.generic.sequence.sort(run=run)
-
-
- def write(self, run=None, file=None, dir=None, force=0):
- """Function for writing the sequence to a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
-
- file: The name of the file.
-
- dir: The directory name.
-
- force: A flag which, if set to 1, will cause the file to be
overwritten.
-
-
- Description
- ~~~~~~~~~~~
-
- If no directory name is given, the file will be placed in the
current working directory.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.write("
- text = text + "run=" + `run`
- text = text + ", file=" + `file`
- text = text + ", dir=" + `dir`
- text = text + ", force=" + `force` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # File.
- if type(file) != str:
- raise RelaxStrError, ('file name', file)
-
- # Directory.
- if dir != None and type(dir) != str:
- raise RelaxNoneStrError, ('directory name', dir)
-
- # The force flag.
- if type(force) != int or (force != 0 and force != 1):
- raise RelaxBinError, ('force flag', force)
-
- # Execute the functional code.
- self.__relax__.generic.sequence.write(run=run, file=file, dir=dir,
force=force)
-
# Docstring modification.
#########################
r3401 - /1.3/prompt/residue.py