Author: bugman
Date: Thu Nov 22 00:03:47 2007
New Revision: 3778
URL: http://svn.gna.org/viewcvs/relax?rev=3778&view=rev
Log:
Removed all the user functions of prompt.sequence which are not in the
redesign document.
The axed user functions are:
sequence.add()
sequence.copy()
sequnece.delete()
sequence.sort()
These no longer have any use.
Modified:
1.3/prompt/sequence.py
Modified: 1.3/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/sequence.py?rev=3778&r1=3777&r2=3778&view=diff
==============================================================================
--- 1.3/prompt/sequence.py (original)
+++ 1.3/prompt/sequence.py Thu Nov 22 00:03:47 2007
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004 Edward d'Auvergne
#
+# Copyright (C) 2003, 2004, 2007 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -20,8 +20,10 @@
#
#
###############################################################################
+# Python module imports.
import sys
+# relax module imports.
import help
from relax_errors import RelaxBinError, RelaxIntError, RelaxNoneStrError,
RelaxStrError
@@ -37,146 +39,6 @@
# Place relax in the class namespace.
self.__relax__ = relax
-
-
- def add(self, run=None, res_num=None, res_name=None, select=1):
- """Function for adding a residue onto the sequence.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
-
- res_num: The residue number.
-
- res_name: The name of the residue.
-
- select: A flag specifying if the residue should be selected.
-
-
- Description
- ~~~~~~~~~~~
-
- Using this function a new sequence can be generated without having
to load the sequence from
- a file. However if the sequence already exists, the new residue
will be added to the end.
- The same residue number cannot be used more than once.
-
-
- Examples
- ~~~~~~~~
-
- The following sequence of commands will generate the sequence 1 ALA,
2 GLY, 3 LYS and assign
- it to the run 'm3':
-
- relax> run = 'm3'
- relax> sequence.add(run, 1, 'ALA')
- relax> sequence.add(run, 2, 'GLY')
- relax> sequence.add(run, 3, 'LYS')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.add("
- text = text + "run=" + `run`
- text = text + ", res_num=" + `res_num`
- text = text + ", res_name=" + `res_name`
- text = text + ", select=" + `select` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
-
- # Residue number.
- if type(res_num) != int:
- raise RelaxIntError, ('residue number', res_num)
-
- # Residue name.
- if type(res_name) != str:
- raise RelaxStrError, ('residue name', res_name)
-
- # Select flag.
- if type(select) != int or (select != 0 and select != 1):
- raise RelaxBinError, ('select', select)
-
- # Execute the functional code.
- self.__relax__.generic.sequence.add(run=run, res_num=res_num,
res_name=res_name, select=select)
-
-
- def copy(self, run1=None, run2=None):
- """Function for copying the sequence from run1 to run2.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run1: The name of the run to copy the sequence from.
-
- run2: The name of the run to copy the sequence to.
-
-
- Description
- ~~~~~~~~~~~
-
- This function will copy the sequence from 'run1' to 'run2'. 'run1'
must contain sequence
- information, while 'run2' must have no sequence loaded.
-
-
- Examples
- ~~~~~~~~
-
- To copy the sequence from the run 'm1' to the run 'm2', type:
-
- relax> sequence.copy('m1', 'm2')
- relax> sequence.copy(run1='m1', run2='m2')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.copy("
- text = text + "run1=" + `run1`
- text = text + ", run2=" + `run2` + ")"
- print text
-
- # The run1 argument.
- if type(run1) != str:
- raise RelaxStrError, ('run1', run1)
-
- # The run2 argument.
- if type(run2) != str:
- raise RelaxStrError, ('run2', run2)
-
- # Execute the functional code.
- self.__relax__.generic.sequence.copy(run1=run1, run2=run2)
-
-
- def delete(self, run=None):
- """Function for deleting the sequence.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
-
-
- Description
- ~~~~~~~~~~~
-
- This function has the same effect as using the 'delete' function to
delete all residue
- specific data.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.delete("
- 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.delete(run=run)
def display(self, run=None):
@@ -294,29 +156,6 @@
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.
r3778 - /1.3/prompt/sequence.py