Author: bugman
Date: Sun Nov 11 10:57:42 2007
New Revision: 3463
URL: http://svn.gna.org/viewcvs/relax?rev=3463&view=rev
Log:
Removed the prompt.spin module. This will be replaced by the current residue
module instead.
Removed:
1.3/prompt/spin.py
Removed: 1.3/prompt/spin.py
URL: http://svn.gna.org/viewcvs/relax/1.3/prompt/spin.py?rev=3462&view=auto
==============================================================================
--- 1.3/prompt/spin.py (original)
+++ 1.3/prompt/spin.py (removed)
@@ -1,191 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2007 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Python module imports.
-import sys
-
-# relax module imports.
-import help
-from generic_fns import residue
-from relax_errors import RelaxBinError, RelaxIntError, RelaxNoneStrError,
RelaxStrError
-
-
-class Residue:
- def __init__(self, relax):
- # Help.
- self.__relax_help__ = \
- """Class for manipulating the residue data."""
-
- # Add the generic help string.
- self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
-
- # Place relax in the class namespace.
- self.__relax__ = relax
-
-
- def create(self, res_num=None, res_name=None):
- """Function for creating a new residue.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- res_num: The residue number.
-
- res_name: The name of the residue.
-
-
- Description
- ~~~~~~~~~~~
-
- Using this function a new sequence can be generated without using
the sequence user
- functions. However if the sequence already exists, the new residue
will be added to the end
- of the residue list (the residue numbers of this list need not be
sequential). The same
- residue number cannot be used more than once. A corresponding
single spin system will be
- created for this residue. The spin system number and name or
additional spin systems can be
- added later if desired.
-
-
- Examples
- ~~~~~~~~
-
- The following sequence of commands will generate the sequence 1 ALA,
2 GLY, 3 LYS:
-
- relax> residue.create(1, 'ALA')
- relax> residue.create(2, 'GLY')
- relax> residue.create(3, 'LYS')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "residue.create("
- text = text + ", res_num=" + `res_num`
- text = text + ", res_name=" + `res_name` + ")"
- print text
-
- # 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)
-
- # Execute the functional code.
- residue.create(res_num=res_num, res_name=res_name)
-
-
- 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, res_id=None):
- """Function for deleting residues.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- res_id: The residue identifier string.
-
-
- Description
- ~~~~~~~~~~~
-
- This function can be used to delete a single or sets of residues.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "residue.delete("
- text = text + "res_id=" + `res_id` + ")"
- print text
-
- # The residue identifier argument.
- if type(res_id) != str:
- raise RelaxStrError, ('residue identifier', res_id)
-
- # Execute the functional code.
- residue.delete(res_id=res_id)
-
-
- def display(self, run=None):
- """Function for displaying the sequence.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- run: The name of the run.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "sequence.display("
- 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.display(run=run)
r3463 - /1.3/prompt/spin.py