Author: bugman
Date: Wed Mar 14 09:30:56 2007
New Revision: 3188
URL: http://svn.gna.org/viewcvs/relax?rev=3188&view=rev
Log:
Added initial support for the residue user function class.
The file 'prompt/residue.py' was copied from 'prompt/sequence.py' and the
function 'add()' renamed
to 'create' (generating the 'residue.create()' user function). All the other
sequence user
functions still remain unchanged.
Added:
1.3/prompt/residue.py
- copied, changed from r3177, 1.3/prompt/sequence.py
Modified:
1.3/prompt/interpreter.py
Modified: 1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/interpreter.py?rev=3188&r1=3187&r2=3188&view=diff
==============================================================================
--- 1.3/prompt/interpreter.py (original)
+++ 1.3/prompt/interpreter.py Wed Mar 14 09:30:56 2007
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2005 Edward d'Auvergne
#
+# Copyright (C) 2003-2007 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -60,6 +60,7 @@
from monte_carlo import Monte_carlo
from noe import Noe
from palmer import Palmer
+from residue import Residue
from structure import Structure
from pymol import Pymol
from relax_data import Relax_data
@@ -118,6 +119,7 @@
self._Monte_carlo = Monte_carlo(relax)
self._Noe = Noe(relax)
self._Palmer = Palmer(relax)
+ self._Residue = Residue(relax)
self._Structure = Structure(relax)
self._Pymol = Pymol(relax)
self._Relax_data = Relax_data(relax)
@@ -180,6 +182,7 @@
pymol = self._Pymol
relax_data = self._Relax_data
relax_fit = self._Relax_fit
+ residue = self._Residue
results = self._Results
pipe = self._Pipe
select = self._Select
Copied: 1.3/prompt/residue.py (from r3177, 1.3/prompt/sequence.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/residue.py?p2=1.3/prompt/residue.py&p1=1.3/prompt/sequence.py&r1=3177&r2=3188&rev=3188&view=diff
==============================================================================
--- 1.3/prompt/sequence.py (original)
+++ 1.3/prompt/residue.py Wed Mar 14 09:30:56 2007
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004 Edward d'Auvergne
#
+# Copyright (C) 2007 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -26,11 +26,11 @@
from relax_errors import RelaxBinError, RelaxIntError, RelaxNoneStrError,
RelaxStrError
-class Sequence:
+class Residue:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for manipulating sequence data."""
+ """Class for manipulating the residue data."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -39,53 +39,44 @@
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.
+ 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.
- 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.
+
+ 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 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`
+ 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`
- text = text + ", select=" + `select` + ")"
- print text
-
- # The run argument.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
+ text = text + ", res_name=" + `res_name` + ")"
+ print text
# Residue number.
if type(res_num) != int:
@@ -95,12 +86,8 @@
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)
+ # Execute the functional code.
+ residue.create(res_num=res_num, res_name=res_name)
def copy(self, run1=None, run2=None):
r3188 - in /1.3/prompt: interpreter.py residue.py