Author: bugman
Date: Sat Mar 10 01:28:20 2007
New Revision: 3143
URL: http://svn.gna.org/viewcvs/relax?rev=3143&view=rev
Log:
Renamed 'run' to 'pipe' in the 'run' user function class.
The file 'prompt/run.py' was renamed to 'prompt/pipe.py' and all instances of
'run' renamed to
'pipe'. The placing of the user function class into the interpreter
namespace was also updated.
The docstrings of all the user functions where modified to use the new
terminology.
Added:
1.3/prompt/pipe.py
- copied, changed from r3141, 1.3/prompt/run.py
Removed:
1.3/prompt/run.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=3143&r1=3142&r2=3143&view=diff
==============================================================================
--- 1.3/prompt/interpreter.py (original)
+++ 1.3/prompt/interpreter.py Sat Mar 10 01:28:20 2007
@@ -65,7 +65,7 @@
from relax_data import Relax_data
from relax_fit import Relax_fit
from results import Results
-from run import Run
+from pipe import Pipe
from select import Select
from sequence import Sequence
from state import State
@@ -123,7 +123,7 @@
self._Relax_data = Relax_data(relax)
self._Relax_fit = Relax_fit(relax)
self._Results = Results(relax)
- self._Run = Run(relax)
+ self._Pipe = Pipe(relax)
self._Select = Select(relax)
self._Sequence = Sequence(relax)
self._State = State(relax)
@@ -181,7 +181,7 @@
relax_data = self._Relax_data
relax_fit = self._Relax_fit
results = self._Results
- run = self._Run
+ pipe = self._Pipe
select = self._Select
sequence = self._Sequence
state = self._State
Copied: 1.3/prompt/pipe.py (from r3141, 1.3/prompt/run.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pipe.py?p2=1.3/prompt/pipe.py&p1=1.3/prompt/run.py&r1=3141&r2=3143&rev=3143&view=diff
==============================================================================
--- 1.3/prompt/run.py (original)
+++ 1.3/prompt/pipe.py Sat Mar 10 01:28:20 2007
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2006 Edward d'Auvergne
#
+# Copyright (C) 2004-2007 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -20,17 +20,19 @@
#
#
###############################################################################
+# Python module imports.
import sys
+# relax module imports.
import help
from relax_errors import RelaxListStrError, RelaxNoneListError,
RelaxNoneStrError, RelaxStrError
-class Run:
+class Pipe:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for holding the functions for manipulating runs."""
+ """Class for holding the functions for manipulating data pipes."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -39,21 +41,22 @@
self.__relax__ = relax
- def create(self, run=None, run_type=None):
- """Function for setting up a run type.
+ def create(self, pipe_name=None, pipe_type=None):
+ """Function for initialising a data pipe.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
+ pipe_name: The name of the data pipe.
- type: The type of run.
+ pipe_type: The type of data pipe.
Description
~~~~~~~~~~~
- The run name can be any string however the run type can only be one
of the following
+ The data pipe name can be any string however the data pipe type can
only be one of the
+ following:
'jw': Reduced spectral density mapping,
'mf': Model-free analysis,
@@ -65,68 +68,68 @@
Examples
~~~~~~~~
- To set up a model-free analysis run with the name 'm5', type:
+ To set up a model-free analysis data pipe with the name 'm5', type:
- relax> run.create('m5', 'mf')
+ relax> pipe.create('m5', 'mf')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "run.create("
- text = text + "run=" + `run`
- text = text + ", run_type=" + `run_type` + ")"
+ text = sys.ps3 + "pipe.create("
+ text = text + "pipe_name=" + `pipe_name`
+ text = text + ", pipe_type=" + `pipe_type` + ")"
print text
- # The name of the run.
- if type(run) != str:
- raise RelaxStrError, ('run', run)
+ # The name of the data pipe.
+ if type(pipe_name) != str:
+ raise RelaxStrError, ('data pipe name', pipe_name)
- # The run type.
- if type(run_type) != str:
- raise RelaxStrError, ('run_type', run_type)
+ # The data pipe type.
+ if type(pipe_type) != str:
+ raise RelaxStrError, ('data pipe type', pipe_type)
# Execute the functional code.
- self.__relax__.generic.runs.create(run=run, run_type=run_type)
+ self.__relax__.generic.pipes.create(pipe_name=pipe_name,
pipe_type=pipe_type)
- def delete(self, run=None):
- """Function for deleting a run.
+ def delete(self, pipe_name=None):
+ """Function for deleting a data pipe.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- run: The name of the run.
+ pipe_name: The name of the name.
Description
~~~~~~~~~~~
- This function will destroy all data corresponding to the given run.
+ This function will permanently remove the data pipe and all its
contents.
"""
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "run.delete("
- text = text + "run=" + `run` + ")"
+ text = sys.ps3 + "pipe.delete("
+ text = text + "pipe_name=" + `pipe_name` + ")"
print text
- # The run argument.
- if run != None and type(run) != str:
- raise RelaxNoneStrError, ('run', run)
+ # The data pipe name argument.
+ if pipe_name != None and type(pipe_name) != str:
+ raise RelaxNoneStrError, ('data pipe name', pipe_name)
# Execute the functional code.
- self.__relax__.generic.runs.delete(run=run)
+ self.__relax__.generic.pipes.delete(pipe_name=pipe_name)
- def hybridise(self, hybrid=None, runs=None):
- """Function for a hybridised run from a number of other runs.
+ def hybridise(self, hybrid=None, pipes=None):
+ """Create a hybrid data pipe by fusing a number of other data pipes.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- hybrid: The name of the hybrid run to create.
+ hybrid: The name of the hybrid data pipe to create.
- runs: An array containing the names of all runs to hybridise.
+ pipes: An array containing the names of all data pipes to hybridise.
Description
@@ -135,40 +138,40 @@
This user function can be used to construct hybrid models. An
example of the use of a
hybrid model could be if the protein consists of two independent
domains. These two domains
could be analysed separately, each having their own optimised
diffusion tensors. The
- N-terminal domain run could be called 'N_sphere' while the
C-terminal domain could be called
- 'C_ellipsoid'. These two runs could then be hybridised into a run
called 'mixed model' by
- typing
+ N-terminal domain data pipe could be called 'N_sphere' while the
C-terminal domain could be
+ called 'C_ellipsoid'. These two data pipes could then be hybridised
into a single data pipe
+ called 'mixed model' by typing:
- relax> run.hybridise('mixed model', ['N_sphere', 'C_ellipsoid'])
- relax> run.hybridise(hybrid='mixed model', runs=['N_sphere',
'C_ellipsoid'])
+ relax> pipe.hybridise('mixed model', ['N_sphere', 'C_ellipsoid'])
+ relax> pipe.hybridise(hybrid='mixed model', pipes=['N_sphere',
'C_ellipsoid'])
- This hybrid run can then be compared via model selection to a run
where the entire protein
- is assumed to have a single diffusion tensor.
+ This hybrid data pipe can then be compared via model selection to a
data pipe whereby the
+ entire protein is assumed to have a single diffusion tensor.
- The only requirements for runs to be hybridised is that, at minimum,
a sequence has been
- loaded, that the sequence for all hybridised runs is the same, and
that no residue is
- allowed to be selected in two or more runs. The last condition is
to ensure that overlap
- does not occur to allow statistically significant comparisons.
+ The requirements for data pipes to be hybridised is that the
molecules, sequences, and spin
+ systems for all the data pipes is the same, and that no spin system
is allowed to be
+ selected in two or more data pipes. The selections must not overlap
to allow for
+ rigorous statistical comparisons.
"""
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "run.hybridise("
+ text = sys.ps3 + "pipe.hybridise("
text = text + "hybrid=" + `hybrid`
- text = text + ", runs=" + `runs` + ")"
+ text = text + ", pipes=" + `pipes` + ")"
print text
# The hybrid argument.
if hybrid != None and type(hybrid) != str:
- raise RelaxNoneStrError, ('hybrid run', hybrid)
+ raise RelaxNoneStrError, ('hybrid data pipe', hybrid)
- # Runs.
- if type(runs) != list:
- raise RelaxNoneListError, ('runs', runs)
+ # Data pipes.
+ if type(pipes) != list:
+ raise RelaxNoneListError, ('data pipes', pipes)
else:
- for name in runs:
+ for name in pipes:
if type(name) != str:
- raise RelaxListStrError, ('runs', runs)
+ raise RelaxListStrError, ('data pipes', pipes)
# Execute the functional code.
- self.__relax__.specific.hybrid.hybridise(hybrid=hybrid, runs=runs)
+ self.__relax__.specific.hybrid.hybridise(hybrid=hybrid, pipes=pipes)
r3143 - in /1.3/prompt: interpreter.py pipe.py run.py