Author: bugman
Date: Mon Dec 5 15:47:19 2011
New Revision: 15027
URL: http://svn.gna.org/viewcvs/relax?rev=15027&view=rev
Log:
Created the prompt/script front end for the domain user function.
Added:
branches/frame_order_testing/prompt/domain.py
- copied, changed from r15025,
branches/frame_order_testing/prompt/eliminate.py
Modified:
branches/frame_order_testing/prompt/interpreter.py
Copied: branches/frame_order_testing/prompt/domain.py (from r15025,
branches/frame_order_testing/prompt/eliminate.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/prompt/domain.py?p2=branches/frame_order_testing/prompt/domain.py&p1=branches/frame_order_testing/prompt/eliminate.py&r1=15025&r2=15027&rev=15027&view=diff
==============================================================================
--- branches/frame_order_testing/prompt/eliminate.py (original)
+++ branches/frame_order_testing/prompt/domain.py Mon Dec 5 15:47:19 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004, 2009-2010 Edward d'Auvergne
#
+# Copyright (C) 2003, 2004, 2009-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -21,53 +21,43 @@
###############################################################################
# Module docstring.
-"""Module containing the 'eliminate' user function for removing failed
models."""
+"""Module containing the 'domain' user function for defining structural
domains."""
__docformat__ = 'plaintext'
# relax module imports.
from base_class import Basic_class, _build_doc
import arg_check
-from generic_fns import eliminate
-from relax_errors import RelaxFunctionError, RelaxListStrError,
RelaxNoneStrListError, RelaxNoneTupleError
+from generic_fns import domain
+from relax_errors import RelaxListStrError, RelaxNoneStrListError,
RelaxNoneTupleError
from specific_fns.model_free import Model_free
-class Eliminate(Basic_class):
- """Class containing the function for model elimination."""
+class Domain(Basic_class):
+ """Class containing the user function for defining domains."""
- def eliminate(self, function=None, args=None):
+ def domain(self, id=None, spin_id=None):
# Function intro text.
if self._exec_info.intro:
- text = self._exec_info.ps3 + "eliminate("
- text = text + "function=" + repr(function)
- text = text + ", args=" + repr(args) + ")"
+ text = self._exec_info.ps3 + "domain("
+ text = text + "id=" + repr(id)
+ text = text + ", spin_id=" + repr(spin_id) + ")"
print(text)
# The argument checks.
- arg_check.is_func(function, 'function', can_be_none=True)
- if function:
- arg_check.is_tuple(args, 'args')
+ arg_check.is_str(id, 'domain ID string')
+ arg_check.is_str(spin_id, 'spin ID string')
# Execute the functional code.
- eliminate.eliminate(function=function, args=args)
+ domain.define(id=id, spin_id=spin_id)
# The function doc info.
- eliminate._doc_title = "Elimination or rejection of models."
- eliminate._doc_title_short = "Model elimination."
- eliminate._doc_args = [
- ["function", "A user supplied function for model elimination."],
- ["args", "A tuple of arguments for model elimination."]
+ domain._doc_title = "Definition of structural domains."
+ domain._doc_title_short = "Domain definition."
+ domain._doc_args = [
+ ["id", "The domain ID string."],
+ ["spin_id", "The spin ID string of all atomic members of the
domain."]
]
- eliminate._doc_desc = """
- This is used for model validation to eliminate or reject models
prior to model selection. Model validation is a part of mathematical
modelling whereby models are either accepted or rejected.
-
- Empirical rules are used for model rejection and are listed below.
However these can be overridden by supplying a function in the prompt and
scripting modes. The function should accept five arguments, a string
defining a certain parameter, the value of the parameter, the minimisation
instance (ie the residue index if the model is residue specific), and the
function arguments. If the model is rejected, the function should return
True, otherwise it should return False. The function will be executed
multiple times, once for each parameter of the model.
-
- The 'args' keyword argument should be a tuple, a list enclosed in
round brackets, and will be passed to the user supplied function or the
inbuilt function. For a description of the arguments accepted by the inbuilt
functions, see below.
-
- Once a model is rejected, the select flag corresponding to that
model will be set to False so that model selection, or any other function,
will then skip the model.
+ domain._doc_desc = """
+ This is used to define structural domains. Multiple domains can be
defined, and these can overlap. Rather than labelling the currently loaded
spins with the ID string, the spin ID string is stored for later use. This
allows new spins to be loaded later and still be included within the same
domain.
"""
- eliminate._doc_additional = []
- for i in range(len(Model_free.eliminate_doc)):
- eliminate._doc_additional.append(Model_free.eliminate_doc[i])
- _build_doc(eliminate)
+ _build_doc(domain)
Modified: branches/frame_order_testing/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/prompt/interpreter.py?rev=15027&r1=15026&r2=15027&view=diff
==============================================================================
--- branches/frame_order_testing/prompt/interpreter.py (original)
+++ branches/frame_order_testing/prompt/interpreter.py Mon Dec 5 15:47:19
2011
@@ -54,6 +54,7 @@
# User functions.
from angles import Angles
+from domain import Domain
from dx import OpenDX
from eliminate import Eliminate
from fix import Fix
@@ -168,6 +169,7 @@
# Initialise the user functions (those not in user function classes)
angles = Angles(self._exec_info)
+ domain = Domain(self._exec_info)
eliminate = Eliminate(self._exec_info)
fix = Fix(self._exec_info)
reset = Reset(self._exec_info)
@@ -180,6 +182,7 @@
# Place the user functions in the local namespace.
objects['angle_diff_frame'] = angles.angle_diff_frame
objects['calc'] = minimisation.calc
+ objects['domain'] = domain.domain
objects['eliminate'] = eliminate.eliminate
objects['fix'] = fix.fix
objects['grid_search'] = minimisation.grid_search
r15027 - in /branches/frame_order_testing/prompt: domain.py interpreter.py