Author: bugman
Date: Wed Jul 9 10:59:43 2008
New Revision: 6854
URL: http://svn.gna.org/viewcvs/relax?rev=6854&view=rev
Log:
Split up the n_state_model.model() user function.
The new user functions are:
n_state_model.number_of_states()
n_state_model.ref_domain()
n_state_model.setup_model()
Modified:
branches/rdc_analysis/prompt/n_state_model.py
Modified: branches/rdc_analysis/prompt/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/prompt/n_state_model.py?rev=6854&r1=6853&r2=6854&view=diff
==============================================================================
--- branches/rdc_analysis/prompt/n_state_model.py (original)
+++ branches/rdc_analysis/prompt/n_state_model.py Wed Jul 9 10:59:43 2008
@@ -200,51 +200,134 @@
n_state_model_obj.cone_pdb(cone_type=cone_type, scale=scale,
file=file, dir=dir, force=force)
- def model(self, N=None, ref=None):
- """Set up the N-state model by specifying the number of states N and
the reference domain.
+ def number_of_states(self, N=None):
+ """Set the number of states in the N-state model.
Keyword Arguments
~~~~~~~~~~~~~~~~~
N: The number of states.
- ref: The domain which will act as the frame of reference.
-
-
- Description
- ~~~~~~~~~~~
-
- Prior to optimisation, the N-state model must be set up. This
simply involves the setting
- of the number of states N and which of the two domains will act as
the frame of reference.
- The N-states will be rotations of the other domain. To switch the
frame of reference to the
- other domain, transpose the rotation matrices.
-
-
- Examples
- ~~~~~~~~
-
- To set up a 5-state model with 'C' domain being the frame of
reference, type:
-
- relax> n_state_model.model(N=5, ref='C')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "n_state_model.model("
- text = text + "N=" + `N`
- text = text + ", ref=" + `ref` + ")"
+
+ Description
+ ~~~~~~~~~~~
+
+ Prior to optimisation, the number of states in the N-state model can
be specified. If the
+ number of states is not set, then this parameter will be equal to
the number of loaded
+ structures.
+
+
+ Examples
+ ~~~~~~~~
+
+ To set up an 8-state model, type:
+
+ relax> n_state_model.number_of_states(N=8)
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "n_state_model.number_of_states("
+ text = text + "N=" + `N` + ")"
print text
# Number of states argument.
if type(N) != int:
raise RelaxIntError, ('the number of states N', N)
+ # Execute the functional code.
+ n_state_model_obj.number_of_states(N=N)
+
+
+ def ref_domain(self, ref=None):
+ """Set the reference domain for the '2-domain' N-state model.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ ref: The domain which will act as the frame of reference. This is
only valid for the
+ '2-domain' N-state model.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ Prior to optimisation of the '2-domain' N-state model, which of the
two domains will act as
+ the frame of reference must be specified. The N-states will be
rotations of the other
+ domain, so to switch the frame of reference to the other domain
simply transpose the
+ rotation matrices.
+
+
+ Examples
+ ~~~~~~~~
+
+ To set up a 5-state model with 'C' domain being the frame of
reference, type:
+
+ relax> n_state_model.ref_domain(ref='C')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "n_state_model.ref_domain("
+ text = text + "ref=" + `ref` + ")"
+ print text
+
# Ref frame argument.
if type(ref) != str:
raise RelaxStrError, ('reference frame', ref)
# Execute the functional code.
- n_state_model_obj.model_setup(N=N, ref=ref)
+ n_state_model_obj.ref_domain(ref=ref)
+
+
+ def setup_model(self, model=None):
+ """Select the N-state model type and set up the model.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ model: The name of the preset N-state model.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ Prior to optimisation, the N-state model type should be selected.
The preset models are:
+
+ '2-domain' - The N-state model for a system of two domains, where
one domain experiences a
+ a reduced tensor.
+
+ 'population' - The N-state model whereby only populations are
optimised. The structures
+ loaded into relax are assumed to be fixed. I.e. if two domains are
present, the Euler
+ angles for each state are fixed. The parameters of the model
include the weight or
+ probability for each state and the alignment tensor - {p0, p1, ...,
pN, Axx, Ayy, Axy, Axz,
+ Ayz}.
+
+ 'fixed' - The N-state model whereby all motions are fixed and all
populations are fixed to
+ the set probabilities. The parameters of the model are simply the
alignment tensor, {Axx,
+ Ayy, Axy, Axz, Ayz}.
+
+
+ Examples
+ ~~~~~~~~
+
+ To analyse populations of states, type:
+
+ relax> n_state_model.select_model(model='populations')
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "n_state_model.select_model("
+ text = text + "model=" + `model` + ")"
+ print text
+
+ # Model argument.
+ if type(model) != str:
+ raise RelaxStrError, ('model', model)
+
+ # Execute the functional code.
+ n_state_model_obj.select_model(model=model)
def set_domain(self, tensor=None, domain=None):
r6854 - /branches/rdc_analysis/prompt/n_state_model.py