Author: bugman
Date: Wed Feb 13 15:38:46 2008
New Revision: 4978
URL: http://svn.gna.org/viewcvs/relax?rev=4978&view=rev
Log:
Merged the N-state model pivot_point() and CoM() user functions to a single
CoM analysis function.
Modified:
branches/N_state_model/prompt/n_state_model.py
Modified: branches/N_state_model/prompt/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/n_state_model.py?rev=4978&r1=4977&r2=4978&view=diff
==============================================================================
--- branches/N_state_model/prompt/n_state_model.py (original)
+++ branches/N_state_model/prompt/n_state_model.py Wed Feb 13 15:38:46 2008
@@ -42,59 +42,77 @@
self.__relax__ = relax
- def CoM(self, centre=None):
- """Set the centre of mass (CoM) for the initial position of the
moving domain.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- centre: The optional argument for manually specifying the CoM.
-
-
- Description
- ~~~~~~~~~~~
-
- Prior to the calculation of the pivot to centre of mass (pivot-CoM)
order parameter and
- subsequent cone of motions, both the pivot point and centre of mass
must be specified. This
- function is used to calculate the centre of mass from the selected
parts of the structure
- previously loaded. That is unless the centre keyword argument has
been supplied, in which
- case this vector floating point numbers (of length 3) will be used
as the CoM. This CoM is
- the initial position prior to its N rotations to the positions of
the N states.
-
-
- Examples
- ~~~~~~~~
-
- To set the CoM to the N-terminal domain of a previously loaded PDB
file (the C-terminal
- domain has been deselected), type:
+ def CoM(self, pivot_point=[0.0, 0.0, 0.0], centre=None):
+ """Centre of mass (CoM) analysis.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ pivot_point: The pivot point of the motions between the two domains.
+
+ centre: The optional argument for manually specifying the CoM of
the initial position prior
+ to the N rotations to the positions of the N states.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function is used for analysing the domain motion information
content of the N states
+ from the N-state model. The states do not correspond to physical
states, hence nothing can
+ be extracted from the individual states. This analysis involves the
calculation of the
+ pivot to centre of mass (pivot-CoM) order parameter and subsequent
cone of motions.
+
+ For the analysis, both the pivot point and centre of mass must be
specified. The supplied
+ pivot point must be a vector of floating point numbers of length 3.
If the centre keyword
+ argument is supplied, it must also be a vector of floating point
numbers (of length 3). If
+ the centre argument is not supplied, then the CoM will be calulcated
from the selected parts
+ of a previously loaded structure.
+
+
+ Examples
+ ~~~~~~~~
+
+ To perform an analysis where the pivot is at the origin and the CoM
is set to the N-terminal
+ domain of a previously loaded PDB file (the C-terminal domain has
been deselected), type:
relax> n_state_model.CoM()
- To set the CoM to the position [0, 0, 1], type one of:
-
- relax> n_state_model.CoM([0, 0, 1])
- relax> n_state_model.CoM([0.0, 0.0, 1.0])
+ To perform an analysis where the pivot is at the origin (because the
real pivot has been
+ shifted to this position) and the CoM is at the position [0, 0, 1],
type one of:
+
+ relax> n_state_model.CoM(centre=[0, 0, 1])
relax> n_state_model.CoM(centre=[0.0, 0.0, 1.0])
+ relax> n_state_model.CoM(pivot_point=[0.0, 0.0, 0.0], centre=[0.0,
0.0, 1.0])
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "n_state_model.CoM("
- text = text + "centre=" + `centre` + ")"
- print text
+ text = text + "pivot_point=" + `pivot_point`
+ text = text + ", centre=" + `centre` + ")"
+ print text
+
+ # Pivot point argument.
+ if type(pivot_point) != list:
+ raise RelaxListError, ('pivot point', pivot_point)
+ if len(pivot_point) != 3:
+ raise RelaxLenError, ('pivot point', 3)
+ for i in xrange(len(pivot_point)):
+ if type(pivot_point[i]) != int and type(pivot_point[i]) != float:
+ raise RelaxListNumError, ('pivot point', pivot_point)
# CoM argument.
if type(centre) != list:
- raise RelaxListError, ('centre', centre)
+ raise RelaxListError, ('centre of mass', centre)
if len(centre) != 3:
- raise RelaxLenError, ("centre of mass", 3)
+ raise RelaxLenError, ('centre of mass', 3)
for i in xrange(len(centre)):
if type(centre[i]) != int and type(centre[i]) != float:
raise RelaxListNumError, ('centre of mass', centre)
# Execute the functional code.
- n_state_model_obj.CoM(centre=centre)
+ n_state_model_obj.CoM(pivot_point=pivot_point, centre=centre)
def model(self, N=None, ref=None):
@@ -144,53 +162,6 @@
n_state_model_obj.model_setup(N=N, ref=ref)
- def pivot_point(self, pivot=[0.0, 0.0, 0.0]):
- """Set the pivot point for the domain motions.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- pivot: The pivot point of the motions between the two domains.
-
-
- Description
- ~~~~~~~~~~~
-
- Prior to the calculation of the pivot to centre of mass (pivot-CoM)
order parameter and
- subsequent cone of motions, both the pivot point and centre of mass
must be specified. The
- supplied pivot point must be a vector of floating point numbers of
length 3.
-
-
- Examples
- ~~~~~~~~
-
- To set the pivot point to the origin in the PDB file (because the
real pivot has been
- shifted to this position), type one of:
-
- relax> n_state_model.pivot_point()
- relax> n_state_model.pivot_point([0.0, 0.0, 0.0])
- relax> n_state_model.pivot_point(pivot=[0.0, 0.0, 0.0])
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "n_state_model.pivot_point("
- text = text + "pivot=" + `pivot` + ")"
- print text
-
- # Pivot argument.
- if type(pivot) != list:
- raise RelaxListError, ('pivot', pivot)
- if len(pivot) != 3:
- raise RelaxLenError, ("pivot point", 3)
- for i in xrange(len(pivot)):
- if type(pivot[i]) != int and type(pivot[i]) != float:
- raise RelaxListNumError, ('pivot point', pivot)
-
- # Execute the functional code.
- n_state_model_obj.pivot_point(pivot=pivot)
-
-
def set_domain(self, tensor=None, domain=None):
"""Set the domain label for the alignment tensor.
r4978 - /branches/N_state_model/prompt/n_state_model.py