Author: bugman
Date: Wed Dec 7 16:32:01 2011
New Revision: 15044
URL: http://svn.gna.org/viewcvs/relax?rev=15044&view=rev
Log:
Converted the align_tensor.init user function to accept the align_id and
domain arguments.
The domain argument complements the align_tensor.set_domain user function
whereas the align_id arg
is new and is used to associate a tensor with an alignment. This is part of
a redesign of how
alignment tensors are handled, as there can be multiple tensors per alignment
if the molecule is
multi-domain.
Modified:
branches/frame_order_testing/generic_fns/align_tensor.py
branches/frame_order_testing/prompt/align_tensor.py
Modified: branches/frame_order_testing/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/align_tensor.py?rev=15044&r1=15043&r2=15044&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/align_tensor.py (original)
+++ branches/frame_order_testing/generic_fns/align_tensor.py Wed Dec 7
16:32:01 2011
@@ -631,7 +631,7 @@
return data
-def init(tensor=None, params=None, scale=1.0, angle_units='deg',
param_types=0, errors=False):
+def init(tensor=None, params=None, scale=1.0, angle_units='deg',
param_types=0, align_id=None, domain=None, errors=False):
"""Function for initialising the alignment tensor.
@keyword tensor: The alignment tensor identification string.
@@ -642,11 +642,13 @@
@type scale: float
@keyword angle_units: The units for the angle parameters (either 'deg'
or 'rad').
@type angle_units: str
- @keyword param_types: The type of parameters supplied. The flag
values correspond to, 0:
- {Axx, Ayy, Axy, Axz, Ayz}, and 1: {Azz, Axx-yy,
Axy, Axz, Ayz}.
+ @keyword param_types: The type of parameters supplied. The flag
values correspond to, 0: {Axx, Ayy, Axy, Axz, Ayz}, and 1: {Azz, Axx-yy, Axy,
Axz, Ayz}.
@type param_types: int
- @keyword errors: A flag which determines if the alignment tensor
data or its errors are
- being input.
+ @keyword align_id: The alignment ID string that the tensor
corresponds to.
+ @type align_id: str or None
+ @keyword domain: The domain label.
+ @type domain: str or None
+ @keyword errors: A flag which determines if the alignment tensor
data or its errors are being input.
@type errors: bool
"""
@@ -661,6 +663,10 @@
valid_types = ['deg', 'rad']
if not angle_units in valid_types:
raise RelaxError("The alignment tensor 'angle_units' argument " +
repr(angle_units) + " should be either 'deg' or 'rad'.")
+
+ # Check that the domain is defined.
+ if domain and (not hasattr(cdp, 'domain') or domain not in
cdp.domain.keys()):
+ raise RelaxError("The domain '%s' has not been defined. Please use
the domain user function." % domain)
# Add the tensor ID to the current data pipe.
if not hasattr(cdp, 'align_ids'):
@@ -828,6 +834,12 @@
# Unknown parameter combination.
else:
raise RelaxUnknownParamCombError('param_types', param_types)
+
+ # Set the domain and alignment ID.
+ if domain:
+ set_domain(tensor=tensor, domain=domain)
+ if align_id:
+ set_domain(tensor=tensor, align_id=align_id)
def map_bounds(param):
@@ -1789,6 +1801,28 @@
"""
+def set_align_id(tensor=None, align_id=None):
+ """Set the align ID string for the given tensor.
+
+ @keyword tensor: The alignment tensor label.
+ @type tensor: str
+ @keyword align_id: The alignment ID string.
+ @type align_id: str
+ """
+
+ # Loop over the tensors.
+ match = False
+ for tensor_cont in cdp.align_tensors:
+ # Find the matching tensor and then store the ID.
+ if tensor_cont.name == tensor:
+ tensor_cont.align_id = align_id
+ match = True
+
+ # The tensor label doesn't exist.
+ if not match:
+ raise RelaxNoTensorError('alignment', tensor)
+
+
def set_domain(tensor=None, domain=None):
"""Set the domain label for the given tensor.
Modified: branches/frame_order_testing/prompt/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/prompt/align_tensor.py?rev=15044&r1=15043&r2=15044&view=diff
==============================================================================
--- branches/frame_order_testing/prompt/align_tensor.py (original)
+++ branches/frame_order_testing/prompt/align_tensor.py Wed Dec 7 16:32:01
2011
@@ -185,32 +185,48 @@
align_tensor.fix(id=id, fixed=fixed)
- def init(self, tensor=None, params=None, scale=1.0, angle_units='deg',
param_types=0, errors=False):
- """Function for initialising the alignment tensor.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- tensor: The alignment tensor identification string.
-
- params: The alignment tensor data.
-
- scale: The alignment tensor eigenvalue scaling value.
-
- angle_units: The units for the angle parameters.
-
- param_types: A flag to select different parameter combinations.
-
- errors: A flag which determines if the alignment tensor data or its
errors are being input.
-
-
- Description
- ~~~~~~~~~~~
-
- Using this function, the alignment tensor data can be set up. The
params argument should be
- a tuple of floating point numbers (a list surrounded by round
brakets). These correspond to
- the parameters of the tensor, which can be specified by the
param_types argument, where the
- values correspond to
+ def init(self, tensor=None, params=None, scale=1.0, angle_units='deg',
param_types=0, align_id=None, domain=None, errors=False):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "align_tensor.init("
+ text = text + "tensor=" + repr(tensor)
+ text = text + ", params=" + repr(params)
+ text = text + ", scale=" + repr(scale)
+ text = text + ", angle_units=" + repr(angle_units)
+ text = text + ", param_types=" + repr(param_types)
+ text = text + ", align_id=" + repr(align_id)
+ text = text + ", domain=" + repr(domain)
+ text = text + ", errors=" + repr(errors) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(tensor, 'tensor')
+ arg_check.is_num_tuple(params, 'alignment tensor parameters', size=5)
+ arg_check.is_float(scale, 'scale')
+ arg_check.is_str(angle_units, 'angle units')
+ arg_check.is_int(param_types, 'parameter types')
+ arg_check.is_str(align_id, 'errors flag', can_be_none=True)
+ arg_check.is_str(domain, 'domain', can_be_none=True)
+ arg_check.is_bool(errors, 'errors flag')
+
+ # Execute the functional code.
+ align_tensor.init(tensor=tensor, params=params, scale=scale,
angle_units=angle_units, param_types=param_types, align_id=align_id,
domain=domain, errors=errors)
+
+ # The function doc info.
+ init._doc_title = "Initialise the alignment tensor."
+ init._doc_title_short = "Alignment tensor initialisation."
+ init._doc_args = [
+ ["tensor", "The alignment tensor identification string."],
+ ["params", "The alignment tensor data."],
+ ["scale", "The alignment tensor eigenvalue scaling value."],
+ ["angle_units", "The units for the angle parameters."],
+ ["param_types", "A flag to select different parameter
combinations."],
+ ["align_id", "The alignment ID string."],
+ ["domain", "The domain ID string."],
+ ["errors", "A flag which determines if the alignment tensor data or
its errors are being input."]
+ ]
+ init._doc_desc = """
+ This allows an alignment tensor data to be set up. The params
argument should be a tuple of floating point numbers (a list surrounded by
round brakets). These correspond to the parameters of the tensor, which can
be specified by the param_types argument, where the values correspond to
0: {Sxx, Syy, Sxy, Sxz, Syz} (unitless),
1: {Szz, Sxx-yy, Sxy, Sxz, Syz} (Pales default format),
@@ -221,8 +237,7 @@
6: {Pxx, Pyy, Pxy, Pxz, Pyz} (unitless),
7: {Pzz, Pxx-yy, Pxy, Pxz, Pyz} (unitless),
- Other formats may be added later. The relationship between the
Saupe order matrix S and the
- alignment tensor A is
+ Other formats may be added later. The relationship between the
Saupe order matrix S and the alignment tensor A is
S = 3/2 A.
@@ -230,13 +245,9 @@
A = P - 1/3 I,
- where I is the identity matrix. For the alignment tensor to be
supplied in Hertz, the bond
- vectors must all be of equal length.
-
-
- Examples
- ~~~~~~~~
-
+ where I is the identity matrix. For the alignment tensor to be
supplied in Hertz, the bond vectors must all be of equal length.
+ """
+ init._doc_examples = """
To set a rhombic tensor to the run 'CaM', type one of:
relax> align_tensor.init('super media', (-8.6322e-05, -5.5786e-04,
-3.1732e-05, 2.2927e-05,
@@ -244,28 +255,7 @@
relax> align_tensor.init(tensor='super media', params=(-8.6322e-05,
-5.5786e-04,
-3.1732e-05, 2.2927e-05, 2.8599e-04),
param_types=1)
"""
-
- # Function intro text.
- if self._exec_info.intro:
- text = self._exec_info.ps3 + "align_tensor.init("
- text = text + "tensor=" + repr(tensor)
- text = text + ", params=" + repr(params)
- text = text + ", scale=" + repr(scale)
- text = text + ", angle_units=" + repr(angle_units)
- text = text + ", param_types=" + repr(param_types)
- text = text + ", errors=" + repr(errors) + ")"
- print(text)
-
- # The argument checks.
- arg_check.is_str(tensor, 'tensor')
- arg_check.is_num_tuple(params, 'alignment tensor parameters', size=5)
- arg_check.is_float(scale, 'scale')
- arg_check.is_str(angle_units, 'angle units')
- arg_check.is_int(param_types, 'parameter types')
- arg_check.is_bool(errors, 'errors flag')
-
- # Execute the functional code.
- align_tensor.init(tensor=tensor, params=params, scale=scale,
angle_units=angle_units, param_types=param_types, errors=errors)
+ _build_doc(init)
def matrix_angles(self, basis_set=0, tensors=None):
r15044 - in /branches/frame_order_testing: generic_fns/align_tensor.py prompt/align_tensor.py