Author: bugman
Date: Tue May 8 19:02:18 2012
New Revision: 16118
URL: http://svn.gna.org/viewcvs/relax?rev=16118&view=rev
Log:
Whitespace clean up.
Modified:
branches/uf_redesign/user_functions/align_tensor.py
Modified: branches/uf_redesign/user_functions/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/align_tensor.py?rev=16118&r1=16117&r2=16118&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/align_tensor.py (original)
+++ branches/uf_redesign/user_functions/align_tensor.py Tue May 8 19:02:18
2012
@@ -42,39 +42,39 @@
uf.title = "Copy alignment tensor data."
uf.title_short = "Alignment tensor copying."
uf.add_keyarg(
- name = "tensor_from",
- default = None,
- py_type = "str",
- desc_short = "tensor from",
- desc = "The identification string of the alignment tensor to copy
the data from."
-)
-uf.add_keyarg(
- name = "pipe_from",
- default = None,
- py_type = "str",
- desc_short = "pipe from",
- desc = "The name of the data pipe to copy the alignment tensor data
from.",
- wiz_element_type = 'combo',
- wiz_combo_iter = pipes.pipe_names,
- can_be_none = True
-)
-uf.add_keyarg(
- name = "tensor_to",
- default = None,
- py_type = "str",
- desc_short = "tensor to",
- desc = "The identification string of the alignment tensor to copy
the data to.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "pipe_to",
- default = None,
- py_type = "str",
- desc_short = "pipe to",
- desc = "The name of the data pipe to copy the alignment tensor data
to.",
- wiz_element_type = 'combo',
- wiz_combo_iter = pipes.pipe_names,
- can_be_none = True
+ name = "tensor_from",
+ default = None,
+ py_type = "str",
+ desc_short = "tensor from",
+ desc = "The identification string of the alignment tensor to copy the
data from."
+)
+uf.add_keyarg(
+ name = "pipe_from",
+ default = None,
+ py_type = "str",
+ desc_short = "pipe from",
+ desc = "The name of the data pipe to copy the alignment tensor data
from.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = pipes.pipe_names,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "tensor_to",
+ default = None,
+ py_type = "str",
+ desc_short = "tensor to",
+ desc = "The identification string of the alignment tensor to copy the
data to.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "pipe_to",
+ default = None,
+ py_type = "str",
+ desc_short = "pipe to",
+ desc = "The name of the data pipe to copy the alignment tensor data to.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = pipes.pipe_names,
+ can_be_none = True
)
uf.desc = """
This will copy the alignment tensor data to a new tensor or a new data pipe.
The destination data pipe must not contain any alignment tensor data
corresponding to the tensor_to label. If the pipe_from or pipe_to arguments
are not supplied, then both will default to the current data pipe. Both the
tensor_from and tensor_to arguments must be supplied.
@@ -111,14 +111,14 @@
uf.title = "Delete alignment tensor data from the relax data store."
uf.title_short = "Alignment tensor pipe deletion."
uf.add_keyarg(
- name = "tensor",
- py_type = "str",
- desc_short = "tensor",
- desc = "The alignment tensor identification string.",
- wiz_element_type = 'combo',
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True,
- can_be_none = True
+ name = "tensor",
+ py_type = "str",
+ desc_short = "tensor",
+ desc = "The alignment tensor identification string.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
)
uf.desc = """
This will delete the specified alignment tensor data from the current data
pipe. If no tensor is specified, all tensors will be deleted.
@@ -135,14 +135,14 @@
uf.title_short = "Align tensor display."
uf.display = True
uf.add_keyarg(
- name = "tensor",
- py_type = "str",
- desc_short = "tensor",
- desc = "The alignment tensor identification string.",
- wiz_element_type = 'combo',
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True,
- can_be_none = True
+ name = "tensor",
+ py_type = "str",
+ desc_short = "tensor",
+ desc = "The alignment tensor identification string.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
)
uf.desc = """
This will show all information relating to the alignment tensor, including
the different tensor forms:
@@ -168,21 +168,21 @@
uf.title = "Fix all alignment tensors so that they do not change during
optimisation."
uf.title_short = "Fix alignment tensors."
uf.add_keyarg(
- name = "id",
- py_type = "str",
- desc_short = "tensor ID",
- desc = "The alignment tensor identification string.",
- wiz_element_type = 'combo',
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True,
- can_be_none = True
-)
-uf.add_keyarg(
- name = "fixed",
- default = True,
- py_type = "bool",
- desc_short = "fixed flag",
- desc = "The flag specifying if the tensors should be fixed or
variable."
+ name = "id",
+ py_type = "str",
+ desc_short = "tensor ID",
+ desc = "The alignment tensor identification string.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "fixed",
+ default = True,
+ py_type = "bool",
+ desc_short = "fixed flag",
+ desc = "The flag specifying if the tensors should be fixed or variable."
)
uf.desc = """
If the ID string is left unset, then all alignment tensors will be fixed.
@@ -198,32 +198,32 @@
uf.title = "Initialise an alignment tensor."
uf.title_short = "Alignment tensor initialisation."
uf.add_keyarg(
- name = "tensor",
- py_type = "str",
- desc_short = "tensor ID",
- desc = "The alignment tensor identification string."
-)
-uf.add_keyarg(
- name = "params",
- py_type = "num_tuple",
- desc_short = "alignment tensor parameters",
- size = 5,
- desc = "The alignment tensor data.",
- wiz_read_only = False
-)
-uf.add_keyarg(
- name = "scale",
- default = 1.0,
- py_type = "float",
- desc_short = "scale",
- desc = "The alignment tensor eigenvalue scaling value."
-)
-uf.add_keyarg(
- name = "angle_units",
- default = "deg",
- py_type = "str",
- desc_short = "angle units",
- desc = "The units for the angle parameters."
+ name = "tensor",
+ py_type = "str",
+ desc_short = "tensor ID",
+ desc = "The alignment tensor identification string."
+)
+uf.add_keyarg(
+ name = "params",
+ py_type = "num_tuple",
+ desc_short = "alignment tensor parameters",
+ size = 5,
+ desc = "The alignment tensor data.",
+ wiz_read_only = False
+)
+uf.add_keyarg(
+ name = "scale",
+ default = 1.0,
+ py_type = "float",
+ desc_short = "scale",
+ desc = "The alignment tensor eigenvalue scaling value."
+)
+uf.add_keyarg(
+ name = "angle_units",
+ default = "deg",
+ py_type = "str",
+ desc_short = "angle units",
+ desc = "The units for the angle parameters."
)
uf.add_keyarg(
name = "param_types",
@@ -255,11 +255,11 @@
wiz_read_only = True
)
uf.add_keyarg(
- name = "errors",
- default = False,
- py_type = "bool",
- desc_short = "errors flag",
- desc = "A flag which determines if the alignment tensor data or its
errors are being input."
+ name = "errors",
+ default = False,
+ py_type = "bool",
+ desc_short = "errors flag",
+ desc = "A flag which determines if the alignment tensor data or its
errors are being input."
)
uf.desc = """
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:
@@ -304,24 +304,24 @@
uf.title_short = "Alignment tensor angle calculation."
uf.display = True
uf.add_keyarg(
- name = "basis_set",
- default = 0,
- py_type = "int",
- desc_short = "basis set",
- desc = "The basis set to operate with.",
- wiz_element_type = "combo",
- wiz_combo_choices = ["{Sxx, Syy, Sxy, Sxz, Syz}", "{Szz, Sxxyy, Sxy,
Sxz, Syz}"],
- wiz_combo_data = [0, 1]
-)
-uf.add_keyarg(
- name = "tensors",
- py_type = "str_list",
- desc_short = "alignment tensor IDs",
- desc = "A list of the tensors to apply the calculation to. If None,
all tensors are used.",
- wiz_element_type = "combo_list",
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True,
- can_be_none = True
+ name = "basis_set",
+ default = 0,
+ py_type = "int",
+ desc_short = "basis set",
+ desc = "The basis set to operate with.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["{Sxx, Syy, Sxy, Sxz, Syz}", "{Szz, Sxxyy, Sxy,
Sxz, Syz}"],
+ wiz_combo_data = [0, 1]
+)
+uf.add_keyarg(
+ name = "tensors",
+ py_type = "str_list",
+ desc_short = "alignment tensor IDs",
+ desc = "A list of the tensors to apply the calculation to. If None, all
tensors are used.",
+ wiz_element_type = "combo_list",
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
)
uf.desc = """
This will calculate the angles between all loaded alignment tensors for the
current data pipe. The matrices are first converted to a 5D vector form and
then then angles are calculated. The angles are dependent on the basis set.
If the basis_set argument is set to the default of 0, the vectors {Sxx, Syy,
Sxy, Sxz, Syz} are used. If the basis_set argument is set to 1, the vectors
{Szz, Sxxyy, Sxy, Sxz, Syz} are used instead.
@@ -338,22 +338,22 @@
uf.title = "Specify that one tensor is a reduction of another."
uf.title_short = "Specify tensor reductions."
uf.add_keyarg(
- name = "full_tensor",
- py_type = "str",
- desc_short = "full tensor",
- desc = "The full alignment tensor.",
- wiz_element_type = 'combo',
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True
-)
-uf.add_keyarg(
- name = "red_tensor",
- py_type = "str",
- desc_short = "reduced tensor",
- desc = "The reduced alignment tensor.",
- wiz_element_type = 'combo',
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True
+ name = "full_tensor",
+ py_type = "str",
+ desc_short = "full tensor",
+ desc = "The full alignment tensor.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True
+)
+uf.add_keyarg(
+ name = "red_tensor",
+ py_type = "str",
+ desc_short = "reduced tensor",
+ desc = "The reduced alignment tensor.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True
)
uf.desc = """
Prior to optimisation of the N-state model and Frame Order theories using
alignment tensors, which tensor is a reduction of which other tensor must be
specified through this user function.
@@ -373,19 +373,19 @@
uf.title = "Set the domain label for the alignment tensor."
uf.title_short = "Tensor domain labelling."
uf.add_keyarg(
- name = "tensor",
- py_type = "str",
- desc_short = "tensor ID",
- desc = "The alignment tensor to assign the domain label to.",
- wiz_element_type = 'combo',
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True,
-)
-uf.add_keyarg(
- name = "domain",
- py_type = "str",
- desc_short = "domain",
- desc = "The domain label."
+ name = "tensor",
+ py_type = "str",
+ desc_short = "tensor ID",
+ desc = "The alignment tensor to assign the domain label to.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+)
+uf.add_keyarg(
+ name = "domain",
+ py_type = "str",
+ desc_short = "domain",
+ desc = "The domain label."
)
uf.desc = """
Prior to optimisation of the N-state model or Frame Order theories, the
domain to which each alignment tensor belongs must be specified.
@@ -407,24 +407,24 @@
uf.title_short = "Alignment tensor SVD calculation."
uf.display = True
uf.add_keyarg(
- name = "basis_set",
- default = 0,
- py_type = "int",
- desc_short = "basis set",
- desc = "The basis set to operate with.",
- wiz_element_type = "combo",
- wiz_combo_choices = ["{Sxx, Syy, Sxy, Sxz, Syz}", "{Szz, Sxxyy, Sxy,
Sxz, Syz}"],
- wiz_combo_data = [0, 1]
-)
-uf.add_keyarg(
- name = "tensors",
- py_type = "str_list",
- desc_short = "alignment tensor IDs",
- desc = "A list of the tensors to apply the calculation to. If None,
all tensors are used.",
- wiz_element_type = "combo_list",
- wiz_combo_iter = align_tensor.get_ids,
- wiz_read_only = True,
- can_be_none = True
+ name = "basis_set",
+ default = 0,
+ py_type = "int",
+ desc_short = "basis set",
+ desc = "The basis set to operate with.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["{Sxx, Syy, Sxy, Sxz, Syz}", "{Szz, Sxxyy, Sxy,
Sxz, Syz}"],
+ wiz_combo_data = [0, 1]
+)
+uf.add_keyarg(
+ name = "tensors",
+ py_type = "str_list",
+ desc_short = "alignment tensor IDs",
+ desc = "A list of the tensors to apply the calculation to. If None, all
tensors are used.",
+ wiz_element_type = "combo_list",
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
)
uf.desc = """
This will perform a singular value decomposition of all tensors loaded for
the current data pipe. If the basis_set argument is set to the default of 0,
the matrix on which SVD will be performed is composed of the unitary basis
set {Sxx, Syy, Sxy, Sxz, Syz} layed out as:
r16118 - /branches/uf_redesign/user_functions/align_tensor.py