Author: bugman
Date: Fri Mar 22 17:15:19 2013
New Revision: 18994
URL: http://svn.gna.org/viewcvs/relax?rev=18994&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18552:18553
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18563:18564
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18564:18565
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18565:18566
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18566:18567
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18568:18569
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18569:18570
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18552:18553
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18553 into '.':
U generic_fns/align_tensor.py
[edau@localhost relax-trunk]$ svn merge -r18563:18564
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18564 into '.':
U specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18564:18565
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18565 into '.':
U maths_fns/frame_order/__init__.py
[edau@localhost relax-trunk]$ svn merge -r18565:18566
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18566 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18566:18567
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18567 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18568:18569
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18569 into '.':
U auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18569:18570
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18570 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$
Modified:
trunk/auto_analyses/frame_order.py
trunk/generic_fns/align_tensor.py
trunk/maths_fns/frame_order/__init__.py
trunk/specific_fns/frame_order.py
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=18994&r1=18993&r2=18994&view=diff
==============================================================================
--- trunk/auto_analyses/frame_order.py (original)
+++ trunk/auto_analyses/frame_order.py Fri Mar 22 17:15:19 2013
@@ -209,39 +209,49 @@
@param model: The frame order model.
@type model: str
- """
+ @return: The list of increment values.
+ @rtype: list of int and None
+ """
+
+ # Initialise the structure.
+ incs = []
+ if hasattr(cdp, 'pivot_fixed') and not cdp.pivot_fixed:
+ incs += [None, None, None]
# The rotor model.
if model == 'rotor':
- return [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc]
+ incs += [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc]
# The free rotor model.
if model == 'free rotor':
- return [None, None, self.grid_inc, self.grid_inc]
+ incs += [None, None, self.grid_inc, self.grid_inc]
# The torsionless isotropic cone model.
if model == 'iso cone, torsionless':
- return [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc]
+ incs += [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc]
# The free rotor isotropic cone model.
if model == 'iso cone, free rotor':
- return [None, None, None, None, self.grid_inc]
+ incs += [None, None, None, None, self.grid_inc]
# The isotropic cone model.
if model == 'iso cone':
- return [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, None]
+ incs += [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, None]
# The torsionless pseudo-elliptic cone model.
if model == 'pseudo-ellipse, torsionless':
- return [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, self.grid_inc, None]
+ incs += [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, self.grid_inc, None]
# The free rotor pseudo-elliptic cone model.
if model == 'pseudo-ellipse, free rotor':
- return [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, self.grid_inc, None]
+ incs += [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, self.grid_inc, None]
# The pseudo-elliptic cone model.
if model == 'pseudo-ellipse':
- return [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, self.grid_inc, None, None]
+ incs += [None, None, None, self.grid_inc, self.grid_inc,
self.grid_inc, self.grid_inc, None, None]
+
+ # Return the increment list.
+ return incs
def nested_params(self, model):
Modified: trunk/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/align_tensor.py?rev=18994&r1=18993&r2=18994&view=diff
==============================================================================
--- trunk/generic_fns/align_tensor.py (original)
+++ trunk/generic_fns/align_tensor.py Fri Mar 22 17:15:19 2013
@@ -1157,12 +1157,18 @@
# The table header.
table.append([''])
for i in range(tensor_num):
- table[0].append(cdp.align_tensors[i].name)
+ if cdp.align_tensors[i].name == None:
+ table[0].append(repr(i))
+ else:
+ table[0].append(cdp.align_tensors[i].name)
# First loop over the rows.
for i in range(tensor_num):
# Add the tensor name.
- table.append([cdp.align_tensors[i].name])
+ if cdp.align_tensors[i].name == None:
+ table.append([repr(i)])
+ else:
+ table.append([cdp.align_tensors[i].name])
# Second loop over the columns.
for j in range(tensor_num):
Modified: trunk/maths_fns/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/frame_order/__init__.py?rev=18994&r1=18993&r2=18994&view=diff
==============================================================================
--- trunk/maths_fns/frame_order/__init__.py (original)
+++ trunk/maths_fns/frame_order/__init__.py Fri Mar 22 17:15:19 2013
@@ -193,8 +193,8 @@
if err:
self.pcs_error = pcs_errors
else:
- # Missing errors (the values need to be small, close to ppm
units, so the chi-squared value is comparable to the RDC).
- self.pcs_error = 0.03 * 1e-6 * ones((self.num_align,
self.num_spins), float64)
+ # Missing errors (default to 0.1 ppm errors).
+ self.pcs_error = 0.1 * 1e-6 * ones((self.num_align,
self.num_spins), float64)
# RDC errors.
if self.rdc_flag_sum:
@@ -206,7 +206,7 @@
if err:
self.rdc_error = rdc_errors
else:
- # Missing errors.
+ # Missing errors (default to 1 Hz errors).
self.rdc_error = ones((self.num_align, self.num_interatom),
float64)
# Missing data matrices (RDC).
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=18994&r1=18993&r2=18994&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 17:15:19 2013
@@ -241,13 +241,13 @@
list = []
# RDC search.
- for interatom in interatomic_loop():
+ for interatom in interatomic_loop(selection1=self._domain_moving()):
if hasattr(interatom, 'rdc'):
list.append('rdc')
break
# PCS search.
- for spin in spin_loop():
+ for spin in spin_loop(selection=self._domain_moving()):
if hasattr(spin, 'pcs'):
list.append('pcs')
break
@@ -517,9 +517,9 @@
def _domain_moving(self):
- """Return the domain ID of the moving domain.
-
- @return: The domain ID of the moving domain.
+ """Return the spin ID string corresponding to the moving domain.
+
+ @return: The spin ID string defining the moving domain.
@rtype: str
"""
@@ -530,6 +530,10 @@
# Only support for 2 domains.
if len(list(cdp.domain.keys())) > 2:
raise RelaxError("Only two domains are supported in the frame
order analysis.")
+
+ # Reference domain not set yet, so return nothing.
+ if not hasattr(cdp, 'ref_domain'):
+ return None
# Loop over the domains.
for id in list(cdp.domain.keys()):
@@ -538,7 +542,7 @@
continue
# Return the ID.
- return id
+ return cdp.domain[id]
def _domain_to_pdb(self, domain=None, pdb=None):
@@ -629,7 +633,7 @@
atomic_pos = []
# Store the atomic positions.
- for spin, spin_id in spin_loop(return_id=True):
+ for spin, spin_id in spin_loop(selection=self._domain_moving(),
return_id=True):
# Skip deselected spins.
if not spin.select:
continue
@@ -728,9 +732,8 @@
raise RelaxError("The spectrometer frequency for the
alignment ID '%s' has not been set." % align_id)
# Spin loop over the domain.
- id = cdp.domain[self._domain_moving()]
j = 0
- for spin in spin_loop(id):
+ for spin in spin_loop(selection=self._domain_moving()):
# Skip deselected spins.
if not spin.select:
continue
@@ -800,7 +803,7 @@
absolute = []
# The unit vectors and RDC constants.
- for interatom in interatomic_loop():
+ for interatom in interatomic_loop(selection1=self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -874,8 +877,7 @@
absolute.append([])
# Interatom loop over the domain.
- id = cdp.domain[self._domain_moving()]
- for interatom in interatomic_loop(id):
+ for interatom in interatomic_loop(self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -1274,9 +1276,8 @@
pcs_flag = True
# Spin loop over the domain.
- id = cdp.domain[self._domain_moving()]
pcs_index = 0
- for spin in spin_loop(id):
+ for spin in spin_loop(self._domain_moving()):
# Skip deselected spins.
if not spin.select:
continue
@@ -1295,7 +1296,7 @@
# Interatomic data container loop.
rdc_index = 0
- for interatom in interatomic_loop(id):
+ for interatom in interatomic_loop(self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -1648,17 +1649,14 @@
@rtype: list of str
"""
- # The moving domain ID.
- id = cdp.domain[self._domain_moving()]
-
# Loop over the interatomic data containers for the moving domain
(for the RDC data).
- for interatom in interatomic_loop(id):
- # Skip deselected containers.
- if not interatom.select:
- continue
-
- # No RDC, so skip.
- if not hasattr(interatom, 'rdc'):
+ for interatom in interatomic_loop(selection1=self._domain_moving()):
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
+ # RDC checks.
+ if not self._check_rdcs(interatom, spin1, spin2):
continue
# Loop over the alignment IDs.
@@ -1667,7 +1665,7 @@
yield ['rdc', interatom.spin_id1, interatom.spin_id2,
align_id]
# Loop over the spin containers for the moving domain (for the PCS
data).
- for spin, spin_id in spin_loop(id, return_id=True):
+ for spin, spin_id in spin_loop(selection=self._domain_moving(),
return_id=True):
# Skip deselected spins.
if not spin.select:
continue
@@ -2033,8 +2031,13 @@
for j in range(n):
# Fixed parameter.
if grid[j] == None:
- # Get the current parameter value.
- pts[i, j] = getattr(cdp, cdp.params[j]) /
scaling_matrix[j, j]
+ # Get the current parameter value (pivot, assuming the
pivot point is always at the start of the parameter array).
+ if cdp.params[j] in ['pivot_x', 'pivot_y', 'pivot_z']:
+ pts[i, j] = cdp.pivot[j] / scaling_matrix[j, j]
+
+ # Get the current parameter value (normal parameter).
+ else:
+ pts[i, j] = getattr(cdp, cdp.params[j]) /
scaling_matrix[j, j]
# Add the point coordinate.
else:
r18994 - in /trunk: auto_analyses/ generic_fns/ maths_fns/frame_order/ specific_fns/