Author: bugman
Date: Fri Feb 22 14:42:49 2013
New Revision: 18567
URL: http://svn.gna.org/viewcvs/relax?rev=18567&view=rev
Log:
Fix for the frame order analysis for a bug introduced at r18566.
The _domain_moving() method has been redefined to return the spin ID string
corresponding to the
moving domain rather than the domain ID, as this method is only used for
restricting the spin_loop()
and interatomic_loop() methods. The changes allows the loop methods to
function prior to defining
the moving domain.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18567&r1=18566&r2=18567&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Fri Feb 22
14:42:49 2013
@@ -239,16 +239,15 @@
# Array of data types.
list = []
- domain_id = cdp.domain[self._domain_moving()]
# RDC search.
- for interatom in interatomic_loop(selection1=domain_id):
+ for interatom in interatomic_loop(selection1=self._domain_moving()):
if hasattr(interatom, 'rdc'):
list.append('rdc')
break
# PCS search.
- for spin in spin_loop(selection=domain_id):
+ for spin in spin_loop(selection=self._domain_moving()):
if hasattr(spin, 'pcs'):
list.append('pcs')
break
@@ -519,9 +518,9 @@
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
"""
@@ -532,6 +531,10 @@
# 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()):
@@ -540,7 +543,7 @@
continue
# Return the ID.
- return id
+ return cdp.domain[id]
def _domain_to_pdb(self, domain=None, pdb=None):
@@ -629,10 +632,9 @@
# Initialise.
atomic_pos = []
- domain_id = cdp.domain[self._domain_moving()]
# Store the atomic positions.
- for spin, spin_id in spin_loop(selection=domain_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
@@ -731,9 +733,8 @@
raise RelaxError("The spectrometer frequency for the
alignment ID '%s' has not been set." % align_id)
# Spin loop over the domain.
- domain_id = cdp.domain[self._domain_moving()]
j = 0
- for spin in spin_loop(selection=domain_id):
+ for spin in spin_loop(selection=self._domain_moving()):
# Skip deselected spins.
if not spin.select:
continue
@@ -801,10 +802,9 @@
unit_vect = []
rdc_const = []
absolute = []
- domain_id = cdp.domain[self._domain_moving()]
# The unit vectors and RDC constants.
- for interatom in interatomic_loop(selection1=domain_id):
+ for interatom in interatomic_loop(selection1=self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -878,8 +878,7 @@
absolute.append([])
# Interatom loop over the domain.
- domain_id = cdp.domain[self._domain_moving()]
- for interatom in interatomic_loop(domain_id):
+ for interatom in interatomic_loop(self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -1278,9 +1277,8 @@
pcs_flag = True
# Spin loop over the domain.
- domain_id = cdp.domain[self._domain_moving()]
pcs_index = 0
- for spin in spin_loop(domain_id):
+ for spin in spin_loop(self._domain_moving()):
# Skip deselected spins.
if not spin.select:
continue
@@ -1299,7 +1297,7 @@
# Interatomic data container loop.
rdc_index = 0
- for interatom in interatomic_loop(domain_id):
+ for interatom in interatomic_loop(self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -1652,11 +1650,8 @@
@rtype: list of str
"""
- # The moving domain ID.
- domain_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(selection1=domain_id):
+ for interatom in interatomic_loop(selection1=self._domain_moving()):
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
@@ -1671,7 +1666,7 @@
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(selection=domain_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
r18567 - /branches/frame_order_testing/specific_fns/frame_order.py