Author: bugman
Date: Thu Apr 10 15:49:03 2014
New Revision: 22679
URL: http://svn.gna.org/viewcvs/relax?rev=22679&view=rev
Log:
Elimination of the specific_analyses.frame_order.checks.check_rdcs() function.
This function duplicates the functionality of pipe_control.rdc.check_rdcs()
while not being as
comprehensive. Switching to the pipe_control.rdc version minimises the
amount of code in the frame
order analysis, decreasing the potential for bugs.
Modified:
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/checks.py
trunk/specific_analyses/frame_order/optimisation.py
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=22679&r1=22678&r2=22679&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/api.py (original)
+++ trunk/specific_analyses/frame_order/api.py Thu Apr 10 15:49:03 2014
@@ -37,9 +37,9 @@
from pipe_control import pipes
from pipe_control.interatomic import interatomic_loop, return_interatom
from pipe_control.mol_res_spin import return_spin, spin_loop
+from pipe_control.rdc import check_rdcs
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
-from specific_analyses.frame_order.checks import check_rdcs
from specific_analyses.frame_order.data import base_data_types, domain_moving
from specific_analyses.frame_order.optimisation import grid_row,
store_bc_data, target_fn_setup, unpack_opt_results
from specific_analyses.frame_order.parameter_object import Frame_order_params
@@ -81,12 +81,8 @@
# Loop over the interatomic data containers for the moving domain
(for the RDC data).
for interatom in interatomic_loop(selection1=domain_moving()):
- # Get the spins.
- spin1 = return_spin(interatom.spin_id1)
- spin2 = return_spin(interatom.spin_id2)
-
# RDC checks.
- if not check_rdcs(interatom, spin1, spin2):
+ if not check_rdcs(interatom):
continue
# Loop over the alignment IDs.
Modified: trunk/specific_analyses/frame_order/checks.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/checks.py?rev=22679&r1=22678&r2=22679&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/checks.py (original)
+++ trunk/specific_analyses/frame_order/checks.py Thu Apr 10 15:49:03
2014
@@ -36,53 +36,3 @@
# Check for the pivot.
if not hasattr(cdp, 'ave_pos_pivot') or not hasattr(cdp,
'ave_pos_translation'):
raise RelaxError("The mechanics of the average domain displacements
have not been set up, please use the frame_order.average_position user
function.")
-
-
-def check_rdcs(interatom, spin1, spin2):
- """Check if the RDCs for the given interatomic data container should be
used.
-
- @param interatom: The interatomic data container.
- @type interatom: InteratomContainer instance
- @param spin1: The first spin container.
- @type spin1: SpinContainer instance
- @param spin2: The second spin container.
- @type spin2: SpinContainer instance
- @return: True if the RDCs should be used, False otherwise.
- """
-
- # Skip deselected spins.
- if not spin1.select or not spin2.select:
- return False
-
- # Only use interatomic data containers with RDC data.
- if not hasattr(interatom, 'rdc'):
- return False
-
- # RDC data exists but the interatomic vectors are missing?
- if not hasattr(interatom, 'vector'):
- # Throw a warning.
- warn(RelaxWarning("RDC data exists but the interatomic vectors are
missing, skipping the spin pair '%s' and '%s'." % (interatom.spin_id1,
interatom.spin_id2)))
-
- # Jump to the next spin.
- return False
-
- # Skip non-Me pseudo-atoms for the first spin.
- if hasattr(spin1, 'members') and len(spin1.members) != 3:
- warn(RelaxWarning("Only methyl group pseudo atoms are supported due
to their fast rotation, skipping the spin pair '%s' and '%s'." %
(interatom.spin_id1, interatom.spin_id2)))
- return False
-
- # Skip non-Me pseudo-atoms for the second spin.
- if hasattr(spin2, 'members') and len(spin2.members) != 3:
- warn(RelaxWarning("Only methyl group pseudo atoms are supported due
to their fast rotation, skipping the spin pair '%s' and '%s'." %
(interatom.spin_id1, interatom.spin_id2)))
- return False
-
- # Checks.
- if not hasattr(spin1, 'isotope'):
- raise RelaxSpinTypeError(interatom.spin_id1)
- if not hasattr(spin2, 'isotope'):
- raise RelaxSpinTypeError(interatom.spin_id2)
- if not hasattr(interatom, 'r'):
- raise RelaxNoValueError("averaged interatomic distance")
-
- # Everything is ok.
- return True
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=22679&r1=22678&r2=22679&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/optimisation.py (original)
+++ trunk/specific_analyses/frame_order/optimisation.py Thu Apr 10 15:49:03
2014
@@ -38,8 +38,9 @@
from lib.warnings import RelaxWarning
from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import return_spin, spin_loop
+from pipe_control.rdc import check_rdcs
from pipe_control.structure.mass import pipe_centre_of_mass
-from specific_analyses.frame_order.checks import check_ave_domain_setup,
check_rdcs
+from specific_analyses.frame_order.checks import check_ave_domain_setup
from specific_analyses.frame_order.data import base_data_types,
domain_moving, pivot_fixed, tensor_loop, translation_fixed
from specific_analyses.frame_order.parameters import assemble_param_vector,
assemble_scaling_matrix
from target_functions import frame_order
@@ -281,13 +282,13 @@
# The unit vectors and RDC constants.
for interatom in interatomic_loop(selection1=domain_moving()):
+ # RDC checks.
+ if not check_rdcs(interatom):
+ continue
+
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
-
- # RDC checks.
- if not check_rdcs(interatom, spin1, spin2):
- continue
# A single unit vector.
if interatom.vector.shape == (3,):
@@ -591,12 +592,8 @@
# Interatomic data container loop.
rdc_index = 0
for interatom in interatomic_loop(domain_moving()):
- # Get the spins.
- spin1 = return_spin(interatom.spin_id1)
- spin2 = return_spin(interatom.spin_id2)
-
# RDC checks.
- if not check_rdcs(interatom, spin1, spin2):
+ if not check_rdcs(interatom):
continue
# Initialise the data structure.
r22679 - in /trunk/specific_analyses/frame_order: api.py checks.py optimisation.py