Author: bugman
Date: Wed Oct 22 14:22:11 2014
New Revision: 26344
URL: http://svn.gna.org/viewcvs/relax?rev=26344&view=rev
Log:
Added printouts to pipe_control.pcs.return_pcs_data() and
pipe_control.rdc.return_rdc_data().
These functions now accept the verbosity argument which if greater than 0 will
activate printouts of
how many RDCs or PCSs have been assembled for each alignment. This will be
useful for user feedback
as the spin verses interatomic data container selections can be difficult to
understand.
Modified:
trunk/pipe_control/pcs.py
trunk/pipe_control/rdc.py
Modified: trunk/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/pcs.py?rev=26344&r1=26343&r2=26344&view=diff
==============================================================================
--- trunk/pipe_control/pcs.py (original)
+++ trunk/pipe_control/pcs.py Wed Oct 22 14:22:11 2014
@@ -752,11 +752,13 @@
cdp.pcs_ids.append(align_id)
-def return_pcs_data(sim_index=None):
+def return_pcs_data(sim_index=None, verbosity=0):
"""Set up the data structures for optimisation using PCSs as base data
sets.
@keyword sim_index: The index of the simulation to optimise. This should
be None if normal optimisation is desired.
@type sim_index: None or int
+ @keyword verbosity: A flag specifying the amount of information to print.
The higher the value, the greater the verbosity.
+ @type verbosity: int
@return: The assembled data structures for using PCSs as the
base data for optimisation. These include:
- the PCS values.
- the unit vectors connecting the paramagnetic
centre (the electron spin) to the spin.
@@ -767,6 +769,10 @@
@rtype: tuple of (numpy rank-2 float64 array, numpy rank-2
float64 array, numpy rank-2 float64 array, list of float, list of float, numpy
rank-1 int32 array)
"""
+ # Initial printout.
+ if verbosity:
+ print("\nPCS data counts:")
+
# Data setup tests.
if not hasattr(cdp, 'paramagnetic_centre') and (hasattr(cdp,
'paramag_centre_fixed') and cdp.paramag_centre_fixed):
raise RelaxError("The paramagnetic centre has not yet been specified.")
@@ -850,6 +856,10 @@
# Spin index.
j = j + 1
+
+ # ID and PCS count printout.
+ if verbosity:
+ print(" Alignment ID '%s': %i" % (align_id, j))
# Pseudo-atom.
for spin in spin_loop():
Modified: trunk/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/rdc.py?rev=26344&r1=26343&r2=26344&view=diff
==============================================================================
--- trunk/pipe_control/rdc.py (original)
+++ trunk/pipe_control/rdc.py Wed Oct 22 14:22:11 2014
@@ -926,11 +926,13 @@
cdp.rdc_ids.append(align_id)
-def return_rdc_data(sim_index=None):
+def return_rdc_data(sim_index=None, verbosity=0):
"""Set up the data structures for optimisation using RDCs as base data
sets.
@keyword sim_index: The index of the simulation to optimise. This should
be None if normal optimisation is desired.
@type sim_index: None or int
+ @keyword verbosity: A flag specifying the amount of information to print.
The higher the value, the greater the verbosity.
+ @type verbosity: int
@return: The assembled data structures for using RDCs as the
base data for optimisation. These include:
- rdc, the RDC values.
- rdc_err, the RDC errors.
@@ -944,6 +946,10 @@
@rtype: tuple of (numpy rank-2 float64 array, numpy rank-2
float64 array, numpy rank-2 float64 array, list of numpy rank-3 float64 arrays,
list of lists of floats, numpy rank-2 int32 array, numpy rank-2 int32 array,
numpy rank-2 float64 array, numpy rank-1 int32 array)
"""
+ # Initial printout.
+ if verbosity:
+ print("\nRDC data counts:")
+
# Sort out pseudo-atoms first. This only needs to be called once.
setup_pseudoatom_rdc()
@@ -1078,6 +1084,7 @@
T_flags.append([])
# Interatom loop.
+ j = 0
for interatom in interatomic_loop():
# Get the spins.
spin1 = return_spin(interatom.spin_id1)
@@ -1136,6 +1143,13 @@
absolute[-1].append(interatom.absolute_rdc[align_id])
else:
absolute[-1].append(False)
+
+ # Interatom index.
+ j = j + 1
+
+ # ID and RDC count printout.
+ if verbosity:
+ print(" Alignment ID '%s': %i" % (align_id, j))
# Convert to numpy objects.
rdc = array(rdc, float64)
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