On Jan 11, 2008 6:03 PM, <sebastien.morin.1@xxxxxxxxx> wrote:
Author: semor
Date: Fri Jan 11 18:02:57 2008
New Revision: 4650
URL: http://svn.gna.org/viewcvs/relax?rev=4650&view=rev
Log:
Continued the shifting of the consistency tests code to the new relax
design started at r4583.
Modified:
branches/consistency_tests_1.3/specific_fns/consistency_tests.py
Modified: branches/consistency_tests_1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/consistency_tests.py?rev=4650&r1=4649&r2=4650&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/consistency_tests.py
(original)
+++ branches/consistency_tests_1.3/specific_fns/consistency_tests.py Fri
Jan 11 18:02:57 2008
@@ -49,7 +49,7 @@
raise RelaxError, "The frequency has not been set up."
# Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
+ if not cdp.res.has_key:
The data structure 'res' no longer exists in the PipeContainer. It is
replaced by this (these are the classes, not the actual names):
PipeContainer.MoleculeList[MoleculeContainer].ResidueList[ResidueContainer].SpinList[SpinContainer]
These are defined in the 'data' directory. In variable form, this
might look like:
cdp.mol[i].res[j].spin[k]
Because of this complexity, I have written the function
exists_mol_res_spin_data(). This is located in the
generic_fns.selection module.
@@ -76,8 +76,8 @@
raise RelaxNoValueError, "correlation time"
# Frequency index.
- if relax_data_store.ct_frq[self.run] not in
relax_data_store.frq[self.run]:
- raise RelaxError, "No relaxation data corresponding to the
frequency " + `relax_data_store.ct_frq[self.run]` + " has been loaded."
+ if cdp.ct_frq not in cdp.frq:
+ raise RelaxError, "No relaxation data corresponding to the
frequency " + `cdp.ct_frq` + " has been loaded."
# Consistency testing.
for spin in spin_loop(spin_id):
@@ -91,7 +91,7 @@
# Residue specific frequency index.
frq_index = None
for j in xrange(data.num_frq):
- if data.frq[j] == relax_data_store.ct_frq[self.run]:
+ if data.frq[j] == cdp.ct_frq:
frq_index = j
if frq_index == None:
continue
In this spin loop, all 'data' variables should be replaced with
'spin'. The "data = cdp" statement should also be removed.
@@ -129,7 +129,7 @@
continue
# Initialise the function to calculate.
- self.ct = Consistency(frq=relax_data_store.ct_frq[self.run],
gx=relax_data_store.gx, gh=relax_data_store.gh, mu0=relax_data_store.mu0,
h_bar=relax_data_store.h_bar)
+ self.ct = Consistency(frq=cdp.ct_frq, gx=relax_data_store.gx,
gh=relax_data_store.gh, mu0=relax_data_store.mu0,
h_bar=relax_data_store.h_bar)
# Calculate the consistency tests values.
j0, f_eta, f_r2 = self.ct.func(orientation=data.orientation,
tc=data.tc, r=data.r, csa=data.csa, r1=r1, r2=r2, noe=noe)
The "relax_data_store.gx" should be replaced by "spin.gx". This is
because gx is a spin specific parameter. Also, as mu0 and h_bar are
now defined in the physical_constants module, these do not need to be
passed in as arguments. The necessary code in 'math_fns' can import
the values for itself.
@@ -270,11 +270,11 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
+ if not cdp.res.has_key:
return 0
This again requires the call to exists_mol_res_spin_data().
# Return the number of residues.
- return len(relax_data_store.res[self.run])
+ return len(cdp.res)
Actually the whole contents of the num_instances() method can be
replaced with a call to generic_fns.selection.count_spins()
I'll comment on the rest in a separate post to keep things short.
Regards,
Edward
Re: r4650 - /branches/consistency_tests_1.3/specific_fns/consistency_tests.py