Seb,
I've had a close look at the changes of this revision and noticed a few
important bugs introduced. Please see below.
On Fri, 2008-04-11 at 14:46 +0000, sebastien.morin.1@xxxxxxxxx wrote:
Author: semor
Date: Fri Apr 11 16:46:39 2008
New Revision: 5587
URL: http://svn.gna.org/viewcvs/relax?rev=5587&view=rev
Log:
Aliased the current data pipe and removed the run arguments.
Modified:
1.3/generic_fns/palmer.py
Modified: 1.3/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/palmer.py?rev=5587&r1=5586&r2=5587&view=diff
==============================================================================
--- 1.3/generic_fns/palmer.py (original)
+++ 1.3/generic_fns/palmer.py Fri Apr 11 16:46:39 2008
@@ -34,6 +34,7 @@
# relax module imports.
from data import Data as relax_data_store
+from generic_fns.selection import exists_mol_res_spin_data, spin_loop
from relax_errors import RelaxDirError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoPdbError, RelaxNoPipeError,
RelaxNoSequenceError, RelaxNucleusError, RelaxProgFailError
@@ -48,7 +49,7 @@
self.relax = relax
- def create(self, run, dir, force, binary, diff_search, sims, sim_type,
trim, steps, constraints, nucleus, atom1, atom2):
+ def create(self, dir, force, binary, diff_search, sims, sim_type,
trim, steps, constraints, nucleus, atom1, atom2, spin_id=None):
"""Function for creating the Modelfree4 input files.
This spin_id argument could come in handy!
The following files are created:
@@ -59,29 +60,24 @@
dir/run.sh
"""
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
This test should be replaced rather than deleted. For example see line
442 of specific_fns/consistency_tests.py (1.3 line, r5603).
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
# Test if sequence data is loaded.
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Test if the PDB file is loaded (for the spheroid and ellipsoid).
- if not relax_data_store.diff[run].type == 'sphere' and not
relax_data_store.pdb.has_key(run):
- raise RelaxNoPdbError, run
-
- # Test if the nucleus type has been set.
- if not hasattr(relax_data_store, 'gx'):
- raise RelaxNucleusError
+ if not cdp.diff.type == 'sphere' and not cdp.pdb.has_key:
+ raise RelaxNoPdbError
Here an important bug has been introduced. has_key() is a method of the
Python dictionary to determine if the dictionary has the key. The two
data structures have also been renamed. It gets a bit more complicated
because of the possible absence of the structures. So the line should
actually be:
if hasattr(cdp, 'diff_tensor') and not cdp.diff_tensor.type == 'sphere'
and not hasattr(cdp, 'structure'):
# Directory creation.
if dir == None:
- dir = run
+ dir = pipe
self.relax.IO.mkdir(dir, verbosity=0)
# Place the arguments into 'self'.
- self.run = run
+ self.pipe = pipe
self.dir = dir
self.force = force
self.binary = binary
@@ -98,14 +94,14 @@
# Number of field strengths and values.
self.num_frq = 0
self.frq = []
- for i in xrange(len(relax_data_store.res[self.run])):
- if hasattr(relax_data_store.res[self.run][i], 'num_frq'):
- if relax_data_store.res[self.run][i].num_frq >
self.num_frq:
+ for spin in spin_loop(spin_id):
+ if hasattr(cdp.res[i], 'num_frq'):
+ if cdp.res[i].num_frq > self.num_frq:
Here is another bug. To fix, simply replace 'cdp.res[i]' with 'spin'.
# Number of field strengths.
- self.num_frq =
relax_data_store.res[self.run][i].num_frq
+ self.num_frq = cdp.res[i].num_frq
Same fix.
# Field strength values.
- for frq in relax_data_store.res[self.run][i].frq:
+ for frq in cdp.res[i].frq:
Again the same fix.
if frq not in self.frq:
self.frq.append(frq)
@@ -120,8 +116,8 @@
mfpar = self.open_file('mfpar')
# Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
- if hasattr(relax_data_store.res[self.run][i], 'num_frq'):
+ for spin in spin_loop(spin_id):
+ if hasattr(cdp.res[i], 'num_frq'):
Here too.
# The 'mfdata' file.
if not self.create_mfdata(i, mfdata):
continue
@@ -138,9 +134,9 @@
mfpar.close()
# The 'run.sh' script.
- run = self.open_file('run.sh')
- self.create_run(run)
- run.close()
+ pipe = self.open_file('run.sh')
+ self.create_pipe(pipe)
+ pipe.close()
This should not have changed. The run here means one execution of
Modelfree, not the runs of the relax data store.
chmod(self.dir + '/run.sh', 0755)
@@ -148,7 +144,7 @@
"""Create the Modelfree4 input file 'mfmodel'."""
# Spin title.
- file.write("\nspin " + relax_data_store.res[self.run][i].name
+ "_" + `relax_data_store.res[self.run][i].num` + "\n")
+ file.write("\nspin " + cdp.res[i].name + "_" +
`cdp.res[i].num` + "\n")
Same bug as above. I won't point out all the positions where
'cdp.res[i]' should be changed to 'spin'.
# Data written flag.
written = 0
@@ -159,24 +155,24 @@
r1, r2, noe = None, None, None
# Loop over the relevant relaxation data.
- for k in xrange(relax_data_store.res[self.run][i].num_ri):
- if self.frq[j] !=
relax_data_store.res[self.run][i].frq[relax_data_store.res[self.run][i].remap_table[k]]:
+ for k in xrange(cdp.res[i].num_ri):
+ if self.frq[j] !=
cdp.res[i].frq[cdp.res[i].remap_table[k]]:
continue
# Find the corresponding R1.
- if relax_data_store.res[self.run][i].ri_labels[k] == 'R1':
- r1 = relax_data_store.res[self.run][i].relax_data[k]
- r1_err =
relax_data_store.res[self.run][i].relax_error[k]
+ if cdp.res[i].ri_labels[k] == 'R1':
+ r1 = cdp.res[i].relax_data[k]
+ r1_err = cdp.res[i].relax_error[k]
# Find the corresponding R2.
- elif relax_data_store.res[self.run][i].ri_labels[k] ==
'R2':
- r2 = relax_data_store.res[self.run][i].relax_data[k]
- r2_err =
relax_data_store.res[self.run][i].relax_error[k]
+ elif cdp.res[i].ri_labels[k] == 'R2':
+ r2 = cdp.res[i].relax_data[k]
+ r2_err = cdp.res[i].relax_error[k]
# Find the corresponding NOE.
- elif relax_data_store.res[self.run][i].ri_labels[k] ==
'NOE':
- noe = relax_data_store.res[self.run][i].relax_data[k]
- noe_err =
relax_data_store.res[self.run][i].relax_error[k]
+ elif cdp.res[i].ri_labels[k] == 'NOE':
+ noe = cdp.res[i].relax_data[k]
+ noe_err = cdp.res[i].relax_error[k]
# Test if the R1 exists for this frequency, otherwise skip the
data.
if r1:
@@ -205,24 +201,24 @@
"""Create the Modelfree4 input file 'mfin'."""
# Set the diffusion tensor specific values.
- if relax_data_store.diff[self.run].type == 'sphere':
+ if cdp.diff.type == 'sphere':
here it should be 'cdp.diff_tensor.type'.
diff = 'isotropic'
algorithm = 'brent'
- tm = relax_data_store.diff[self.run].tm / 1e-9
+ tm = cdp.diff.tm / 1e-9
here too, etc.
dratio = 1
theta = 0
phi = 0
- elif relax_data_store.diff[self.run].type == 'spheroid':
+ elif cdp.diff.type == 'spheroid':
diff = 'axial'
algorithm = 'powell'
- tm = relax_data_store.diff[self.run].tm / 1e-9
- dratio = relax_data_store.diff[self.run].Dratio
- theta = relax_data_store.diff[self.run].theta * 360.0 / (2.0 *
pi)
- phi = relax_data_store.diff[self.run].phi * 360.0 / (2.0 * pi)
- elif relax_data_store.diff[self.run].type == 'ellipsoid':
+ tm = cdp.diff.tm / 1e-9
+ dratio = cdp.diff.Dratio
+ theta = cdp.diff.theta * 360.0 / (2.0 * pi)
+ phi = cdp.diff.phi * 360.0 / (2.0 * pi)
+ elif cdp.diff.type == 'ellipsoid':
diff = 'anisotropic'
algorithm = 'powell'
- tm = relax_data_store.diff[self.run].tm / 1e-9
+ tm = cdp.diff.tm / 1e-9
dratio = 0
theta = 0
phi = 0
@@ -233,7 +229,7 @@
file.write("search grid\n\n")
# Diffusion type.
- if relax_data_store.diff[self.run].fixed:
+ if cdp.diff.fixed:
algorithm = 'fix'
file.write("diffusion " + diff + " " + self.diff_search +
"\n\n")
@@ -294,12 +290,15 @@
def create_mfmodel(self, i, file):
"""Create the Modelfree4 input file 'mfmodel'."""
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
# Spin title.
- file.write("\nspin " + relax_data_store.res[self.run][i].name
+ "_" + `relax_data_store.res[self.run][i].num` + "\n")
+ file.write("\nspin " + cdp.res[i].name + "_" +
`cdp.res[i].num` + "\n")
# tloc.
file.write('%-3s%-6s%-6.1f' % ('M1', 'tloc', 0))
- if 'tm' in relax_data_store.res[self.run][i].params:
+ if 'tm' in cdp.res[i].params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -324,7 +323,7 @@
# S2f.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Sf2', 1))
- if 'S2f' in relax_data_store.res[self.run][i].params:
+ if 'S2f' in cdp.res[i].params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -338,7 +337,7 @@
# S2s.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Ss2', 1))
- if 'S2s' in relax_data_store.res[self.run][i].params or 'S2' in
relax_data_store.res[self.run][i].params:
+ if 'S2s' in cdp.res[i].params or 'S2' in cdp.res[i].params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -352,7 +351,7 @@
# te.
file.write('%-3s%-6s%-6.1f' % ('M1', 'te', 0))
- if 'te' in relax_data_store.res[self.run][i].params or 'ts' in
relax_data_store.res[self.run][i].params:
+ if 'te' in cdp.res[i].params or 'ts' in cdp.res[i].params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -366,7 +365,7 @@
# Rex.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Rex', 0))
- if 'Rex' in relax_data_store.res[self.run][i].params:
+ if 'Rex' in cdp.res[i].params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -382,15 +381,18 @@
def create_mfpar(self, i, file):
"""Create the Modelfree4 input file 'mfpar'."""
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
# Spin title.
- file.write("\nspin " + relax_data_store.res[self.run][i].name
+ "_" + `relax_data_store.res[self.run][i].num` + "\n")
+ file.write("\nspin " + cdp.res[i].name + "_" +
`cdp.res[i].num` + "\n")
file.write('%-14s' % "constants")
- file.write('%-6i' % relax_data_store.res[self.run][i].num)
+ file.write('%-6i' % cdp.res[i].num)
file.write('%-7s' % self.nucleus)
- file.write('%-8.4f' % (relax_data_store.gx / 1e7))
- file.write('%-8.3f' % (relax_data_store.res[self.run][i].r * 1e10))
- file.write('%-8.3f\n' % (relax_data_store.res[self.run][i].csa *
1e6))
+ file.write('%-8.4f' % (cdp.gx / 1e7))
+ file.write('%-8.3f' % (cdp.res[i].r * 1e10))
+ file.write('%-8.3f\n' % (cdp.res[i].csa * 1e6))
The gyromagnetic ratios don't exist anymore. See
https://mail.gna.org/public/relax-devel/2008-04/msg00055.html
(Message-id: <1208028698.8064.23.camel@localhost>).
file.write('%-10s' % "vector")
file.write('%-4s' % self.atom1)
@@ -400,23 +402,29 @@
def create_run(self, file):
"""Create the script 'run.sh' for the execution of Modelfree4."""
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
file.write("#! /bin/sh\n")
file.write(self.binary + " -i mfin -d mfdata -p mfpar -m mfmodel
-o mfout -e out")
- if relax_data_store.diff[self.run].type != 'sphere':
+ if cdp.diff.type != 'sphere':
# Copy the pdb file to the model directory so there are no
problems with the existance of *.rotate files.
- system('cp ' + relax_data_store.pdb[self.run].file_name + ' '
+ self.dir)
- file.write(" -s " +
relax_data_store.pdb[self.run].file_name.split('/')[-1])
+ system('cp ' + cdp.pdb.file_name + ' ' + self.dir)
+ file.write(" -s " + cdp.pdb.file_name.split('/')[-1])
'cdp.pdb' is now 'cdp.structure'. Note that this structure has
completely changed because of the recent structural API I have been
constructing, so 'cdp.structure.file_name' may need to be replaced in
the future. It's not something you need to worry about though.
file.write("\n")
- def execute(self, run, dir, force, binary):
+ def execute(self,pipe, dir, force, binary):
The pipe argument should be axed.
"""Function for executing Modelfree4.
BUG: Control-C during execution causes the cwd to stay as dir.
"""
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
# Arguments.
- self.run = run
+ self.pipe = pipe
self.dir = dir
self.force = force
self.binary = binary
@@ -426,7 +434,7 @@
# The directory.
if dir == None:
- dir = run
+ dir = pipe
if not access(dir, F_OK):
raise RelaxDirError, ('Modelfree4', dir)
@@ -452,8 +460,8 @@
raise RelaxFileError, ('mfpar input', 'mfpar')
# Test if the 'PDB' input file exists.
- if relax_data_store.diff[run].type != 'sphere':
- pdb =
relax_data_store.pdb[self.run].file_name.split('/')[-1]
+ if cdp.diff.type != 'sphere':
+ pdb = cdp.pdb.file_name.split('/')[-1]
if not access(pdb, F_OK):
raise RelaxFileError, ('PDB', pdb)
else:
@@ -493,19 +501,22 @@
chdir(orig_dir)
- def extract(self, run, dir):
+ def extract(self, pipe, dir):
Again the pipe arg should not exist.
"""Function for extracting the Modelfree4 results out of the
'mfout' file."""
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
# Arguments.
- self.run = run
+ self.pipe = pipe
# Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# The directory.
if dir == None:
- dir = run
+ dir = pipe
if not access(dir, F_OK):
raise RelaxDirError, ('Modelfree4', dir)
@@ -531,9 +542,9 @@
# Loop over the sequence.
pos = 0
- for i in xrange(len(relax_data_store.res[self.run])):
+ for i in xrange(len(cdp.res)):
This requires the spin_loop().
# Reassign the data structure.
- data = relax_data_store.res[self.run][i]
+ data = cdp.res[i]
This can be deleted and from the spin_loop() down, the 'data' object can
be replaced by the 'spin' SpinContainer.
Cheers,
Edward
Re: r5587 - /1.3/generic_fns/palmer.py