Author: semor
Date: Sat Apr 12 22:29:26 2008
New Revision: 5606
URL: http://svn.gna.org/viewcvs/relax?rev=5606&view=rev
Log:
Corrected some of many bugs introduced in former revisions as part of the
move to the new design.
These were spotted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00056.html (# Message-id:
<1208030368.8064.47.camel@localhost>)
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=5606&r1=5605&r2=5606&view=diff
==============================================================================
--- 1.3/generic_fns/palmer.py (original)
+++ 1.3/generic_fns/palmer.py Sat Apr 12 22:29:26 2008
@@ -49,7 +49,7 @@
self.relax = relax
- def create(self, dir, force, binary, diff_search, sims, sim_type, trim,
steps, constraints, heteronuc_type, atom1, atom2, spin_id=None):
+ def create(self, dir, force, binary, diff_search, sims, sim_type, trim,
steps, constraints, heteronuc_type, atom1, atom2, spin_id):
"""Function for creating the Modelfree4 input files.
The following files are created:
@@ -60,6 +60,10 @@
dir/run.sh
"""
+ # Test if the current pipe exists.
+ if not relax_data_store.current_pipe:
+ raise RelaxNoPipeError
+
# Alias the current data pipe.
cdp = relax_data_store[relax_data_store.current_pipe]
@@ -68,7 +72,7 @@
raise RelaxNoSequenceError
# Test if the PDB file is loaded (for the spheroid and ellipsoid).
- if not cdp.diff.type == 'sphere' and not cdp.pdb.has_key:
+ if hasattr(cdp, 'diff_tensor') and not cdp.diff_tensor.type ==
'sphere' and not hasattr(cdp, 'structure'):
raise RelaxNoPdbError
# Directory creation.
@@ -95,13 +99,13 @@
self.num_frq = 0
self.frq = []
for spin in spin_loop(spin_id):
- if hasattr(cdp.res[i], 'num_frq'):
- if cdp.res[i].num_frq > self.num_frq:
+ if hasattr(spin, 'num_frq'):
+ if spin.num_frq > self.num_frq:
# Number of field strengths.
- self.num_frq = cdp.res[i].num_frq
+ self.num_frq = spin.num_frq
# Field strength values.
- for frq in cdp.res[i].frq:
+ for frq in spin.frq:
if frq not in self.frq:
self.frq.append(frq)
@@ -117,7 +121,7 @@
# Loop over the sequence.
for spin in spin_loop(spin_id):
- if hasattr(cdp.res[i], 'num_frq'):
+ if hasattr(spin, 'num_frq'):
# The 'mfdata' file.
if not self.create_mfdata(i, mfdata):
continue
@@ -134,9 +138,9 @@
mfpar.close()
# The 'run.sh' script.
- pipe = self.open_file('run.sh')
- self.create_pipe(pipe)
- pipe.close()
+ run = self.open_file('run.sh')
+ self.create_run(run)
+ run.close()
chmod(self.dir + '/run.sh', 0755)
@@ -144,7 +148,7 @@
"""Create the Modelfree4 input file 'mfmodel'."""
# Spin title.
- file.write("\nspin " + cdp.res[i].name + "_" + `cdp.res[i].num`
+ "\n")
+ file.write("\nspin " + spin.name + "_" + `spin.num` + "\n")
# Data written flag.
written = 0
@@ -155,24 +159,24 @@
r1, r2, noe = None, None, None
# Loop over the relevant relaxation data.
- for k in xrange(cdp.res[i].num_ri):
- if self.frq[j] != cdp.res[i].frq[cdp.res[i].remap_table[k]]:
+ for k in xrange(spin.num_ri):
+ if self.frq[j] != spin.frq[spin.remap_table[k]]:
continue
# Find the corresponding R1.
- if cdp.res[i].ri_labels[k] == 'R1':
- r1 = cdp.res[i].relax_data[k]
- r1_err = cdp.res[i].relax_error[k]
+ if spin.ri_labels[k] == 'R1':
+ r1 = spin.relax_data[k]
+ r1_err = spin.relax_error[k]
# Find the corresponding R2.
- elif cdp.res[i].ri_labels[k] == 'R2':
- r2 = cdp.res[i].relax_data[k]
- r2_err = cdp.res[i].relax_error[k]
+ elif spin.ri_labels[k] == 'R2':
+ r2 = spin.relax_data[k]
+ r2_err = spin.relax_error[k]
# Find the corresponding NOE.
- elif cdp.res[i].ri_labels[k] == 'NOE':
- noe = cdp.res[i].relax_data[k]
- noe_err = cdp.res[i].relax_error[k]
+ elif spin.ri_labels[k] == 'NOE':
+ noe = spin.relax_data[k]
+ noe_err = spin.relax_error[k]
# Test if the R1 exists for this frequency, otherwise skip the
data.
if r1:
@@ -201,21 +205,21 @@
"""Create the Modelfree4 input file 'mfin'."""
# Set the diffusion tensor specific values.
- if cdp.diff.type == 'sphere':
+ if cdp.diff_tensor.type == 'sphere':
diff = 'isotropic'
algorithm = 'brent'
tm = cdp.diff.tm / 1e-9
dratio = 1
theta = 0
phi = 0
- elif cdp.diff.type == 'spheroid':
+ elif cdp.diff_tensor.type == 'spheroid':
diff = 'axial'
algorithm = 'powell'
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':
+ elif cdp.diff_tensor.type == 'ellipsoid':
diff = 'anisotropic'
algorithm = 'powell'
tm = cdp.diff.tm / 1e-9
@@ -294,11 +298,11 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Spin title.
- file.write("\nspin " + cdp.res[i].name + "_" + `cdp.res[i].num`
+ "\n")
+ file.write("\nspin " + spin.name + "_" + `spin.num` + "\n")
# tloc.
file.write('%-3s%-6s%-6.1f' % ('M1', 'tloc', 0))
- if 'tm' in cdp.res[i].params:
+ if 'tm' in spin.params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -323,7 +327,7 @@
# S2f.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Sf2', 1))
- if 'S2f' in cdp.res[i].params:
+ if 'S2f' in spin.params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -337,7 +341,7 @@
# S2s.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Ss2', 1))
- if 'S2s' in cdp.res[i].params or 'S2' in cdp.res[i].params:
+ if 'S2s' in spin.params or 'S2' in spin.params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -351,7 +355,7 @@
# te.
file.write('%-3s%-6s%-6.1f' % ('M1', 'te', 0))
- if 'te' in cdp.res[i].params or 'ts' in cdp.res[i].params:
+ if 'te' in spin.params or 'ts' in spin.params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -365,7 +369,7 @@
# Rex.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Rex', 0))
- if 'Rex' in cdp.res[i].params:
+ if 'Rex' in spin.params:
file.write('%-4i' % 1)
else:
file.write('%-4i' % 0)
@@ -385,14 +389,14 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Spin title.
- file.write("\nspin " + cdp.res[i].name + "_" + `cdp.res[i].num`
+ "\n")
+ file.write("\nspin " + spin.name + "_" + `spin.num` + "\n")
file.write('%-14s' % "constants")
- file.write('%-6i' % cdp.res[i].num)
+ file.write('%-6i' % spin.num)
file.write('%-7s' % self.heteronuc_type)
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))
+ file.write('%-8.3f' % (spin.r * 1e10))
+ file.write('%-8.3f\n' % (spin.csa * 1e6))
file.write('%-10s' % "vector")
file.write('%-4s' % self.atom1)
@@ -407,14 +411,14 @@
file.write("#! /bin/sh\n")
file.write(self.binary + " -i mfin -d mfdata -p mfpar -m mfmodel -o
mfout -e out")
- if cdp.diff.type != 'sphere':
+ if cdp.diff_tensor.type != 'sphere':
# Copy the pdb file to the model directory so there are no
problems with the existance of *.rotate files.
- system('cp ' + cdp.pdb.file_name + ' ' + self.dir)
- file.write(" -s " + cdp.pdb.file_name.split('/')[-1])
+ system('cp ' + cdp.structure.file_name + ' ' + self.dir)
+ file.write(" -s " + cdp.structure.file_name.split('/')[-1])
file.write("\n")
- def execute(self,pipe, dir, force, binary):
+ def execute(self, dir, force, binary):
"""Function for executing Modelfree4.
BUG: Control-C during execution causes the cwd to stay as dir.
@@ -460,8 +464,8 @@
raise RelaxFileError, ('mfpar input', 'mfpar')
# Test if the 'PDB' input file exists.
- if cdp.diff.type != 'sphere':
- pdb = cdp.pdb.file_name.split('/')[-1]
+ if cdp.diff_tensor.type != 'sphere':
+ pdb = cdp.structure.file_name.split('/')[-1]
if not access(pdb, F_OK):
raise RelaxFileError, ('PDB', pdb)
else:
@@ -501,7 +505,7 @@
chdir(orig_dir)
- def extract(self, pipe, dir):
+ def extract(self, dir):
"""Function for extracting the Modelfree4 results out of the 'mfout'
file."""
# Alias the current data pipe.
r5606 - /1.3/generic_fns/palmer.py