Author: bugman
Date: Sat Oct 11 23:47:44 2008
New Revision: 7623
URL: http://svn.gna.org/viewcvs/relax?rev=7623&view=rev
Log:
Converted the create_mfmodel() and create_mfpar() functions to the new design.
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=7623&r1=7622&r2=7623&view=diff
==============================================================================
--- 1.3/generic_fns/palmer.py (original)
+++ 1.3/generic_fns/palmer.py Sat Oct 11 23:47:44 2008
@@ -39,6 +39,7 @@
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
from generic_fns import pipes
+from physical_constants import return_gyromagnetic_ratio
from relax_errors import RelaxDirError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoModelError, RelaxNoPdbError,
RelaxNoSequenceError, RelaxNucleusError, RelaxProgFailError
from relax_io import mkdir_nofail, open_write_file, test_binary
@@ -133,17 +134,17 @@
mfpar = open_write_file('mfpar', dir, force)
# Loop over the sequence.
- for spin, id in spin_loop(spin_id, return_id=True):
+ for spin, mol_name, res_num, res_name, id in spin_loop(spin_id,
full_info=True, return_id=True):
if hasattr(spin, 'num_frq'):
# The 'mfdata' file.
if not create_mfdata(mfdata, spin=spin, spin_id=id,
num_frq=num_frq, frq=frq):
continue
# The 'mfmodel' file.
- create_mfmodel(spin, mfmodel)
+ create_mfmodel(mfmodel, spin=spin, spin_id=id, steps=steps,
constraints=constraints)
# The 'mfpar' file.
- create_mfpar(spin, mfpar)
+ create_mfpar(mfpar, spin=spin, spin_id=id, res_num=res_num,
atom1=atom1, atom2=atom2)
# Close the 'mfdata', 'mfmodel', and 'mfpar' files.
mfdata.close()
@@ -338,14 +339,26 @@
file.write('%4i\n' % 10)
-def create_mfmodel(i, file):
- """Create the Modelfree4 input file 'mfmodel'."""
+def create_mfmodel(file, spin=None, spin_id=None, steps=None,
constraints=None):
+ """Create the Modelfree4 input file 'mfmodel'.
+
+ @param file: The writable file object.
+ @type file: file object
+ @keyword spin: The spin container.
+ @type spin: SpinContainer instance
+ @keyword spin_id: The spin identification string.
+ @type spin_id str
+ @keyword steps: The grid search size (see the Modelfree4 manual
for details).
+ @type steps: int
+ @keyword constraints: A flag which if True will result in constrained
optimisation.
+ @type constraints: bool
+ """
# Alias the current data pipe.
cdp = pipes.get_pipe()
# Spin title.
- file.write("\nspin " + spin.name + "_" + `spin.num` + "\n")
+ file.write("\nspin " + spin_id + "\n")
# tloc.
file.write('%-3s%-6s%-6.1f' % ('M1', 'tloc', 0))
@@ -354,23 +367,23 @@
else:
file.write('%-4i' % 0)
- if self.constraints:
+ if constraints:
file.write('%-2i' % 2)
else:
file.write('%-2i' % 0)
- file.write('%11.3f%12.3f %-4s\n' % (0, 20, self.steps))
+ file.write('%11.3f%12.3f %-4s\n' % (0, 20, steps))
# Theta.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Theta', 0))
file.write('%-4i' % 0)
- if self.constraints:
+ if constraints:
file.write('%-2i' % 2)
else:
file.write('%-2i' % 0)
- file.write('%11.3f%12.3f %-4s\n' % (0, 90, self.steps))
+ file.write('%11.3f%12.3f %-4s\n' % (0, 90, steps))
# S2f.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Sf2', 1))
@@ -379,12 +392,12 @@
else:
file.write('%-4i' % 0)
- if self.constraints:
+ if constraints:
file.write('%-2i' % 2)
else:
file.write('%-2i' % 0)
- file.write('%11.3f%12.3f %-4s\n' % (0, 1, self.steps))
+ file.write('%11.3f%12.3f %-4s\n' % (0, 1, steps))
# S2s.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Ss2', 1))
@@ -393,12 +406,12 @@
else:
file.write('%-4i' % 0)
- if self.constraints:
+ if constraints:
file.write('%-2i' % 2)
else:
file.write('%-2i' % 0)
- file.write('%11.3f%12.3f %-4s\n' % (0, 1, self.steps))
+ file.write('%11.3f%12.3f %-4s\n' % (0, 1, steps))
# te.
file.write('%-3s%-6s%-6.1f' % ('M1', 'te', 0))
@@ -407,12 +420,12 @@
else:
file.write('%-4i' % 0)
- if self.constraints:
+ if constraints:
file.write('%-2i' % 2)
else:
file.write('%-2i' % 0)
- file.write('%11.3f%12.3f %-4s\n' % (0, 10000, self.steps))
+ file.write('%11.3f%12.3f %-4s\n' % (0, 10000, steps))
# Rex.
file.write('%-3s%-6s%-6.1f' % ('M1', 'Rex', 0))
@@ -421,33 +434,47 @@
else:
file.write('%-4i' % 0)
- if self.constraints:
+ if constraints:
file.write('%-2i' % -1)
else:
file.write('%-2i' % 0)
- file.write('%11.3f%12.3f %-4s\n' % (0, 20, self.steps))
-
-
-def create_mfpar(i, file):
- """Create the Modelfree4 input file 'mfpar'."""
+ file.write('%11.3f%12.3f %-4s\n' % (0, 20, steps))
+
+
+def create_mfpar(file, spin=None, spin_id=None, res_num=None, atom1=None,
atom2=None):
+ """Create the Modelfree4 input file 'mfpar'.
+
+ @param file: The writable file object.
+ @type file: file object
+ @keyword spin: The spin container.
+ @type spin: SpinContainer instance
+ @keyword spin_id: The spin identification string.
+ @type spin_id str
+ @keyword res_num: The residue number from the PDB file corresponding
to the spin.
+ @type res_num: int
+ @keyword atom1: The name of the heteronucleus in the PDB file.
+ @type atom1: str
+ @keyword atom2: The name of the proton in the PDB file.
+ @type atom2: str
+ """
# Alias the current data pipe.
cdp = pipes.get_pipe()
# Spin title.
- file.write("\nspin " + spin.name + "_" + `spin.num` + "\n")
+ file.write("\nspin " + spin_id + "\n")
file.write('%-14s' % "constants")
- file.write('%-6i' % spin.num)
+ file.write('%-6i' % res_num)
file.write('%-7s' % spin.heteronuc_type)
- file.write('%-8.4f' % ([return_gyromagnetic_ratio(spin.heteronuc_type)]
/ 1e7))
+ file.write('%-8.4f' % (return_gyromagnetic_ratio(spin.heteronuc_type) /
1e7))
file.write('%-8.3f' % (spin.r * 1e10))
file.write('%-8.3f\n' % (spin.csa * 1e6))
file.write('%-10s' % "vector")
- file.write('%-4s' % self.atom1)
- file.write('%-4s\n' % self.atom2)
+ file.write('%-4s' % atom1)
+ file.write('%-4s\n' % atom2)
def create_run(file):
r7623 - /1.3/generic_fns/palmer.py