Author: bugman
Date: Thu May 30 15:45:13 2013
New Revision: 19793
URL: http://svn.gna.org/viewcvs/relax?rev=19793&view=rev
Log:
Redesign of the relax_disp.sherekhan_input user function to handle spin
clustering.
Modified:
branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/sherekhan.py?rev=19793&r1=19792&r2=19793&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/sherekhan.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/sherekhan.py Thu May 30
15:45:13 2013
@@ -40,15 +40,13 @@
from lib.physical_constants import g1H, g15N
from pipe_control import pipes
from pipe_control.spectrometer import get_frequencies
-from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
-from specific_analyses.relax_disp.disp_data import loop_frq, loop_point,
return_param_key_from_data
+from pipe_control.mol_res_spin import exists_mol_res_spin_data,
return_residue, spin_loop
+from specific_analyses.relax_disp.disp_data import loop_cluster, loop_frq,
loop_point, return_param_key_from_data
-def sherekhan_input(dir=None, spin_id=None, force=False):
+def sherekhan_input(spin_id=None, force=False):
"""Create the ShereKhan input files.
- @keyword dir: The optional directory to place the files
into. If None, then the files will be placed into a directory named after
the dispersion model.
- @type dir: str or None
@keyword spin_id: The spin ID string to restrict the file
creation to.
@type spin_id: str
@keyword force: A flag which if True will cause all
pre-existing files to be overwritten.
@@ -74,49 +72,67 @@
if len(cdp.relax_time_list) != 1:
raise RelaxError("ShereKhan only supports the fixed time
relaxation dispersion experiments.")
- # Directory creation.
- if dir == None:
- dir = lower(cdp.model)
- mkdir_nofail(dir, verbosity=0)
+ # Loop over the spin blocks.
+ cluster_index = 0
+ for spins, spin_ids in loop_cluster():
+ # Loop over the magnetic fields.
+ frq_index = 0
+ for frq in loop_frq():
+ # The ShereKhan input file for the spin cluster.
+ file_name = 'sherekhan_frq%s.in' % (frq_index+1)
+ dir_name = 'cluster%s' % (cluster_index+1)
+ file = open_write_file(file_name=file_name, dir=dir_name,
force=force)
- # Loop over the magnetic fields.
- frq_index = 0
- for frq in loop_frq():
- # The ShereKhan input file.
- file = open_write_file('sherekhan_%s.py' % (frq_index+1), dir, force)
+ # The B0 field for the nuclei of interest in MHz (must be
positive to be accepted by the server).
+ file.write("%s\n" % abs(frq / g1H * g15N / 1e6))
- # The B0 field for the nuclei of interest in MHz.
- file.write("%s\n" % (frq / g1H * g15N / 1e6))
+ # The constant relaxation time for the CPMG experiment in
seconds.
+ file.write("%s\n" % (cdp.relax_time_list[0]))
- # The constant relaxation time for the CPMG experiment in seconds.
- file.write("%s\n" % (cdp.relax_time_list[0]))
+ # The comment line.
+ file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff
(rad/s)", "Error"))
- # The comment line.#nu_cpmg(Hz) R2(1/s) Esd(R2))
- file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff
(rad/s)", "Error"))
+ # Loop over the spins of the cluster.
+ for i in range(len(spins)):
+ # Get the residue container.
+ res = return_residue(spin_ids[i])
- # Generate the input files for each spin.
- for spin, mol_name, res_num, res_name, id in
spin_loop(full_info=True, selection=spin_id, return_id=True, skip_desel=True):
- # Name the residue if needed.
- if res_name == None:
- res_name = 'X'
+ # Name the residue if needed.
+ res_name = res.name
+ if res_name == None:
+ res_name = 'X'
- # The residue ID line.
- file.write("# %s%s\n" % (res_name, res_num))
+ # Initialise the lines to output (to be able to catch
missing data).
+ lines = []
- # Loop over the dispersion points.
- for point in loop_point(skip_ref=True):
- # The parameter key.
- param_key = return_param_key_from_data(frq=frq, point=point)
+ # The residue ID line.
+ lines.append("# %s%s\n" % (res_name, res.num))
+
+ # Loop over the dispersion points.
+ for point in loop_point(skip_ref=True):
+ # The parameter key.
+ param_key = return_param_key_from_data(frq=frq,
point=point)
+
+ # No data.
+ if param_key not in spins[i].r2eff:
+ continue
+
+ # Store the data.
+ lines.append("%20.15g %20.15g %20.15g\n" % (point,
spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
# No data.
- if param_key not in spin.r2eff:
+ if len(lines) == 1:
continue
# Write out the data.
- file.write("%20.15g %20.15g %20.15g\n" % (point,
spin.r2eff[param_key], spin.r2eff_err[param_key]))
+ for line in lines:
+ file.write(line)
- # Close the file.
- file.close()
+ # Close the file.
+ file.close()
- # Increment the field index.
- frq_index += 1
+ # Increment the field index.
+ frq_index += 1
+
+ # Increment the cluster index.
+ cluster_index += 1
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=19793&r1=19792&r2=19793&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Thu May 30 15:45:13 2013
@@ -562,14 +562,6 @@
uf.title = "Create the input files for Adam Mazur's ShereKhan program."
uf.title_short = "ShereKhan input file creation."
uf.add_keyarg(
- name = "dir",
- py_type = "str",
- arg_type = "dir sel",
- desc_short = "directory name",
- desc = "The directory to place the files. If not given, this defaults
to the model name in lower case.",
- can_be_none = True
-)
-uf.add_keyarg(
name = "force",
default = False,
py_type = "bool",
@@ -585,7 +577,7 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This creates the files required for the ShereKhan
server located at http://sherekhan.bionmr.org/. One file per field strength
will be created. These will be named 'dir/sherekhan_x.in', where x is a
number starting from 1 and dir is the specified directory which if not given
defaults to the model name in lower case.")
+uf.desc[-1].add_paragraph("This creates the files required for the ShereKhan
server located at http://sherekhan.bionmr.org/. One file per spin cluster
per field strength will be created. These will be placed in the directory
'clusterx' and named 'sherekhan_frqy.in', where x is the cluster index
starting from 1 and y is the magnetic field strength index starting from 1.")
uf.backend = sherekhan_input
uf.menu_text = "&sherekhan_input"
uf.gui_icon = "relax.sherekhan"
r19793 - in /branches/relax_disp: specific_analyses/relax_disp/sherekhan.py user_functions/relax_disp.py