Author: bugman
Date: Thu May 30 13:44:49 2013
New Revision: 19790
URL: http://svn.gna.org/viewcvs/relax?rev=19790&view=rev
Log:
Created the relax_disp.sherekhan_input user function.
This includes an icon for the GUI, and the full front and backends.
Added:
branches/relax_disp/graphics/relax_icons/16x16/sherekhan.png (with
props)
branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
- copied, changed from r19778,
branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
Modified:
branches/relax_disp/user_functions/relax_disp.py
Added: branches/relax_disp/graphics/relax_icons/16x16/sherekhan.png
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/graphics/relax_icons/16x16/sherekhan.png?rev=19790&view=auto
==============================================================================
Binary file - no diff available.
Propchange: branches/relax_disp/graphics/relax_icons/16x16/sherekhan.png
------------------------------------------------------------------------------
svn:mime-type = image/png
Copied: branches/relax_disp/specific_analyses/relax_disp/sherekhan.py (from
r19778, branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/sherekhan.py?p2=branches/relax_disp/specific_analyses/relax_disp/sherekhan.py&p1=branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py&r1=19778&r2=19790&rev=19790&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/sherekhan.py Thu May 30
13:44:49 2013
@@ -20,7 +20,7 @@
###############################################################################
# Module docstring.
-"""Functions for interfacing with Art Palmer's CPMGFit program."""
+"""Functions for interfacing with Adam Mazur's ShereKhan program."""
# Dependencies.
import dep_check
@@ -36,96 +36,19 @@
# relax module imports.
from lib.errors import RelaxError, RelaxDirError, RelaxFileError,
RelaxNoSequenceError
-from lib.io import mkdir_nofail, open_write_file, test_binary
-from lib.physical_constants import g1H
+from lib.io import mkdir_nofail, open_write_file
+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_point,
return_param_key_from_data
+from specific_analyses.relax_disp.disp_data import loop_frq, loop_point,
return_param_key_from_data
-def cpmgfit_execute(dir=None, binary='cpmgfit', force=False):
- """Execute CPMGFit for each spin input file.
-
- @keyword dir: The directory where the input files are located. If
None, this defaults to the dispersion model name in lowercase.
- @type dir: str or None
- @keyword binary: The name of the CPMGFit binary file. This can
include the path to the binary.
- @type binary: str
- @keyword force: A flag which if True will cause any pre-existing
files to be overwritten by CPMGFit.
- @type force: bool
- """
-
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if the experiment type has been set.
- if not hasattr(cdp, 'exp_type'):
- raise RelaxError("The relaxation dispersion experiment type has not
been specified.")
-
- # Test if the model has been set.
- if not hasattr(cdp, 'model'):
- raise RelaxError("The relaxation dispersion model has not been
specified.")
-
- # Translate the model.
- function = translate_model()
-
- # The directory.
- if dir == None:
- dir = lower(cdp.model)
- if not access(dir, F_OK):
- raise RelaxDirError('CPMGFit', dir)
-
- # Loop over each spin.
- for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
- # The spin input file name.
- file_in = dir + sep + spin_file_name(spin_id=spin_id)
- if not access(file_in, F_OK):
- raise RelaxFileError("spin input", file_in)
-
- # The spin output file name.
- file_out = dir + sep + spin_file_name(spin_id=spin_id, output=True)
-
- # Test the binary file string corresponds to a valid executable.
- test_binary(binary)
-
- # Execute CPMGFit.
- cmd = "%s -grid -xmgr -f %s | tee %s\n" % (binary, file_in, file_out)
- print("\n\n%s" % cmd)
- pipe = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE,
close_fds=False)
-
- # Close the pipe.
- pipe.stdin.close()
-
- # Write to stdout.
- for line in pipe.stdout.readlines():
- # Decode Python 3 byte arrays.
- if hasattr(line, 'decode'):
- line = line.decode()
-
- # Write.
- sys.stdout.write(line)
-
- # Write to stderr.
- for line in pipe.stderr.readlines():
- # Decode Python 3 byte arrays.
- if hasattr(line, 'decode'):
- line = line.decode()
-
- # Write.
- sys.stderr.write(line)
-
-
-def cpmgfit_input(dir=None, binary='cpmgfit', spin_id=None, force=False):
- """Create the CPMGFit input files.
+def sherekhan_input(dir=None, 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 binary: The name of the CPMGFit binary file. This
can include the path to the binary.
- @type binary: str
@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.
@@ -147,141 +70,53 @@
if not hasattr(cdp, 'model'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
- # Translate the model.
- function = translate_model()
+ # Test that this is a fixed time period experiment.
+ 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)
- # The 'run.sh' script.
- batch = open_write_file('batch_run.sh', dir, force)
- batch.write("#! /bin/sh\n\n")
+ # 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)
- # Generate the input files for each spin.
- for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
- file_name = create_spin_input(function=function, spin=spin,
spin_id=spin_id, dir=dir)
+ # The B0 field for the nuclei of interest in MHz.
+ file.write("%s\n" % (frq / g1H * g15N / 1e6))
- # Add the file to the batch script.
- batch.write("%s -xmgr -f %s\n" % (binary, file_name))
+ # The constant relaxation time for the CPMG experiment in seconds.
+ file.write("%s\n" % (cdp.relax_time_list[0]))
- # Close the batch script, then make it executable.
- batch.close()
- chmod(dir + sep + 'batch_run.sh', 0755)
+ # The comment line.#nu_cpmg(Hz) R2(1/s) Esd(R2))
+ file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff
(rad/s)", "Error"))
+ # 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'
-def create_spin_input(function=None, spin=None, spin_id=None, dir=None):
- """Generate the CPMGFit file for the given spin.
+ # The residue ID line.
+ file.write("# %s%s\n" % (res_name, res_num))
- @keyword function: The CPMGFit model or function name.
- @type function: str
- @keyword spin: The spin container to generate the input file for.
- @type spin: SpinContainer instance
- @keyword spin_id: The spin ID string corresponding to the spin
container.
- @type spin_id: str
- @keyword dir: The directory to place the file into.
- @type dir: str or None
- @return: The name of the file created.
- @rtype: str
- """
+ # 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 output file.
- file_name = spin_file_name(spin_id=spin_id)
- file = open_write_file(file_name=file_name, dir=dir, force=True)
+ # No data.
+ if param_key not in spin.r2eff:
+ continue
- # The title.
- file.write("title %s\n" % spin_id)
+ # Write out the data.
+ file.write("%20.15g %20.15g %20.15g\n" % (point,
spin.r2eff[param_key], spin.r2eff_err[param_key]))
- # The proton frequencies.
- frq = get_frequencies(units='T')
+ # Close the file.
+ file.close()
- # The frequency info.
- file.write("fields %s" % len(frq))
- for i in range(len(frq)):
- file.write(" %s" % frq[i])
- file.write("\n")
-
- # The function and parameters.
- if function == 'CPMG':
- # Function.
- file.write("function CPMG\n")
-
- # Parameters.
- file.write("R2 1 10 20\n")
- file.write("Rex 0 100.0 100\n")
- file.write("tex 0 10.0 100\n")
-
- # The Grace setup.
- file.write("xmgr\n")
- file.write("@ xaxis label \"1/tcp (1/ms)\"\n")
- file.write("@ yaxis label \"R2(tcp) (rad/s)\"\n")
- file.write("@ xaxis ticklabel format decimal\n")
- file.write("@ yaxis ticklabel format decimal\n")
- file.write("@ xaxis ticklabel char size 0.8\n")
- file.write("@ yaxis ticklabel char size 0.8\n")
- file.write("@ world xmin 0.0\n")
-
- # The data.
- file.write("data\n")
- for frq, point in loop_frq_point():
- # The parameter key.
- param_key = return_param_key_from_data(frq=frq, point=point)
-
- # No data.
- if param_key not in spin.r2eff:
- continue
-
- # Tesla units.
- B0 = frq * 2.0 * pi / g1H
-
- # Write out the data and error.
- file.write("%-20f %-20f %-20f %-20f\n" % (point/1000.0,
spin.r2eff[param_key], spin.r2eff_err[param_key], B0))
-
- # Close the file and return its name.
- file.close()
- return file_name
-
-
-def spin_file_name(spin_id=None, output=False):
- """Generate the unique file name for the given spin ID.
-
- @keyword spin_id: The spin ID string.
- @type spin_id: str
- @keyword output: A flag which if True will cause the CPMGFit output
rather than input name to be returned.
- @return: The file name.
- @rtype: str
- """
-
- # Construct the name.
- name = "spin_%s." % spin_id
- if output:
- name += "out"
- else:
- name += "in"
-
- # Return the file name.
- return name
-
-
-def translate_model():
- """Translate the dispersion model from relax notation to CPMGFit
notation.
-
- @return: The CPMGFit model name.
- @rtype: str
- """
-
- # A translation table (relax to CPMGFit models).
- translation = {
- 'LM63': 'CPMG'
- }
-
- # No translation, so fail.
- if cdp.model not in translation:
- raise RelaxError("The conversion of the relax model '%s' to a
CPMGFit model is not supported." % cdp.model)
-
- # Printout.
- print("Translating the relax '%s' model to the CPMGFit '%s' model." %
(cdp.model, translation[cdp.model]))
-
- # Return the translated name.
- return translation[cdp.model]
+ # Increment the field index.
+ frq_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=19790&r1=19789&r2=19790&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Thu May 30 13:44:49 2013
@@ -36,8 +36,9 @@
from pipe_control.mol_res_spin import get_spin_ids
from graphics import ANALYSIS_IMAGE_PATH, WIZARD_IMAGE_PATH
from specific_analyses.relax_disp.cpmgfit import cpmgfit_execute,
cpmgfit_input
+from specific_analyses.relax_disp.disp_data import cpmg_frq, relax_time,
spin_lock_field
from specific_analyses.relax_disp.nessy import nessy_input
-from specific_analyses.relax_disp.disp_data import cpmg_frq, relax_time,
spin_lock_field
+from specific_analyses.relax_disp.sherekhan import sherekhan_input
from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_LM63,
MODEL_R2EFF
from specific_analyses.setup import relax_disp_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
@@ -556,6 +557,43 @@
uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
+# The relax_disp.sherekhan_input user function.
+uf = uf_info.add_uf('relax_disp.sherekhan_input')
+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",
+ desc_short = "force flag",
+ desc = "A flag which if set to True will cause the files to be
overwritten if they already exist."
+)
+uf.add_keyarg(
+ name = "spin_id",
+ py_type = "str",
+ desc_short = "spin ID string",
+ desc = "The spin identification string.",
+ can_be_none = True
+)
+# 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.backend = sherekhan_input
+uf.menu_text = "&sherekhan_input"
+uf.gui_icon = "relax.sherekhan"
+uf.wizard_size = (800, 500)
+uf.wizard_apply_button = False
+uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
+
+
# The relax_disp.spin_lock_field user function.
uf = uf_info.add_uf('relax_disp.spin_lock_field')
uf.title = "Set the relaxation dispersion spin-lock field strength (nu1)."
r19790 - in /branches/relax_disp: graphics/relax_icons/16x16/ specific_analyses/relax_disp/ user_functions/