Author: bugman
Date: Thu May 23 19:21:05 2013
New Revision: 19714
URL: http://svn.gna.org/viewcvs/relax?rev=19714&view=rev
Log:
Added support for interfacing with Art Palmer's CPMGFit program.
The two new user functions relax_disp.cpmgfit_input and
relax_disp.cpmgfit_execute have been created
to interface with CPMGFit. The first creates the per spin system CPMGFit
input files as well as a
batch script for executing CPMGFit with all the input files. The second
bypasses the batch script
and allows CPMGFit to be executed from within relax. This mimics the palmer
and dasha user
functions. The back end code is in the new
specific_analyses.relax_disp.cpmgfit module.
Added:
branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19714&r1=19713&r2=19714&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Thu May 23
19:21:05 2013
@@ -25,6 +25,7 @@
# The available modules.
__all__ = [
+ 'cpmgfit',
'disp_data',
'parameters',
'variables'
Added: branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py?rev=19714&view=auto
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py (added)
+++ branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py Thu May 23
19:21:05 2013
@@ -1,0 +1,276 @@
+###############################################################################
+#
#
+# Copyright (C) 2013 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Functions for interfacing with Art Palmer's CPMGFit program."""
+
+# Dependencies.
+import dep_check
+
+# Python module imports.
+from math import pi
+from os import F_OK, access, chmod, sep
+from string import lower
+PIPE, Popen = None, None
+if dep_check.subprocess_module:
+ from subprocess import PIPE, Popen
+import sys
+
+# 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 pipe_control import pipes
+from pipe_control.frq import get_values
+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
+
+
+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_name = dir + sep + spin_file_name(spin_id=spin_id)
+ if not access(file_name, F_OK):
+ raise RelaxFileError("spin input", file_name)
+
+ # Test the binary file string corresponds to a valid executable.
+ test_binary(binary)
+
+ # Execute CPMGFit.
+ cmd = "%s -xmgr -f %s\n" % (binary, file_name)
+ 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.
+
+ @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.
+ @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()
+
+ # 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")
+
+ # 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)
+
+ # Add the file to the batch script.
+ batch.write("%s -xmgr -f %s\n" % (binary, file_name))
+
+ # Close the batch script, then make it executable.
+ batch.close()
+ chmod(dir + sep + 'batch_run.sh', 0755)
+
+
+def create_spin_input(function=None, spin=None, spin_id=None, dir=None):
+ """Generate the CPMGFit file for the given spin.
+
+ @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
+ """
+
+ # The output file.
+ file_name = spin_file_name(spin_id=spin_id)
+ file = open_write_file(file_name=file_name, dir=dir, force=True)
+
+ # The title.
+ file.write("title %s\n" % spin_id)
+
+ # The proton frequencies.
+ frq = get_values()
+
+ # Loop over each frequency.
+ for i in range(len(frq)):
+ # Convert to Tesla.
+ frq[i] = frq[i] * 2.0 * pi / g1H
+
+ # 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):
+ """Generate the unique file name for the given spin ID.
+
+ @keyword spin_id: The spin ID string.
+ @type spin_id: str
+ @return: The file name.
+ @rtype: str
+ """
+
+ return "spin_%s.in" % spin_id
+
+
+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)
+
+ # Return the translated name.
+ return translation[cdp.model]
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=19714&r1=19713&r2=19714&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Thu May 23 19:21:05 2013
@@ -35,6 +35,7 @@
from pipe_control import spectrum
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.variables import MODEL_CR72, MODEL_LM63,
MODEL_R2EFF
from specific_analyses.setup import relax_disp_obj
@@ -121,6 +122,96 @@
uf.backend = cpmg_frq
uf.menu_text = "&cpmg_frq"
uf.wizard_size = (800, 500)
+uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
+
+
+# The relax_disp.cpmgfit_execute user function.
+uf = uf_info.add_uf('relax_disp.cpmgfit_execute')
+uf.title = "Optimisation of the CPMG data using Art Palmer's CPMGFit
program."
+uf.title_short = "CPMGFit execution."
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir sel",
+ desc_short = "directory name",
+ desc = "The directory containing all of the CPMGFit input 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 results files to be
overwritten if they already exist."
+)
+uf.add_keyarg(
+ name = "binary",
+ default = "cpmgfit",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "CPMGFit executable file",
+ desc = "The name of the executable CPMGFit program file.",
+ wiz_filesel_style = FD_OPEN
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("CPMGFit will be executed once per spin as:")
+uf.desc[-1].add_prompt("$ cpmgfit -xmgr -f dir/spin_x.in")
+uf.desc[-1].add_paragraph("where x is replaced by each spin ID string. If
you would like to use a different CPMGFit executable file, change the binary
name to the appropriate file name. If the file is not located within the
environment's path, be sure to include the full path in front of the binary
file name so it can be found.")
+uf.backend = cpmgfit_execute
+uf.menu_text = "&cpmgfit_execute"
+uf.gui_icon = "oxygen.categories.applications-education"
+uf.wizard_size = (800, 600)
+uf.wizard_apply_button = False
+uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
+
+
+# The relax_disp.cpmgfit_input user function.
+uf = uf_info.add_uf('relax_disp.cpmgfit_input')
+uf.title = "Create the input files for Art Palmer's CPMGFit program."
+uf.title_short = "CPMGFit 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 = "binary",
+ default = "cpmgfit",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "CPMGFit executable file",
+ desc = "The name of the executable CPMGFit program file.",
+ wiz_filesel_style = FD_OPEN
+)
+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("The following files are created:")
+uf.desc[-1].add_list_element("'dir/spin_x.in',")
+uf.desc[-1].add_list_element("'dir/run.sh'.")
+uf.desc[-1].add_paragraph("One CPMGFit input file is created per spin and
named 'dir/spin_x.in', where x is the spin ID string. The file 'dir/run.sh'
is a batch file for executing CPMGFit for all of the spin input files. If
you would like to use a different CPMGFit executable file, change the binary
name to the appropriate file name. If the file is not located within the
environment's path, be sure to include the full path in front of the binary
name so it can be found.")
+uf.backend = cpmgfit_input
+uf.menu_text = "&cpmgfit_input"
+uf.gui_icon = "oxygen.actions.list-add-relax-blue"
+uf.wizard_size = (800, 600)
+uf.wizard_apply_button = False
uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
r19714 - in /branches/relax_disp: specific_analyses/relax_disp/ user_functions/