Author: bugman
Date: Wed Aug 21 11:43:00 2013
New Revision: 20657
URL: http://svn.gna.org/viewcvs/relax?rev=20657&view=rev
Log:
Created the chemical_shift.read user function.
This includes both the front and back end code.
Added:
trunk/pipe_control/chemical_shift.py
trunk/user_functions/chemical_shift.py
Modified:
trunk/pipe_control/__init__.py
trunk/user_functions/__init__.py
Modified: trunk/pipe_control/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/__init__.py?rev=20657&r1=20656&r2=20657&view=diff
==============================================================================
--- trunk/pipe_control/__init__.py (original)
+++ trunk/pipe_control/__init__.py Wed Aug 21 11:43:00 2013
@@ -27,6 +27,7 @@
'angles',
'bmrb',
'bruker',
+ 'chemical_shift',
'dasha',
'diffusion_tensor',
'domain',
Added: trunk/pipe_control/chemical_shift.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/chemical_shift.py?rev=20657&view=auto
==============================================================================
--- trunk/pipe_control/chemical_shift.py (added)
+++ trunk/pipe_control/chemical_shift.py Wed Aug 21 11:43:00 2013
@@ -1,0 +1,116 @@
+###############################################################################
+#
#
+# 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.
+"""Module containing functions for the handling of chemical shifts."""
+
+
+# Python module imports.
+from warnings import warn
+
+# relax module imports.
+from lib.errors import RelaxError, RelaxNoSequenceError
+from lib.spectrum.peak_list import read_peak_list
+from lib.warnings import RelaxNoSpinWarning
+from pipe_control import pipes
+from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin
+
+
+def read(file=None, dir=None, spin_id_col=None, mol_name_col=None,
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, spin_id=None, verbose=True):
+ """Read the peak intensity data.
+
+ @keyword file: The name of the file containing the peak
intensities.
+ @type file: str
+ @keyword dir: The directory where the file is located.
+ @type dir: str
+ @keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity file format). If supplied, the mol_name_col,
res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be
none.
+ @type spin_id_col: int or None
+ @keyword mol_name_col: The column containing the molecule name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type mol_name_col: int or None
+ @keyword res_name_col: The column containing the residue name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type res_name_col: int or None
+ @keyword res_num_col: The column containing the residue number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type res_num_col: int or None
+ @keyword spin_name_col: The column containing the spin name information
(used by the generic intensity file format). If supplied, spin_id_col must
be None.
+ @type spin_name_col: int or None
+ @keyword spin_num_col: The column containing the spin number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type spin_num_col: int or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab
formatted file, the ID's are auto generated in form of Z_Ai.
+ @type spin_id: None or str
+ @keyword verbose: A flag which if True will cause all chemical
shift data loaded to be printed out.
+ @type verbose: bool
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Check the file name.
+ if file == None:
+ raise RelaxError("The file name must be supplied.")
+
+ # Read the peak list data.
+ peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
+
+ # Loop over the assignments.
+ data = []
+ data_flag = False
+ dim = peak_list._dim
+ for assign in peak_list:
+ # Loop over the dimensions of the peak list.
+ for i in range(dim):
+ # Generate the spin_id.
+ spin_id = generate_spin_id_unique(res_num=assign.res_nums[i],
spin_name=assign.spin_names[i])
+
+ # Get the spin container.
+ spin = return_spin(spin_id)
+ if not spin:
+ warn(RelaxNoSpinWarning(spin_id))
+ continue
+
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Store the shift.
+ spin.chemical_shift = assign.shifts[i]
+
+ # Switch the flag.
+ data_flag = True
+
+ # Append the data for printing out.
+ data.append([spin_id, repr(spin.chemical_shift)])
+
+ # No data.
+ if not data_flag:
+ raise RelaxError("No chemical shifts could be loaded from the peak
list")
+
+ # Print out.
+ if verbose:
+ print("\nThe following chemical shifts have been loaded into the
relax data store:\n")
+ write_data(out=sys.stdout, headings=["Spin_ID", "Chemical shift"],
data=data)
+
+
Modified: trunk/user_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/__init__.py?rev=20657&r1=20656&r2=20657&view=diff
==============================================================================
--- trunk/user_functions/__init__.py (original)
+++ trunk/user_functions/__init__.py Wed Aug 21 11:43:00 2013
@@ -37,6 +37,7 @@
'angles',
'bmrb',
'bruker',
+ 'chemical_shift',
'consistency_tests',
'dasha',
'deselect',
@@ -91,6 +92,7 @@
import user_functions.angles
import user_functions.bmrb
import user_functions.bruker
+ import user_functions.chemical_shift
import user_functions.consistency_tests
import user_functions.dasha
import user_functions.deselect
Added: trunk/user_functions/chemical_shift.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/chemical_shift.py?rev=20657&view=auto
==============================================================================
--- trunk/user_functions/chemical_shift.py (added)
+++ trunk/user_functions/chemical_shift.py Wed Aug 21 11:43:00 2013
@@ -1,0 +1,141 @@
+###############################################################################
+#
#
+# 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.
+"""The chemical_shift user function definitions."""
+
+# Python module imports.
+import dep_check
+if dep_check.wx_module:
+ from wx import FD_OPEN
+else:
+ FD_OPEN = -1
+from os import sep
+
+# relax module imports.
+from graphics import WIZARD_IMAGE_PATH
+from pipe_control import chemical_shift
+from user_functions.data import Uf_info; uf_info = Uf_info()
+from user_functions.objects import Desc_container
+
+
+# The user function class.
+uf_class = uf_info.add_class('chemical_shift')
+uf_class.title = "Class for handling chemical shifts."
+uf_class.menu_text = "&chemical_shift"
+uf_class.gui_icon = "relax.chemical_shift"
+
+
+# The chemical_shift.read user function.
+uf = uf_info.add_uf('chemical_shift.read')
+uf.title = "Read chemical shifts from a file."
+uf.title_short = "Chemical shift reading."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the peak list of generic formatted file containing
the chemical shifts.",
+ wiz_filesel_style = FD_OPEN
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory where the file is located.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin ID string column",
+ desc = "The spin ID string column used by the generic file format (an
alternative to the mol, res, and spin name and number columns).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "mol_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "molecule name column",
+ desc = "The molecule name column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "res_num_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "residue number column",
+ desc = "The residue number column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "res_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "residue name column",
+ desc = "The residue name column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_num_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin number column",
+ desc = "The spin number column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_name_col",
+ py_type = "int",
+ arg_type = "free format",
+ desc_short = "spin name column",
+ desc = "The spin name column used by the generic file format
(alternative to the spin ID column).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "sep",
+ py_type = "str",
+ arg_type = "free format",
+ desc_short = "column separator",
+ desc = "The column separator used by the generic format (the default is
white space).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id",
+ py_type = "str",
+ desc_short = "spin ID string",
+ desc = "The spin ID string used to restrict the loading of data to
certain spin subsets.",
+ can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This will read chemical shifts from a peak list
or a generic column formatted file.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("The following commands will read the chemical
shifts out of the Sparky peak list '10ms.list':")
+uf.desc[-1].add_prompt("relax> chemical_shift.read('10ms.list')")
+uf.backend = chemical_shift.read
+uf.menu_text = "&read"
+uf.gui_icon = "oxygen.actions.document-open"
+uf.wizard_size = (800, 500)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
r20657 - in /trunk: pipe_control/ user_functions/