Author: bugman
Date: Fri Aug 16 17:15:24 2013
New Revision: 20599
URL: http://svn.gna.org/viewcvs/relax?rev=20599&view=rev
Log:
Created the new lib.spectrum.objects module.
This will hold temporary data structures for representing peak lists and
other spectral data. The
module currently contains the Peak_list class which is used to hold peak list
data.
Added:
branches/peak_intensities/lib/spectrum/objects.py
Modified:
branches/peak_intensities/lib/spectrum/__init__.py
Modified: branches/peak_intensities/lib/spectrum/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/lib/spectrum/__init__.py?rev=20599&r1=20598&r2=20599&view=diff
==============================================================================
--- branches/peak_intensities/lib/spectrum/__init__.py (original)
+++ branches/peak_intensities/lib/spectrum/__init__.py Fri Aug 16 17:15:24
2013
@@ -23,5 +23,6 @@
"""The relax-lib NMR package - a library of functions for spectral data."""
__all__ = [
- 'peak_list'
+ 'peak_list',
+ 'objects'
]
Added: branches/peak_intensities/lib/spectrum/objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/lib/spectrum/objects.py?rev=20599&view=auto
==============================================================================
--- branches/peak_intensities/lib/spectrum/objects.py (added)
+++ branches/peak_intensities/lib/spectrum/objects.py Fri Aug 16 17:15:24 2013
@@ -1,0 +1,96 @@
+###############################################################################
+#
#
+# 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/>.
#
+#
#
+###############################################################################
+
+# Package docstring.
+"""Module containing objects used to handle peak list data.
+
+These objects are only temporary. In the future, they may be made permanent
by shifting them into the relax data storage object.
+"""
+
+# relax module imports.
+from lib.errors import RelaxError
+
+
+class Assignment:
+ """A special container for a single assignment in a peak list."""
+
+
+
+class Peak_list(list):
+ """The object used to represent a peak list."""
+
+ def __init__(self, dim=2):
+ """Set up the object.
+
+ @keyword dim: The dimensionality of the peak list.
+ @type dim: int
+ """
+
+ # Store the dimensionality.
+ self._dim = dim
+
+
+ def add(self, mol_names=None, res_nums=None, res_names=None,
spin_nums=None, spin_names=None, shifts=None, intensity=None):
+ """Add a peak list element.
+
+
+ @keyword mol_names: The list of molecule names for each
dimension of the assignment.
+ @type mol_names: list of str or None
+ @keyword res_nums: The list of residue numbers for each
dimension of the assignment.
+ @type res_nums: list of int or None
+ @keyword res_names: The list of residue names for each dimension
of the assignment.
+ @type res_names: list of str or None
+ @keyword spin_nums: The list of spin numbers for each dimension
of the assignment.
+ @type spin_nums: list of int or None
+ @keyword spin_names: The list of spin names for each dimension of
the assignment.
+ @type spin_names: list of str or None
+ @keyword shifts: The chemical shifts for each dimension of
the assignment in ppm.
+ @type shifts: list of float or None
+ @keyword intensity: The single intensity value for the peak.
+ @type intensity: float or None
+ """
+
+ # Check the arguments.
+ if mol_names != None and len(mol_names) != self._dim:
+ raise RelaxError("The molecule names %s must be a list of %s
dimensions." % (mol_names, self._dim))
+ if res_nums != None and len(res_nums) != self._dim:
+ raise RelaxError("The residue numbers %s must be a list of %s
dimensions." % (res_nums, self._dim))
+ if res_names != None and len(res_names) != self._dim:
+ raise RelaxError("The residue names %s must be a list of %s
dimensions." % (res_names, self._dim))
+ if spin_nums != None and len(spin_nums) != self._dim:
+ raise RelaxError("The spin numbers %s must be a list of %s
dimensions." % (spin_nums, self._dim))
+ if spin_names != None and len(spin_names) != self._dim:
+ raise RelaxError("The spin names %s must be a list of %s
dimensions." % (spin_names, self._dim))
+ if shifts != None and len(shifts) != self._dim:
+ raise RelaxError("The chemical shifts %s must be a list of %s
dimensions." % (shifts, self._dim))
+
+ # Add a new element.
+ self.append(Assignment)
+
+ # Store the data.
+ assign = self[-1]
+ assign.mol_names = mol_names
+ assign.res_nums = res_nums
+ assign.res_names = res_names
+ assign.spin_nums = spin_nums
+ assign.spin_names = spin_names
+ assign.shifts = shifts
+ assign.intensity = intensity
r20599 - in /branches/peak_intensities/lib/spectrum: __init__.py objects.py