Author: bugman
Date: Fri Aug 16 19:14:57 2013
New Revision: 20612
URL: http://svn.gna.org/viewcvs/relax?rev=20612&view=rev
Log:
The lib.spectrum.peak_list.intensity_generic() function now operates on the
Peak_list object.
Modified:
branches/peak_intensities/lib/spectrum/peak_list.py
Modified: branches/peak_intensities/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/lib/spectrum/peak_list.py?rev=20612&r1=20611&r2=20612&view=diff
==============================================================================
--- branches/peak_intensities/lib/spectrum/peak_list.py (original)
+++ branches/peak_intensities/lib/spectrum/peak_list.py Fri Aug 16 19:14:57
2013
@@ -70,12 +70,11 @@
return 'generic'
-def intensity_generic(file_data=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,
data_col=None, sep=None, spin_id=None):
- """Return the process data from the generic peak intensity file.
-
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
+def intensity_generic(peak_list=None, file_data=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, data_col=None, sep=None, spin_id=None):
+ """Extract the peak intensity information from the generic column
formatted peak list.
+
+ @keyword peak_list: The peak list object to place all data into.
+ @type peak_list: lib.spectrum.objects.Peak_list instance
@keyword file_data: The data extracted from the file converted into
a list of lists.
@type file_data: list of lists of 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.
@@ -95,8 +94,6 @@
@keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins.
@type spin_id: None or str
@raises RelaxError: When the expected peak intensity is not a float.
- @return: The extracted data as a list of lists. The
first dimension corresponds to the spin. The second dimension consists of
the proton name, heteronucleus name, spin ID string, and the intensity value.
- @rtype: list of lists of str, str, str, float
"""
# Check the intensity column argument.
@@ -110,37 +107,25 @@
if not isinstance(data_col, list):
data_col = [data_col]
- # Loop over the data columns.
- data = []
- for i in range(len(data_col)):
- # Loop over the data.
- row_index = 0
- for values in read_spin_data(file_data=file_data,
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, data_col=data_col[i], sep=sep, spin_id=spin_id):
- # Check the values.
- if len(values) != 6:
- raise RelaxError("The molecule name, residue number and
name, spin number and name, and value columns could not be found in the data
%s." % repr(values))
-
- # Unpack.
- mol_name, res_num, res_name, spin_num, spin_name, value = values
-
- # Create the unique spin ID.
- id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
-
- # Store the necessary data.
- if i == 0:
- # Convert the value to a list if multiple columns are
present.
- if len(data_col) > 1:
- data.append([None, None, id, [value], id])
- else:
- data.append([None, None, id, value, id])
- else:
- data[row_index][3].append(value)
-
- # Go to the next row.
- row_index += 1
-
- # Return the data.
- return data
+ # Loop over the file data.
+ for line in file_data:
+ # Loop over the intensity columns, storing the data.
+ intensity = []
+ for i in range(len(data_col)):
+ # Extract the data for the single line (loop of a single
element).
+ for values in read_spin_data(file_data=[line],
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, data_col=data_col[i], sep=sep, spin_id=spin_id):
+ # Check the values.
+ if len(values) != 6:
+ raise RelaxError("The molecule name, residue number and
name, spin number and name, and value columns could not be found in the data
%s." % repr(values))
+
+ # Unpack.
+ mol_name, res_num, res_name, spin_num, spin_name, value =
values
+
+ # Store the intensity.
+ intensity.append(value)
+
+ # Add the assignment to the peak list object.
+ peak_list.add(mol_names=[mol_name, mol_name], res_nums=[res_num,
res_num], res_names=[res_name, res_name], spin_nums=[spin_num, spin_num],
spin_names=[spin_name, spin_name], intensity=intensity)
def read_peak_list(file=None, dir=None, int_col=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):
r20612 - /branches/peak_intensities/lib/spectrum/peak_list.py