Author: bugman
Date: Wed Aug 21 15:08:03 2013
New Revision: 20664
URL: http://svn.gna.org/viewcvs/relax?rev=20664&view=rev
Log:
Expanded the functionality of the lib.spectrum.sparky.read_list() function.
Now the dimensionality of the peak list is automatically determined, and all
peak lists from 1D to
4D are supported. The chemical shifts are also automatically detected and
extracted from the list
and placed into the peak list object. The peak intensity data is also
automatically detected,
therefore the int_col argument is no longer used.
Modified:
trunk/lib/spectrum/peak_list.py
trunk/lib/spectrum/sparky.py
Modified: trunk/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/peak_list.py?rev=20664&r1=20663&r2=20664&view=diff
==============================================================================
--- trunk/lib/spectrum/peak_list.py (original)
+++ trunk/lib/spectrum/peak_list.py Wed Aug 21 15:08:03 2013
@@ -135,7 +135,7 @@
@type file: str
@keyword dir: The directory where the file is located.
@type dir: str
- @keyword int_col: The column containing the peak intensity data.
If set to None, no intensity data will be returned.
+ @keyword int_col: The column containing the peak intensity data.
If set to None, the auto-detection of intensity data will be attempted.
@type int_col: None or int
@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
@@ -196,7 +196,7 @@
print("Sparky formatted data file.\n")
# Extract the data.
- sparky.read_list(peak_list=peak_list, file_data=file_data,
int_col=int_col)
+ sparky.read_list(peak_list=peak_list, file_data=file_data)
# XEasy.
elif format == 'xeasy':
Modified: trunk/lib/spectrum/sparky.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=20664&r1=20663&r2=20664&view=diff
==============================================================================
--- trunk/lib/spectrum/sparky.py (original)
+++ trunk/lib/spectrum/sparky.py Wed Aug 21 15:08:03 2013
@@ -32,15 +32,13 @@
from lib.io import open_write_file, strip
-def read_list(peak_list=None, file_data=None, int_col=3):
+def read_list(peak_list=None, file_data=None):
"""Extract the peak intensity information from the Sparky peak intensity
file.
@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 int_col: The column containing the peak intensity data (for a
non-standard formatted file).
- @type int_col: int
@raises RelaxError: When the expected peak intensity is not a float.
"""
@@ -52,15 +50,45 @@
num = num + 1
print("Number of header lines found: %s" % num)
- # Default intensity column.
- if int_col == None:
- int_col = 3
+ # The columns according to the file.
+ w1_col = None
+ w2_col = None
+ w3_col = None
+ w4_col = None
+ int_col = None
+ for i in range(len(file_data[0])):
+ # The chemical shifts.
+ if file_data[0][i] == 'w1':
+ w1_col = i
+ elif file_data[0][i] == 'w2':
+ w2_col = i
+ elif file_data[0][i] == 'w3':
+ w3_col = i
+ elif file_data[0][i] == 'w4':
+ w4_col = i
+
+ # The peak height.
+ elif file_data[0][i] == 'Data' and file_data[0][i+1] == 'Height':
+ int_col = i
# Remove the header.
file_data = file_data[num:]
# Strip the data.
file_data = strip(file_data)
+
+ # The dimensionality.
+ if w4_col != None:
+ dim = 4
+ elif w3_col != None:
+ dim = 3
+ elif w2_col != None:
+ dim = 2
+ elif w1_col != None:
+ dim = 1
+ else:
+ raise RelaxError("The dimensionality of the peak list cannot be
determined.")
+ print("%sD peak list detected." % dim)
# Loop over the file data.
for line in file_data:
@@ -68,16 +96,29 @@
if line[0] == '?-?':
continue
- # First split by the 2D separator.
- assign1, assign2 = split('-', line[0])
-
- # The assignment of the first dimension.
- row1 = split('([A-Z]+)', assign1)
- name1 = row1[-2] + row1[-1]
-
- # The assignment of the second dimension.
- row2 = split('([A-Z]+)', assign2)
- name2 = row2[-2] + row2[-1]
+ # Split up the assignments.
+ if dim == 1:
+ assign1 = line[0]
+ elif dim == 2:
+ assign1, assign2 = split('-', line[0])
+ elif dim == 3:
+ assign1, assign2, assign3 = split('-', line[0])
+ elif dim == 4:
+ assign1, assign2, assign3, assign4 = split('-', line[0])
+
+ # Process the assignment for each dimension.
+ if dim >= 1:
+ row1 = split('([A-Z]+)', assign1)
+ name1 = row1[-2] + row1[-1]
+ if dim >= 2:
+ row2 = split('([A-Z]+)', assign2)
+ name2 = row2[-2] + row2[-1]
+ if dim >= 3:
+ row3 = split('([A-Z]+)', assign3)
+ name3 = row3[-2] + row3[-1]
+ if dim >= 4:
+ row4 = split('([A-Z]+)', assign4)
+ name4 = row4[-2] + row4[-1]
# The residue number.
try:
@@ -85,14 +126,48 @@
except:
raise RelaxError("Improperly formatted Sparky file, cannot
process the assignment '%s'." % line[0])
+ # Chemical shifts.
+ w1 = None
+ w2 = None
+ w3 = None
+ w4 = None
+ if w1_col != None:
+ try:
+ w1 = float(line[w1_col])
+ except ValueError:
+ raise RelaxError("The chemical shift from the line %s is
invalid." % line)
+ if w2_col != None:
+ try:
+ w2 = float(line[w2_col])
+ except ValueError:
+ raise RelaxError("The chemical shift from the line %s is
invalid." % line)
+ if w3_col != None:
+ try:
+ w3 = float(line[w3_col])
+ except ValueError:
+ raise RelaxError("The chemical shift from the line %s is
invalid." % line)
+ if w4_col != None:
+ try:
+ w4 = float(line[w4_col])
+ except ValueError:
+ raise RelaxError("The chemical shift from the line %s is
invalid." % line)
+
# Intensity.
- try:
- intensity = float(line[int_col])
- except ValueError:
- raise RelaxError("The peak intensity value %s from the line %s
is invalid." % (intensity, line))
+ if int_col != None:
+ try:
+ intensity = float(line[int_col])
+ except ValueError:
+ raise RelaxError("The peak intensity value from the line %s
is invalid." % line)
# Add the assignment to the peak list object.
- peak_list.add(res_nums=[res_num, res_num], spin_names=[name1,
name2], intensity=intensity)
+ if dim == 1:
+ peak_list.add(res_nums=[res_num], spin_names=[name1],
shifts=[w1], intensity=intensity)
+ elif dim == 2:
+ peak_list.add(res_nums=[res_num, res_num], spin_names=[name1,
name2], shifts=[w1, w2], intensity=intensity)
+ elif dim == 3:
+ peak_list.add(res_nums=[res_num, res_num, res_num],
spin_names=[name1, name2, name3], shifts=[w1, w2, w3], intensity=intensity)
+ elif dim == 4:
+ peak_list.add(res_nums=[res_num, res_num, res_num, res_num],
spin_names=[name1, name2, name3, name4], shifts=[w1, w2, w3, w4],
intensity=intensity)
def write_list(file_prefix=None, dir=None, res_names=None, res_nums=None,
atom1_names=None, atom2_names=None, w1=None, w2=None, data_height=None,
force=True):
r20664 - in /trunk/lib/spectrum: peak_list.py sparky.py