Author: bugman
Date: Tue Feb 22 15:33:56 2011
New Revision: 12612
URL: http://svn.gna.org/viewcvs/relax?rev=12612&view=rev
Log:
Convert the pdc.read() back-end to use the \t delimination of the PDC file
for parsing.
Modified:
1.3/generic_fns/pdc.py
Modified: 1.3/generic_fns/pdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pdc.py?rev=12612&r1=12611&r2=12612&view=diff
==============================================================================
--- 1.3/generic_fns/pdc.py (original)
+++ 1.3/generic_fns/pdc.py Tue Feb 22 15:33:56 2011
@@ -25,6 +25,7 @@
# Python module imports.
from re import search, split
+from string import strip
# relax module imports.
from generic_fns import pipes
@@ -33,10 +34,10 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data, name_spin,
spin_loop
from generic_fns.relax_data import pack_data, peak_intensity_type
from relax_errors import RelaxError
-from relax_io import extract_data
-
-
-def get_relax_data(data):
+from relax_io import open_read_file
+
+
+def convert_relax_data(data):
"""Determine the relaxation data from the given PDC data.
@param data: The list of Tx, Tx error, and scaling factor for a given
residue from the PDC file.
@@ -66,17 +67,15 @@
# Init.
res_num = None
- # Loop over the list.
- for i in range(len(data)):
- # Split the data.
- row = split('([0-9]+)', data[i])
-
- # Loop over the new list.
- for j in range(len(row)):
- try:
- res_num = int(row[j])
- except ValueError:
- pass
+ # Split the data.
+ row = split('([0-9]+)', data)
+
+ # Loop over the new list.
+ for j in range(len(row)):
+ try:
+ res_num = int(row[j])
+ except ValueError:
+ pass
# Return the value.
return ":%s" % res_num
@@ -99,7 +98,9 @@
raise RelaxNoSequenceError
# Extract the data from the file.
- file_data = extract_data(file, dir)
+ file_handle = open_read_file(file, dir)
+ lines = file_handle.readlines()
+ file_handle.close()
# Init.
values = []
@@ -108,83 +109,88 @@
# Loop over the data.
in_ri_data = False
- for line in file_data:
+ for line in lines:
+ # Split the line.
+ row = split("\t", line)
+
+ # Strip the rubbish.
+ for j in range(len(row)):
+ row[j] = strip(row[j])
+
+ # Empty line.
+ if len(row) == 0:
+ continue
+
# The PDC version.
- if len(line) > 2 and line[0] == 'generated' and line[1] == 'by:':
- version = line[2]
- for i in range(len(line)-3):
- version = version + ' ' + line[i+3]
+ if row[0] == 'generated by:':
+ version = row[1]
# Check for bad errors.
- if len(line) >= 5 and line[0:5] == ['Systematic', 'error',
'estimation', 'of', 'data:']:
+ if row[0] == 'Systematic error estimation of data:':
# Badness.
- if line[5:] == ['worst', 'case', 'per', 'peak', 'scenario']:
+ if row[1] == 'worst case per peak scenario':
raise RelaxError("The errors estimation method \"worst case
per peak scenario\" is not suitable for model-free analysis. Please go back
to the PDC and switch to \"average variance calculation\".")
-
# The data type.
- if len(line) == 3 and search('T1', line[2]):
- ri_label = 'R1'
- elif len(line) == 3 and search('T2', line[2]):
- ri_label = 'R2'
- elif len(line) == 4 and line[3] == 'NOE':
- ri_label = 'NOE'
+ if row[0] == 'Project:':
+ if search('T1', row[1]):
+ ri_label = 'R1'
+ elif search('T2', row[1]):
+ ri_label = 'R2'
+ elif row[3] == 'NOE':
+ ri_label = 'NOE'
# Get the frequency.
- elif len(line) == 3 and line[0] == 'Proton' and line[1] ==
'frequency[MHz]:':
- frq = float(line[2])
- frq_label = str(int(round(float(line[2])/10)*10))
+ elif row[0] == 'Proton frequency[MHz]:':
+ frq = float(row[1])
+ frq_label = str(int(round(float(row[1])/10)*10))
# Inside the relaxation data section.
- elif len(line) == 2 and line[0] == 'SECTION:' and line[1] ==
'results':
+ elif row[0] == 'SECTION:' and row[1] == 'results':
in_ri_data = True
# The relaxation data.
- elif in_ri_data and line[0] != 'Peak':
- # Differences in the Rx and NOE files.
- if ri_label == 'NOE':
- index1 = -4
- index2 = -4
- else:
- index1 = -5
- index2 = -3
+ elif in_ri_data:
+ # Skip the header.
+ if row[0] == 'Peak name':
+ continue
# The residue info.
- res_nums.append(get_res_num(line[:index1]))
+ res_nums.append(get_res_num(row[0]))
# Get the relaxation data.
if ri_label != 'NOE':
- rx, rx_err = get_relax_data(line[index2:])
+ rx, rx_err = convert_relax_data(row[3:])
else:
- rx = float(line[-2])
- rx_err = float(line[-1])
+ rx = float(row[-2])
+ rx_err = float(row[-1])
# Append the data.
values.append(rx)
errors.append(rx_err)
# The temperature.
- elif len(line) == 3 and line[0] == 'Temperature':
+ elif row[0] == 'Temperature (K):':
# Set the value (not implemented yet).
pass
# The labelling.
- elif len(line) == 2 and line[0] == 'Labelling:':
+ elif row[0] == 'Labelling:':
# Set the heteronucleus value.
- value.set(line[1], 'heteronucleus')
+ value.set(row[1], 'heteronucleus')
# Name the spins.
- name = split('([A-Z]+)', line[1])[1]
+ name = split('([A-Z]+)', row[1])[1]
name_spin(name=name)
# The integration method.
- elif len(line) == 4 and line[0] == 'Used' and line[1] ==
'integrals:':
+ elif row[0] == 'Used integrals:':
# Peak heights.
- if line[2] == 'peak' and line[3] == 'intensities':
+ if row[1] == 'peak intensities':
int_type = 'height'
# Peak volumes:
- if line[2] == 'area' and line[3] == 'integral':
+ if row[1] == 'area integral':
int_type = 'volume'
# Pack the data.
r12612 - /1.3/generic_fns/pdc.py