Author: bugman
Date: Tue Oct 7 23:16:40 2008
New Revision: 7571
URL: http://svn.gna.org/viewcvs/relax?rev=7571&view=rev
Log:
Deletion of a number of methods no longer used in the 1.3 line.
These are:
read_columnar_results()
write_columnar_line()
write_columnar_results()
Modified:
1.3/specific_fns/noe.py
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=7571&r1=7570&r2=7571&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Tue Oct 7 23:16:40 2008
@@ -137,124 +137,6 @@
intensity.read(file=file, dir=dir, format=format,
heteronuc=heteronuc, proton=proton, int_col=int_col,
assign_func=self.assign_function, spectrum_type=spectrum_type)
- def read_columnar_results(self, run, file_data):
- """Function for reading the results file."""
-
- # Arguments.
- self.run = run
-
- # Extract and remove the header.
- header = file_data[0]
- file_data = file_data[1:]
-
- # Sort the column numbers.
- col = {}
- for i in xrange(len(header)):
- if header[i] == 'Num':
- col['num'] = i
- elif header[i] == 'Name':
- col['name'] = i
- elif header[i] == 'Selected':
- col['select'] = i
- elif header[i] == 'Ref_intensity':
- col['ref_int'] = i
- elif header[i] == 'Ref_error':
- col['ref_err'] = i
- elif header[i] == 'Sat_intensity':
- col['sat_int'] = i
- elif header[i] == 'Sat_error':
- col['sat_err'] = i
- elif header[i] == 'NOE':
- col['noe'] = i
- elif header[i] == 'NOE_error':
- col['noe_err'] = i
-
- # Test the file.
- if len(col) < 2:
- raise RelaxInvalidDataError
-
-
- # Sequence.
- ###########
-
- # Generate the sequence.
- for i in xrange(len(file_data)):
- # Residue number and name.
- try:
- res_num = int(file_data[i][col['num']])
- except ValueError:
- raise RelaxError, "The residue number " +
file_data[i][col['num']] + " is not an integer."
- res_name = file_data[i][col['name']]
-
- # Add the residue.
- self.relax.generic.sequence.add(self.run, res_num, res_name,
select=int(file_data[i][col['select']]))
-
-
- # Data.
- #######
-
- # Loop over the file data.
- for i in xrange(len(file_data)):
- # Residue number and name.
- try:
- res_num = int(file_data[i][col['num']])
- except ValueError:
- raise RelaxError, "The residue number " +
file_data[i][col['num']] + " is not an integer."
- res_name = file_data[i][col['name']]
-
- # Find the residue index.
- index = None
- for j in xrange(len(ds.res[self.run])):
- if ds.res[self.run][j].num == res_num and
ds.res[self.run][j].name == res_name:
- index = j
- break
- if index == None:
- raise RelaxError, "Residue " + `res_num` + " " + res_name +
" cannot be found in the sequence."
-
- # Reassign data structure.
- data = ds.res[self.run][index]
-
- # Skip deselected residues.
- if not data.select:
- continue
-
- # Reference intensity.
- try:
- data.ref = float(file_data[i][col['ref_int']])
- except ValueError:
- data.ref = None
-
- # Reference error.
- try:
- data.ref_err = float(file_data[i][col['ref_err']])
- except ValueError:
- data.ref_err = None
-
- # Saturated intensity.
- try:
- data.sat = float(file_data[i][col['sat_int']])
- except ValueError:
- data.sat = None
-
- # Saturated error.
- try:
- data.sat_err = float(file_data[i][col['sat_err']])
- except ValueError:
- data.sat_err = None
-
- # NOE.
- try:
- data.noe = float(file_data[i][col['noe']])
- except ValueError:
- data.noe = None
-
- # NOE error.
- try:
- data.noe_err = float(file_data[i][col['noe_err']])
- except ValueError:
- data.noe_err = None
-
-
def return_data_name(self, name):
"""
NOE calculation data type string matching patterns
@@ -397,95 +279,3 @@
# Close the file.
noe_file.close()
-
-
- def write_columnar_line(self, file=None, num=None, name=None,
select=None, ref_int=None, ref_err=None, sat_int=None, sat_err=None,
noe=None, noe_err=None):
- """Function for printing a single line of the columnar formatted
results."""
-
- # Residue number and name.
- file.write("%-4s %-5s " % (num, name))
-
- # Selected flag and data set.
- file.write("%-9s " % select)
- if not select:
- file.write("\n")
- return
-
- # Reference and saturated data.
- file.write("%-25s %-25s " % (ref_int, ref_err))
- file.write("%-25s %-25s " % (sat_int, sat_err))
-
- # NOE and error.
- file.write("%-25s %-25s " % (noe, noe_err))
-
- # End of the line.
- file.write("\n")
-
-
- def write_columnar_results(self, file, run):
- """Function for printing the results into a file."""
-
- # Arguments.
- self.run = run
-
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
-
- # Header.
- #########
-
-
- # Write the header line.
- self.write_columnar_line(file=file, num='Num', name='Name',
select='Selected', ref_int='Ref_intensity', ref_err='Ref_error',
sat_int='Sat_intensity', sat_err='Sat_error', noe='NOE', noe_err='NOE_error')
-
-
- # Values.
- #########
-
- # Loop over the sequence.
- for i in xrange(len(ds.res[self.run])):
- # Reassign data structure.
- data = ds.res[self.run][i]
-
- # Deselected residues.
- if not data.select:
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=0)
- continue
-
- # Reference intensity.
- ref_int = None
- if hasattr(data, 'ref'):
- ref_int = data.ref
-
- # Reference error.
- ref_err = None
- if hasattr(data, 'ref_err'):
- ref_err = data.ref_err
-
- # Saturated intensity.
- sat_int = None
- if hasattr(data, 'sat'):
- sat_int = data.sat
-
- # Saturated error.
- sat_err = None
- if hasattr(data, 'sat_err'):
- sat_err = data.sat_err
-
- # NOE
- noe = None
- if hasattr(data, 'noe'):
- noe = data.noe
-
- # NOE error.
- noe_err = None
- if hasattr(data, 'noe_err'):
- noe_err = data.noe_err
-
- # Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, ref_int=ref_int, ref_err=ref_err,
sat_int=sat_int, sat_err=sat_err, noe=noe, noe_err=noe_err)
r7571 - /1.3/specific_fns/noe.py