Author: bugman
Date: Tue Mar 26 18:36:41 2013
New Revision: 19164
URL: http://svn.gna.org/viewcvs/relax?rev=19164&view=rev
Log:
Deleted the completely unused pipe_control.spectrum.Bruker_import class.
This was added by Michael Bieri at r11637 in Oct 2011, but the code has never
been used. Other,
simpler code has replaced its functionality.
Modified:
trunk/pipe_control/spectrum.py
Modified: trunk/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/spectrum.py?rev=19164&r1=19163&r2=19164&view=diff
==============================================================================
--- trunk/pipe_control/spectrum.py (original)
+++ trunk/pipe_control/spectrum.py Tue Mar 26 18:36:41 2013
@@ -33,234 +33,9 @@
# relax module imports.
from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
from pipe_control import pipes
-from lib.errors import RelaxArgNotNoneError, RelaxError,
RelaxImplementError, RelaxNoSequenceError, RelaxNoSpectraError
+from lib.errors import RelaxError, RelaxImplementError,
RelaxNoSequenceError, RelaxNoSpectraError
from lib.io import extract_data, read_spin_data, strip, write_data
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
-
-
-
-class Bruker_import:
- def __init__(self, dir=None, exp_type=None, file=None, UI='prompt',
output_file=None):
- """Function to import Bruker Protein Dynamic Center (PDC) files.
-
- @param dir: The directory to save the new file in.
- @type dir: str
- @param file: The Bruker PDC output file.
- @type file: str
- @param exp_type: The type of experiment, e.g. NOE, T1 or T2
- @type exp_type: str
- @param UI: The relax user interface (either 'prompt' or
'GUI').
- @type UI: str
- @param output_file: The file to save the imported list.
- @type output_file: str
- """
-
- # Create experiment type
- self.exp_type = exp_type
-
- # The output file
- self.output_file = output_file
- self.dir = dir
-
- # The user interface.
- self.UI = UI
-
- # Read the file.
- if file:
- self.read_file(file)
- else:
- raise RelaxError('No file selected.')
-
- # Collect the entries for the file.
- self.collect_entries()
-
- # Create dummy file.
- self.create_file()
-
-
- def __str__(self):
- """Function to allow to return a value."""
- return str(self.value)
-
-
- def collect_entries(self):
- """Function to collect entries for the NOE/R1/R2 relax dummy file."""
-
- # storage for file entries
- # [ [Mol_name, Res_num, Res_name, Spin_num, value, error], ... ]
- self.file_entries = []
-
- # Data flag
- is_data = False
-
- # Spin name
- spinname = 'N'
-
- # loop over line
- for line in range(0, len(self.entries)):
- # Detect the experiment
- if 'Project:' in self.entries[line][0]:
- exp_type = ''
-
- # NOE
- if 'Dynamic method/Hetero NOE' in self.entries[line][1]:
- exp_type = 'NOE'
- # T1
- elif 'Dynamic method/T1' in self.entries[line][1]:
- exp_type = 'T1'
- # T2
- elif 'Dynamic method/T2' in self.entries[line][1]:
- exp_type = 'T2'
-
- # Check agreement of file and user input.
- if self.exp_type:
- if not self.exp_type == exp_type:
- raise RelaxError('Selected file is not a
'+self.exp_type+'-file.')
- return
-
- # Feedback
- print("Reading BRUKER PDC "+exp_type+" file.\n")
-
- # The entries
- if 'SECTION:' in self.entries[line][0]:
- # NOE/T1/T2 results
- if 'results' in self.entries[line][1]:
- is_data = True
- continue
-
- # Other entries
- else:
- is_data = False
-
- # Spin name
- if 'Labelling:' in self.entries[line][0]:
- # 15N
- if 'N' in self.entries[line][0]:
- spinname = 'N'
-
- # 13C
- if 'C' in self.entries[line][0]:
- spinname = 'C'
-
- # Collect NOE/T1/T2 values
- if is_data:
- # Exclued header or blank line.
- if self.entries[line][0] in ['Peak name', '']:
- continue
-
- # Label
- label_tmp = self.entries[line][0]
- label_tmp = label_tmp.replace(' ', '')
- label_tmp = label_tmp.replace('[', '')
- label_tmp = label_tmp.replace(']', '')
-
- # Detect residue number
- resnum = label_tmp
- # find start of number
- start = 0
- while resnum[start].isdigit()==False: start = start+1
-
- # find end of number
- end = start
- try:
- while resnum[end].isdigit()==True: end = end+1
- # Label ends with number
- except:
- end = end
-
- # cut out residue number integer
- resnum = resnum[start:end]
-
- # Residue name
- resname = label_tmp[0:start]
-
- # Spin num
- spin_no = line
-
- # The value
- value_tmp = float(self.entries[line][3])
-
- # Convert T1/T2 to R1/R2
- if exp_type in ['T1', 'T2']:
- value_tmp = 1.0/value_tmp
-
- # error
- error = float(self.entries[line][4])
-
- # Store file entry
- self.file_entries.append(['Bruker_PDC_'+exp_type, resnum,
resname, spin_no, spinname, value_tmp, error])
-
-
- def create_file(self):
- """Function to write the file."""
-
- # The Sparky header
- text =
'Mol_name\tRes_num\tRes_name\tSpin_num\tSpin_name\tValue\tError \n'
-
- for line in range(0, len(self.file_entries)):
- # Build entries.
- tmp_text = ''
- for i in range(0, len(self.file_entries[line])):
- tmp_text = tmp_text + str(self.file_entries[line][i])+'\t'
-
- # Add entries.
- text = text+tmp_text + '\n'
-
- # Print entries
- if not self.UI == 'GUI':
- print(text)
-
- # craete output file
- if self.output_file:
- if self.dir:
- file = open(self.dir+sep+self.output_file, 'w')
- else:
- file = open(self.output_file, 'w')
- # create dummy file
- else:
- file = DummyFileObject()
-
- # Write the file
- file.write(text)
- file.close()
-
- # Feedback
- if self.output_file:
- if self.dir:
- print('Created BRUKER PDC file
'+self.dir+sep+self.output_file)
- # The return value
- self.value = self.dir+sep+self.output_file
- else:
- print('Created BRUKER PDC file '+self.output_file)
- # The return value
- self.value = self.output_file
- else:
- print('Created BRUKER PDC file.')
- # Return the dummy file
- self.value = file
-
-
- def read_file(self, filename):
- """Function to read the file."""
-
- # Open the file.
- file = open(filename, 'r')
-
- # Storage of lines.
- self.entries = []
-
- # Loop over line in PDC file
- for line in file:
- # Read entries in line
- entry = line
- entry = line.strip()
- entry = entry.split('\t')
-
- # Add entries to storage
- self.entries.append(entry)
-
- # close the file
- file.close()
def __errors_height_no_repl():
r19164 - /trunk/pipe_control/spectrum.py