Author: michaelbieri
Date: Mon Oct 11 03:42:10 2010
New Revision: 11637
URL: http://svn.gna.org/viewcvs/relax?rev=11637&view=rev
Log:
Function to import BRUKER Protein Dynamic Center project is added.
The import will be converted to a relax formatted parameter file, either as a
dummy file or saved at a specified location.
Modified:
branches/bruker_import/generic_fns/spectrum.py
Modified: branches/bruker_import/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bruker_import/generic_fns/spectrum.py?rev=11637&r1=11636&r2=11637&view=diff
==============================================================================
--- branches/bruker_import/generic_fns/spectrum.py (original)
+++ branches/bruker_import/generic_fns/spectrum.py Mon Oct 11 03:42:10 2010
@@ -37,6 +37,232 @@
from relax_errors import RelaxArgNotNoneError, RelaxError,
RelaxImplementError, RelaxNoSequenceError
from relax_io import extract_data, read_spin_data, strip
from relax_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 __check_args(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):
r11637 - /branches/bruker_import/generic_fns/spectrum.py