Author: bugman
Date: Tue Nov 27 13:23:07 2007
New Revision: 4076
URL: http://svn.gna.org/viewcvs/relax?rev=4076&view=rev
Log:
Converted the specific_fns.relax_data.read() to the new relax design.
Modified:
1.3/specific_fns/relax_data.py
Modified: 1.3/specific_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_data.py?rev=4076&r1=4075&r2=4076&view=diff
==============================================================================
--- 1.3/specific_fns/relax_data.py (original)
+++ 1.3/specific_fns/relax_data.py Tue Nov 27 13:23:07 2007
@@ -531,37 +531,60 @@
return index
- def read(self, run=None, ri_label=None, frq_label=None, frq=None,
file=None, dir=None, file_data=None, num_col=0, name_col=1, data_col=2,
error_col=3, sep=None):
- """Function for reading R1, R2, or NOE relaxation data."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
- self.frq = frq
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
+ def read(self, ri_label=None, frq_label=None, frq=None, file=None,
dir=None, file_data=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None):
+ """Function for reading R1, R2, or NOE relaxation data.
+
+ @param ri_label: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
+ @type ri_label: str
+ @param frq_label: The field strength label.
+ @type frq_label: str
+ @param frq: The spectrometer proton frequency in Hz.
+ @type frq: float
+ @param file: The name of the file to open.
+ @type file: str
+ @param dir: The directory containing the file (defaults
to the current directory
+ if None).
+ @type dir: str or None
+ @param file_data: An alternative opening a file, if the data
already exists in the
+ correct format. The format is a list of
lists where the first index
+ corresponds to the row and the second the
column.
+ @type file_data: list of lists
+ @param mol_name_col: The column containing the molecule name
information.
+ @type mol_name_col: int or None
+ @param res_name_col: The column containing the residue name
information.
+ @type res_name_col: int or None
+ @param res_num_col: The column containing the residue number
information.
+ @type res_num_col: int or None
+ @param spin_name_col: The column containing the spin name
information.
+ @type spin_name_col: int or None
+ @param spin_num_col: The column containing the spin number
information.
+ @type spin_num_col: int or None
+ @param sep: The column seperator which, if None,
defaults to whitespace.
+ @type sep: str or None
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test(relax_data_store.current_pipe)
+
+ # Test if sequence data exists.
+ if not sequence_exists():
+ raise RelaxNoSequenceError
# Test if relaxation data corresponding to 'self.ri_label' and
'self.frq_label' already exists.
- if self.test_labels(run):
+ if self.test_labels():
raise RelaxRiError, (self.ri_label, self.frq_label)
# Minimum number of columns.
- min_col_num = max(num_col, name_col, data_col, error_col)
+ min_col_num = max(mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, data_col, error_col)
# Extract the data from the file.
if not file_data:
# Extract.
- file_data = self.relax.IO.extract_data(file, dir)
+ file_data = extract_data(file, dir)
# Count the number of header lines.
header_lines = 0
+ num_col = max(res_num_col, spin_num_col)
for i in xrange(len(file_data)):
try:
int(file_data[i][num_col])
@@ -574,7 +597,7 @@
file_data = file_data[header_lines:]
# Strip the data.
- file_data = self.relax.IO.strip(file_data)
+ file_data = strip(file_data)
# Test the validity of the relaxation data.
for i in xrange(len(file_data)):
@@ -586,11 +609,14 @@
# Test that the data are numbers.
try:
- int(file_data[i][num_col])
+ if res_num_col != None:
+ int(file_data[i][res_num_col])
+ if spin_num_col != None:
+ int(file_data[i][spin_num_col])
float(file_data[i][data_col])
float(file_data[i][error_col])
except ValueError:
- raise RelaxError, "The relaxation data is invalid (num="
+ file_data[i][num_col] + ", name=" + file_data[i][name_col] + ", data=" +
file_data[i][data_col] + ", error=" + file_data[i][error_col] + ")."
+ raise RelaxError, "The relaxation data in the line " +
`file_data[i]` + " is invalid."
# Global (non-residue specific) data.
@@ -600,7 +626,7 @@
self.global_flag = 1
# Initialise the global data if necessary.
- self.data_init(relax_data_store)
+ self.data_init()
# Update the global data.
self.update_global_data_structures()
@@ -611,9 +637,6 @@
# Global data flag.
self.global_flag = 0
-
- # Store the indecies for which relaxation data has been added.
- index_list = []
# Loop over the relaxation data.
for i in xrange(len(file_data)):
@@ -621,9 +644,10 @@
if len(file_data[i]) <= min_col_num:
continue
+ # Generate the spin identification string.
+ id = generate_spin_id(data=file_data[i],
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
+
# Convert the data.
- res_num = int(file_data[i][num_col])
- res_name = file_data[i][name_col]
value = eval(file_data[i][data_col])
error = eval(file_data[i][error_col])
@@ -631,23 +655,13 @@
if value == None or error == None:
continue
- # Find the index of relax_data_store.res[self.run] which
corresponds to the relaxation data set i.
- index = None
- for j in xrange(len(relax_data_store.res[self.run])):
- if relax_data_store.res[self.run][j].num == res_num and
relax_data_store.res[self.run][j].name == res_name:
- index = j
- break
- if index == None:
- raise RelaxNoResError, (res_num, res_name)
-
- # Remap the data structure
'relax_data_store.res[self.run][index]'.
- data = relax_data_store.res[self.run][index]
+ # Get the corresponding spin container.
+ spin = return_spin(id)
+ if spin == None:
+ raise RelaxNoSpinError, id
# Update all data structures.
- self.update_data_structures(data, value, error)
-
- # Add the index to the list.
- index_list.append(index)
+ self.update_data_structures(spin, value, error)
def return_value(self, run, i, data_type):
r4076 - /1.3/specific_fns/relax_data.py