Author: bugman
Date: Tue Oct 6 20:22:15 2009
New Revision: 9608
URL: http://svn.gna.org/viewcvs/relax?rev=9608&view=rev
Log:
Converted the pcs.read() user fn to use the new
relax_io.read_spin_data_file() function.
Modified:
1.3/generic_fns/pcs.py
1.3/generic_fns/rdc.py
1.3/test_suite/shared_data/align_data/pcs.txt
1.3/test_suite/shared_data/align_data/pcs_err.txt
Modified: 1.3/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pcs.py?rev=9608&r1=9607&r2=9608&view=diff
==============================================================================
--- 1.3/generic_fns/pcs.py (original)
+++ 1.3/generic_fns/pcs.py Tue Oct 6 20:22:15 2009
@@ -31,7 +31,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxPCSError
-from relax_io import extract_data, strip
+from relax_io import read_spin_data_file
def add_data_to_spin(spin=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, values=None, errors=None, sim=False):
@@ -437,10 +437,10 @@
return index
-def read(id=None, file=None, dir=None, file_data=None, spin_id=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, data_col=None, error_col=None, sep=None):
+def read(id=None, file=None, dir=None, file_data=None, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None):
"""Read the PCS data from file.
- @param id: The alignment identification string.
+ @param id: The alignment tensor ID string.
@type id: str
@param file: The name of the file to open.
@type file: str
@@ -453,18 +453,34 @@
@type file_data: list of lists
@keyword spin_id: The spin identification string.
@type spin_id: None or str
- @param mol_name_col: The column containing the molecule name
information.
+ @keyword spin_id_col: The column containing the spin ID strings. If
supplied, the
+ mol_name_col, res_name_col, res_num_col,
spin_name_col, and spin_num_col
+ arguments must be none.
+ @type spin_id_col: int or None
+ @keyword mol_name_col: The column containing the molecule name
information. If supplied,
+ spin_id_col must be None.
@type mol_name_col: int or None
- @param res_name_col: The column containing the residue name
information.
+ @keyword res_name_col: The column containing the residue name
information. If supplied,
+ spin_id_col must be None.
@type res_name_col: int or None
- @param res_num_col: The column containing the residue number
information.
+ @keyword res_num_col: The column containing the residue number
information. If supplied,
+ spin_id_col must be None.
@type res_num_col: int or None
- @param spin_name_col: The column containing the spin name information.
+ @keyword spin_name_col: The column containing the spin name information.
If supplied,
+ spin_id_col must be None.
@type spin_name_col: int or None
- @param spin_num_col: The column containing the spin number
information.
+ @keyword spin_num_col: The column containing the spin number
information. If supplied,
+ spin_id_col must be None.
@type spin_num_col: int or None
- @param sep: The column separator which, if None, defaults to
whitespace.
+ @keyword data_col: The column containing the RDC data in Hz.
+ @type data_col: int or None
+ @keyword error_col: The column containing the RDC errors.
+ @type error_col: int or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
@type sep: str or None
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all
+ spins.
+ @type spin_id: None or str
"""
# Test if the current data pipe exists.
@@ -478,97 +494,22 @@
if data_col == None and error_col == None:
raise RelaxError("One of either the data or error column must be
supplied.")
- # Minimum number of columns.
- 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 = extract_data(file, dir)
-
- # Count the number of header lines.
- header_lines = 0
- for i in xrange(len(file_data)):
- try:
- if data_col != None:
- float(file_data[i][data_col])
- else:
- float(file_data[i][error_col])
- except:
- header_lines = header_lines + 1
- else:
- break
-
- # Remove the header.
- file_data = file_data[header_lines:]
-
- # Strip the data of all comments and empty lines.
- file_data = strip(file_data)
-
- # Test the validity of the PCS data.
- missing = True
- for i in xrange(len(file_data)):
- # Skip missing data.
- if len(file_data[i]) <= min_col_num:
- continue
- elif data_col != None and file_data[i][data_col] == 'None':
- continue
- elif error_col != None and file_data[i][error_col] == 'None':
- continue
-
- # Test that the data are numbers.
- try:
- if res_num_col != None:
- int(file_data[i][res_num_col])
- if spin_num_col != None:
- int(file_data[i][spin_num_col])
- if data_col != None:
- float(file_data[i][data_col])
- if error_col != None:
- float(file_data[i][error_col])
- except ValueError:
- raise RelaxError("The PCS data in the line " +
repr(file_data[i]) + " is invalid.")
-
- # Right, data is ok and exists.
- missing = False
-
- # Hmmm, no data!
- if missing:
- raise RelaxError("No corresponding data could be found within the
file.")
-
-
- # Global (non-spin specific) data.
- ##################################
-
- # Initialise.
- if not hasattr(cdp, 'pcs_ids'):
- cdp.pcs_ids = []
-
- # Add the PCS id string.
- if id not in cdp.pcs_ids:
- cdp.pcs_ids.append(id)
-
# Spin specific data.
#####################
# Loop over the PCS data.
print(("\n%-50s %-15s %-15s" % ("spin_id", "value", "error")))
- for i in xrange(len(file_data)):
- # Skip missing data.
- if len(file_data[i]) <= min_col_num:
- continue
-
- # Generate the spin identification string.
- id = generate_spin_id_data_array(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.
- value = None
- if data_col != None:
- value = eval(file_data[i][data_col])
- error = None
- if error_col != None:
- error = eval(file_data[i][error_col])
+ for data in read_spin_data_file(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, 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, data_col=data_col, error_col=error_col, sep=sep,
spin_id=spin_id):
+ # Unpack.
+ if data_col and error_col:
+ id, value, error = data
+ elif data_col:
+ id, value = data
+ error = None
+ else:
+ id, error = data
+ value = None
# Test the error value (cannot be 0.0).
if error == 0.0:
@@ -580,7 +521,7 @@
raise RelaxNoSpinError(id)
# Add the data.
- if data_col != None:
+ if data_col:
# Initialise.
if not hasattr(spin, 'pcs'):
spin.pcs = []
@@ -589,7 +530,7 @@
spin.pcs.append(value)
# Add the error.
- if error_col != None:
+ if error_col:
# Initialise.
if not hasattr(spin, 'pcs_err'):
spin.pcs_err = []
@@ -599,6 +540,18 @@
# Print out.
print(("%-50s %15s %15s" % (id, value, error)))
+
+
+ # Global (non-spin specific) data.
+ ##################################
+
+ # Initialise.
+ if not hasattr(cdp, 'pcs_ids'):
+ cdp.pcs_ids = []
+
+ # Add the PCS id string.
+ if id not in cdp.pcs_ids:
+ cdp.pcs_ids.append(id)
def return_data_desc(name):
Modified: 1.3/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=9608&r1=9607&r2=9608&view=diff
==============================================================================
--- 1.3/generic_fns/rdc.py (original)
+++ 1.3/generic_fns/rdc.py Tue Oct 6 20:22:15 2009
@@ -417,6 +417,7 @@
if data_col == None and error_col == None:
raise RelaxError("One of either the data or error column must be
supplied.")
+
# Spin specific data.
#####################
@@ -428,8 +429,14 @@
id, value, error = data
elif data_col:
id, value = data
+ error = None
else:
id, error = data
+ value = None
+
+ # Test the error value (cannot be 0.0).
+ if error == 0.0:
+ raise RelaxError("An invalid error value of zero has been
encountered.")
# Get the corresponding spin container.
spin = return_spin([id, spin_id])
Modified: 1.3/test_suite/shared_data/align_data/pcs.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/align_data/pcs.txt?rev=9608&r1=9607&r2=9608&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/align_data/pcs.txt (original)
+++ 1.3/test_suite/shared_data/align_data/pcs.txt Tue Oct 6 20:22:15 2009
@@ -1,4 +1,4 @@
-Name Dy Tb Tm E
+#Name Dy Tb Tm E
C1 0.004 0.040 0.100 0.037
C2 0.008 0.045 0.080 0.045
C3 0.021 0.050 0.090 0.018
Modified: 1.3/test_suite/shared_data/align_data/pcs_err.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/align_data/pcs_err.txt?rev=9608&r1=9607&r2=9608&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/align_data/pcs_err.txt (original)
+++ 1.3/test_suite/shared_data/align_data/pcs_err.txt Tue Oct 6 20:22:15 2009
@@ -1,4 +1,4 @@
-Atom Dy Tb Tm
Er
+#Atom Dy Tb Tm
Er
H1 0.00017778978794241471 0.00020909584759850369 7.88347403825711e-05
0.00026363071804653775
H2 0.00015135068429266831 0.00010896251439994929
0.00010397661534864064 0.00037323554231773827
H3 0.00020797864504014244 0.00017137432686588103
0.00015997346046683463 0.00027037046207674463
r9608 - in /1.3: generic_fns/ test_suite/shared_data/align_data/