Author: bugman
Date: Mon Jun 11 20:16:21 2012
New Revision: 16853
URL: http://svn.gna.org/viewcvs/relax?rev=16853&view=rev
Log:
Converted the rdc.read user function backend to the new interatomic data
design.
Modified:
branches/interatomic/generic_fns/rdc.py
Modified: branches/interatomic/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/rdc.py?rev=16853&r1=16852&r2=16853&view=diff
==============================================================================
--- branches/interatomic/generic_fns/rdc.py (original)
+++ branches/interatomic/generic_fns/rdc.py Mon Jun 11 20:16:21 2012
@@ -32,6 +32,7 @@
from warnings import warn
# relax module imports.
+from data.rdc import Rdc
from float import nan
from generic_fns import grace, pipes
from generic_fns.align_tensor import get_tensor_index
@@ -39,7 +40,7 @@
from maths_fns.rdc import ave_rdc_tensor
from physical_constants import dipolar_constant, return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxNoRDCError, RelaxNoSequenceError,
RelaxSpinTypeError
-from relax_io import open_write_file, read_spin_data, write_spin_data
+from relax_io import extract_data, open_write_file, strip, write_data
from relax_warnings import RelaxWarning, RelaxNoSpinWarning
@@ -409,7 +410,7 @@
cdp.q_rdc_norm2 = sqrt(cdp.q_rdc_norm2 / len(cdp.q_factors_rdc_norm2))
-def read(align_id=None, file=None, dir=None, file_data=None, data_type='D',
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, neg_g_corr=False):
+def read(align_id=None, file=None, dir=None, file_data=None, data_type='D',
spin_id1_col=None, spin_id2_col=None, data_col=None, error_col=None,
sep=None, neg_g_corr=False):
"""Read the RDC data from file.
@keyword align_id: The alignment tensor ID string.
@@ -421,26 +422,16 @@
@keyword file_data: An alternative to 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
@keyword data_type: A string which is set to 'D' means that the
splitting in the aligned sample was assumed to be J + D, or if set to '2D'
then the splitting was taken as J + 2D.
- @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
- @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
- @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
- @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
- @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
+ @keyword spin_id1_col: The column containing the spin ID strings of the
first spin.
+ @type spin_id1_col: int
+ @keyword spin_id2_col: The column containing the spin ID strings of the
second spin.
+ @type spin_id2_col: int
@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
@keyword neg_g_corr: A flag which is used to correct for the negative
gyromagnetic ratio of 15N. If True, a sign inversion will be applied to all
RDC values to be loaded.
@type neg_g_corr: bool
"""
@@ -456,7 +447,7 @@
if data_col == None and error_col == None:
raise RelaxError("One of either the data or error column must be
supplied.")
- # Store the data type as global data (need for the conversion of spin
data).
+ # Store the data type as global data (need for the conversion of RDC
data).
if not hasattr(cdp, 'rdc_data_types'):
cdp.rdc_data_types = {}
if not cdp.rdc_data_types.has_key(align_id):
@@ -465,42 +456,56 @@
# Spin specific data.
#####################
+ # Initialise the RDC data store object.
+ if not hasattr(cdp, 'rdc'):
+ cdp.rdc = Rdc()
+
+ # Extract the data from the file.
+ file_data = extract_data(file, dir, sep=sep)
+
# Loop over the RDC data.
- mol_names = []
- res_nums = []
- res_names = []
- spin_nums = []
- spin_names = []
- values = []
- errors = []
- for data in read_spin_data(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):
+ data = []
+ for line in file_data:
# Unpack.
if data_col and error_col:
- mol_name, res_num, res_name, spin_num, spin_name, value, error =
data
+ spin_id1, spin_id2, value, error = line
elif data_col:
- mol_name, res_num, res_name, spin_num, spin_name, value = data
+ spin_id1, spin_id2, value = line
error = None
else:
- mol_name, res_num, res_name, spin_num, spin_name, error = data
+ spin_id1, spin_id2, error = line
value = None
+
+ # Convert and check the value.
+ if value != None:
+ try:
+ value = float(value)
+ except ValueError:
+ warn(RelaxWarning("The data value of the line '%s' is
invalid." % line))
+ continue
+
+ # Convert and check the error.
+ if error != None:
+ try:
+ error = float(error)
+ except ValueError:
+ warn(RelaxWarning("The error value of the line '%s' is
invalid." % line))
+ continue
# 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.
- id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
- spin = return_spin(id)
+ # Check the spin IDs.
+ spin = return_spin(spin_id1)
if spin == None:
- warn(RelaxNoSpinWarning(id))
- continue
-
- # Add the data.
+ raise RelaxNoSpinWarning(spin_id1)
+ spin = return_spin(spin_id2)
+ if spin == None:
+ raise RelaxNoSpinWarning(spin_id2)
+
+ # Convert the data.
if data_col:
- # Initialise.
- if not hasattr(spin, 'rdc'):
- spin.rdc = {}
-
# Data conversion.
value = convert(value, align_id, to_intern=True)
@@ -508,39 +513,26 @@
if neg_g_corr and value != None:
value = -value
- # Append the value.
- spin.rdc[align_id] = value
-
- # Add the error.
+ # Convert the error.
if error_col:
- # Initialise.
- if not hasattr(spin, 'rdc_err'):
- spin.rdc_err = {}
-
# Data conversion.
error = convert(error, align_id, to_intern=True)
- # Append the error.
- spin.rdc_err[align_id] = error
+ # Store the data.
+ cdp.rdc.add(align_id=align_id, spin_id1=spin_id1, spin_id2=spin_id2,
rdc=value, error=error)
# Append the data for printout.
- mol_names.append(mol_name)
- res_nums.append(res_num)
- res_names.append(res_name)
- spin_nums.append(spin_num)
- spin_names.append(spin_name)
- values.append(value)
- errors.append(error)
+ data.append([spin_id1, spin_id2, repr(value), repr(error)])
# Print out.
- write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums,
res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values,
data_name='RDCs', error=errors, error_name='RDC_error')
+ write_data(out=sys.stdout, headings=["Spin_ID1", "Spin_ID2", "Value",
"Error"], data=data)
# Global (non-spin specific) data.
##################################
# No data, so return.
- if not len(values):
+ if not len(data):
return
# Initialise.
r16853 - /branches/interatomic/generic_fns/rdc.py