Author: bugman
Date: Tue Oct 6 13:01:06 2009
New Revision: 9578
URL: http://svn.gna.org/viewcvs/relax?rev=9578&view=rev
Log:
Converted value.read() to use the new relax_io.read_spin_data_file() function.
This converts the user function to the 1.3 line design as well.
Modified:
1.3/generic_fns/dasha.py
1.3/generic_fns/value.py
1.3/prompt/value.py
Modified: 1.3/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/dasha.py?rev=9578&r1=9577&r2=9578&view=diff
==============================================================================
--- 1.3/generic_fns/dasha.py (original)
+++ 1.3/generic_fns/dasha.py Tue Oct 6 13:01:06 2009
@@ -492,7 +492,7 @@
scaling = 1.0
# Set the values.
- value.read(param=param, scaling=scaling, file=file_name,
res_num_col=0, res_name_col=None, data_col=1, error_col=2)
+ value.read(param=param, scaling=scaling, file=file_name,
res_num_col=1, res_name_col=None, data_col=2, error_col=3)
# Clean up of non-existant parameters (set the parameter to None!).
for spin in spin_loop():
@@ -515,4 +515,4 @@
raise RelaxFileError('Dasha', file_name)
# Set the values.
- value.read(param='chi2', file=file_name, res_num_col=0,
res_name_col=None, data_col=1, error_col=2)
+ value.read(param='chi2', file=file_name, res_num_col=1,
res_name_col=None, data_col=2, error_col=3)
Modified: 1.3/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/value.py?rev=9578&r1=9577&r2=9578&view=diff
==============================================================================
--- 1.3/generic_fns/value.py (original)
+++ 1.3/generic_fns/value.py Tue Oct 6 13:01:06 2009
@@ -31,7 +31,7 @@
from generic_fns import minimise, pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_loop
from generic_fns.sequence import write_header, write_line
-from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoSequenceError, RelaxNoSpinError, RelaxParamSetError, RelaxValueError
+from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxParamSetError, RelaxValueError
from relax_io import extract_data, open_write_file, strip
import specific_fns
@@ -191,7 +191,7 @@
return spin_params, spin_values, other_params, other_values
-def read(param=None, scaling=1.0, file=None, dir=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):
+def read(param=None, scaling=1.0, 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 spin specific data values from a file.
@keyword param: The name of the parameter to read.
@@ -203,22 +203,37 @@
@keyword dir: The directory containing the file (defaults to
the current directory if
None).
@type dir: str or None
- @keyword mol_name_col: The column containing the molecule name
information.
+ @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 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.
+ @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.
+ @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.
+ @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.
+ @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 data_col: The column containing the values.
- @type data_col: int
- @keyword error_col: The column containing the errors.
+ @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.
+ @type spin_id: None or str
"""
# Test if the current pipe exists.
@@ -263,77 +278,18 @@
if value != None or error != None:
raise RelaxValueError(param)
- # Extract the data from the file.
- file_data = extract_data(file, dir=dir, sep=sep)
-
- # 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])
- except:
- header_lines = header_lines + 1
+ # Loop over the data.
+ 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
else:
- break
-
- # Remove the header.
- file_data = file_data[header_lines:]
-
- # Strip the data.
- file_data = strip(file_data)
-
- # Do nothing if the file does not exist.
- if not file_data:
- raise RelaxFileEmptyError
-
- # 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)
-
- # Test the validity of the data.
- for i in xrange(len(file_data)):
- # Skip missing data.
- if len(file_data[i]) <= min_col_num:
- continue
-
- try:
- # Value column.
- if file_data[i][data_col] != 'None':
- float(file_data[i][data_col])
-
- # Error column.
- if error_col != None and file_data[i][error_col] != 'None':
- float(file_data[i][error_col])
-
- except ValueError:
- if error_col != None:
- raise RelaxError("The data is invalid (data=" +
file_data[i][data_col] + ", error=" + file_data[i][error_col] + ").")
- else:
- raise RelaxError("The data is invalid (data=" +
file_data[i][data_col] + ").")
-
- # Loop over the data.
- 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)
-
- # Value.
- if file_data[i][data_col] != 'None':
- value = float(file_data[i][data_col])
- else:
- value = None
-
- # Error.
- if error_col != None and file_data[i][error_col] != 'None':
- error = float(file_data[i][error_col])
- else:
- error = None
+ id, error = data
# Get the corresponding spin container.
- spin = return_spin(id)
+ spin = return_spin([id, spin_id])
if spin == None:
raise RelaxNoSpinError(id)
Modified: 1.3/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/value.py?rev=9578&r1=9577&r2=9578&view=diff
==============================================================================
--- 1.3/prompt/value.py (original)
+++ 1.3/prompt/value.py Tue Oct 6 13:01:06 2009
@@ -128,7 +128,7 @@
self.__relax__.generic.value.display(param=param)
- def read(self, param=None, scaling=1.0, file=None, num_col=0,
name_col=1, data_col=2, error_col=3, sep=None):
+ def read(self, param=None, scaling=1.0, file=None, dir=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 spin specific data values from a file.
Keyword Arguments
@@ -138,40 +138,60 @@
scaling: The factor to scale parameters by.
- file: The name of the file containing the relaxation data.
-
- num_col: The residue number column (the default is 0, ie the first
column).
-
- name_col: The residue name column (the default is 1).
-
- data_col: The relaxation data column (the default is 2).
-
- error_col: The experimental error column (the default is 3).
+ file: The name of the file containing the values.
+
+ dir: The directory where the file is located.
+
+ spin_id_col: The spin ID string column (an alternative to the mol,
res, and spin name and
+ number columns).
+
+ mol_name_col: The molecule name column (alternative to the
spid_id_col).
+
+ res_num_col: The residue number column (alternative to the
spid_id_col).
+
+ res_name_col: The residue name column (alternative to the
spid_id_col).
+
+ spin_num_col: The spin number column (alternative to the
spid_id_col).
+
+ spin_name_col: The spin name column (alternative to the
spid_id_col).
+
+ data_col: The RDC data column.
+
+ error_col: The experimental error column.
sep: The column separator (the default is white space).
+
+ spin_id: The spin ID string to restrict the loading of data to
certain spin subsets.
Description
~~~~~~~~~~~
- Only one parameter may be selected, therefore the 'param' argument
should be a string. If
- the file only contains values and no errors, set the error column
argument to None.
+ The spin system can be identified in the file using two different
formats. The first is the
+ spin ID string column which can include the molecule name, the
residue name and number, and
+ the spin name and number. Alternatively the mol_name_col,
res_num_col, res_name_col,
+ spin_num_col, and/or spin_name_col arguments can be supplied
allowing this information to be
+ in separate columns. Note that the numbering of columns starts at
one. The spin_id
+ argument can be used to restrict the reading to certain spin types,
for example only 15N
+ spins when only residue information is in the file.
+
+ Only one parameter may be selected, therefore the 'param' argument
should be a string.
If this function is used to change values of previously minimised
parameters, then the
minimisation statistics (chi-squared value, iteration count,
function count, gradient count,
- and Hessian count) will be reset to None.
+ and Hessian count) will be reset.
Examples
~~~~~~~~
- To load CSA values from the file 'csa_values' in the directory
'data', type one of the
- following:
-
- relax> value.read('CSA', 'data/csa_value')
- relax> value.read('CSA', 'data/csa_value', 0, 1, 2, 3, None, 1)
- relax> value.read(param='CSA', file='data/csa_value', num_col=0,
name_col=1,
- data_col=2, error_col=3, sep=None)
+ To load 15N CSA values from the file 'csa_values' in the directory
'data', where spins are
+ only identified by residue name and number, type one of the
following:
+
+ relax> value.read('CSA', 'data/csa_value', spin_id='@N')
+ relax> value.read('CSA', 'csa_value', dir='data', spin_id='@N')
+ relax> value.read(param='CSA', file='csa_value', dir='data',
res_num_col=1, res_name_col=2,
+ data_col=3, error_col=4, spin_id='@N')
"""
# Function intro text.
@@ -180,25 +200,37 @@
text = text + "param=" + repr(param)
text = text + ", scaling=" + repr(scaling)
text = text + ", file=" + repr(file)
- text = text + ", num_col=" + repr(num_col)
- text = text + ", name_col=" + repr(name_col)
+ text = text + ", dir=" + repr(dir)
+ text = text + ", spin_id_col=" + repr(spin_id_col)
+ text = text + ", mol_name_col=" + repr(mol_name_col)
+ text = text + ", res_num_col=" + repr(res_num_col)
+ text = text + ", res_name_col=" + repr(res_name_col)
+ text = text + ", spin_num_col=" + repr(spin_num_col)
+ text = text + ", spin_name_col=" + repr(spin_name_col)
text = text + ", data_col=" + repr(data_col)
text = text + ", error_col=" + repr(error_col)
- text = text + ", sep=" + repr(sep) + ")"
+ text = text + ", sep=" + repr(sep)
+ text = text + ", spin_id=" + repr(spin_id) + ")"
print(text)
# The argument checks.
check.is_str(param, 'parameter')
check.is_float(scaling, 'scaling')
check.is_str(file, 'file name')
- check.is_int(num_col, 'residue number column')
- check.is_int(name_col, 'residue name column')
- check.is_int(data_col, 'data column')
- check.is_int(error_col, 'residue name column', can_be_none=True)
+ check.is_str(dir, 'directory name', can_be_none=True)
+ check.is_int(spin_id_col, 'spin ID string column', can_be_none=True)
+ check.is_int(mol_name_col, 'molecule name column', can_be_none=True)
+ check.is_int(res_num_col, 'residue number column', can_be_none=True)
+ check.is_int(res_name_col, 'residue name column', can_be_none=True)
+ check.is_int(spin_num_col, 'spin number column', can_be_none=True)
+ check.is_int(spin_name_col, 'spin name column', can_be_none=True)
+ check.is_int(data_col, 'data column', can_be_none=True)
+ check.is_int(error_col, 'error column', can_be_none=True)
check.is_str(sep, 'column separator', can_be_none=True)
+ check.is_str(spin_id, 'spin ID string', can_be_none=True)
# Execute the functional code.
- self.__relax__.generic.value.read(param=param, scaling=scaling,
file=file, num_col=num_col, name_col=name_col, data_col=data_col,
error_col=error_col, sep=sep)
+ self.__relax__.generic.value.read(param=param, scaling=scaling,
file=file, dir=dir, 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)
def set(self, val=None, param=None, spin_id=None):
r9578 - in /1.3: generic_fns/dasha.py generic_fns/value.py prompt/value.py