Author: bugman
Date: Fri Aug 1 14:53:53 2008
New Revision: 7067
URL: http://svn.gna.org/viewcvs/relax?rev=7067&view=rev
Log:
Converted the generic_fns.value.read() function to the new design.
Modified:
1.3/generic_fns/value.py
Modified: 1.3/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/value.py?rev=7067&r1=7066&r2=7067&view=diff
==============================================================================
--- 1.3/generic_fns/value.py (original)
+++ 1.3/generic_fns/value.py Fri Aug 1 14:53:53 2008
@@ -30,9 +30,8 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
-from generic_fns import diffusion_tensor
-from generic_fns.minimise import reset_min_stats
-from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
+from generic_fns import diffusion_tensor, minimise
+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, RelaxNoResError,
RelaxNoPipeError, RelaxNoSequenceError, RelaxParamSetError, RelaxValueError
from relax_io import extract_data, open_write_file, strip
@@ -96,7 +95,7 @@
set(spin_to, value=value, error=error, param=param)
# Reset all minimisation statistics.
- reset_min_stats(pipe_to)
+ minimise.reset_min_stats(pipe_to)
def display(param=None):
@@ -199,12 +198,35 @@
return spin_params, spin_values, other_params, other_values
-def read(param=None, scaling=1.0, file=None, num_col=0, name_col=1,
data_col=2, error_col=3, sep=None):
- """Function for reading residue specific data values from a file."""
-
- # Arguments.
- self.param = param
- self.scaling = scaling
+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):
+ """Read spin specific data values from a file.
+
+ @keyword param: The name of the parameter to read.
+ @type param: str
+ @keyword scaling: A scaling factor by which all read values are
multiplied by.
+ @type scaling: float
+ @keyword file: The name of the file to open.
+ @type file: str
+ @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.
+ @type mol_name_col: int or None
+ @keyword res_name_col: The column containing the residue name
information.
+ @type res_name_col: int or None
+ @keyword res_num_col: The column containing the residue number
information.
+ @type res_num_col: int or None
+ @keyword spin_name_col The column containing the spin name information.
+ @type spin_name_col: int or None
+ @keyword spin_num_col: The column containing the spin number
information.
+ @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.
+ @type error_col: int or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ """
# Test if the current pipe exists.
if not ds.current_pipe:
@@ -214,49 +236,47 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Function type.
- self.function_type = ds.run_types[ds.run_names.index(self.run)]
-
# Minimisation parameter.
- if self.relax.generic.minimise.return_data_name(param):
+ if minimise.return_data_name(param):
# Minimisation statistic flag.
- min_stat = 1
+ min_stat = True
# Specific value and error returning function.
- return_value = self.relax.generic.minimise.return_value
+ return_value = minimise.return_value
# Specific set function.
- set = self.relax.generic.minimise.set
+ set = minimise.set
# Normal parameter.
else:
# Minimisation statistic flag.
- min_stat = 0
-
- # Specific value and error returning function.
- return_value = self.relax.specific_setup.setup('return_value',
self.function_type)
+ min_stat = False
+
+ # Specific v
+ return_value = get_specific_fn('return_value',
ds[ds.current_pipe].pipe_type)
# Specific set function.
- set = self.relax.specific_setup.setup('set', self.function_type)
+ set = get_specific_fn('set', ds[ds.current_pipe].pipe_type)
# Test data corresponding to param already exists.
- for i in xrange(len(ds.res[self.run])):
- # Skip deselected residues.
- if not ds.res[self.run][i].select:
+ for spin in spin_loop():
+ # Skip deselected spins.
+ if not spin.select:
continue
# Get the value and error.
- value, error = return_value(self.run, i, self.param)
+ value, error = return_value(spin, param)
# Data exists.
if value != None or error != None:
- raise RelaxValueError, (self.param, self.run)
+ raise RelaxValueError, self.param
# Extract the data from the file.
file_data = extract_data(file)
# 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])
@@ -275,16 +295,16 @@
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]) <= data_col or len(file_data[i]) <= error_col:
+ if len(file_data[i]) <= min_col_num:
continue
try:
- # Number column.
- int(file_data[i][num_col])
-
# Value column.
if file_data[i][data_col] != 'None':
float(file_data[i][data_col])
@@ -295,30 +315,18 @@
except ValueError:
if error_col != None:
- if name_col != None:
- raise RelaxError, "The 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] + ")."
- else:
- raise RelaxError, "The data is invalid (num=" +
file_data[i][num_col] + ", data=" + file_data[i][data_col] + ", error=" +
file_data[i][error_col] + ")."
+ raise RelaxError, "The data is invalid (data=" +
file_data[i][data_col] + ", error=" + file_data[i][error_col] + ")."
else:
- if name_col != None:
- raise RelaxError, "The data is invalid (num=" +
file_data[i][num_col] + ", name=" + file_data[i][name_col] + ", data=" +
file_data[i][data_col] + ")."
- else:
- raise RelaxError, "The data is invalid (num=" +
file_data[i][num_col] + ", data=" + file_data[i][data_col] + ")."
+ 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]) <= data_col or len(file_data[i]) <= error_col:
+ if len(file_data[i]) <= min_col_num:
continue
- # Residue number.
- spin_num = int(file_data[i][num_col])
-
- # Residue name.
- if name_col == None:
- spin_name = None
- else:
- spin_name = file_data[i][name_col]
+ # 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':
@@ -332,25 +340,17 @@
else:
error = None
- # Find the index of ds.res[self.run] which corresponds to the
relaxation data set i.
- index = None
- for j in xrange(len(ds.res[self.run])):
- if ds.res[self.run][j].num == spin_num and (spin_name == None or
ds.res[self.run][j].name == spin_name):
- index = j
- break
- if index == None:
- raise RelaxNoResError, (spin_num, spin_name)
+ # Get the corresponding spin container.
+ spin = return_spin(id)
+ if spin == None:
+ raise RelaxNoSpinError, id
# Set the value.
- set(run=run, value=value, error=error, param=self.param,
scaling=scaling, index=index)
-
- # Reset the residue specific minimisation statistics.
- if not min_stat:
- self.relax.generic.minimise.reset_min_stats(self.run, index)
-
- # Reset the global minimisation statistics.
+ set(value=value, error=error, param=param, scaling=scaling,
spin=spin)
+
+ # Reset the minimisation statistics.
if not min_stat:
- self.relax.generic.minimise.reset_min_stats(self.run)
+ reset_min_stats()
def set(val=None, param=None, spin_id=None, force=False):
@@ -440,7 +440,7 @@
set_non_spin_params(value=val, param=param)
# Reset all minimisation statistics.
- reset_min_stats()
+ minimise.reset_min_stats()
def set_spin_params(value=None, error=None, param=None, scaling=1.0,
spin=None):
r7067 - /1.3/generic_fns/value.py