Author: bugman
Date: Wed May 7 16:46:52 2008
New Revision: 6127
URL: http://svn.gna.org/viewcvs/relax?rev=6127&view=rev
Log:
Updated the desel_read() function to the new relax design.
Modified:
1.3/generic_fns/selection.py
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=6127&r1=6126&r2=6127&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Wed May 7 16:46:52 2008
@@ -22,8 +22,9 @@
# relax module imports.
from data import Data as relax_data_store
-from generic_fns.mol_res_spin import spin_loop
-from relax_errors import RelaxError, RelaxNoPipeError, RelaxNoSequenceError
+from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_loop
+from relax_errors import RelaxError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxNoSpinError
+from relax_io import extract_data, strip
def desel_all():
@@ -42,17 +43,52 @@
spin.select = 0
-def desel_read(self, run=None, file=None, dir=None, change_all=None,
column=None):
- """Function for deselecting the residues contained in a file."""
+def desel_read(file=None, dir=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None,
change_all=False):
+ """Deselect the spins contained in a file.
+
+ @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 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
+ @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 sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ @keyword change_all: A flag which if True will cause all spins not
specified in the file to
+ be selected.
+ @type change_all: bool
+ """
+
+ # Test if the current data pipe exists.
+ if not relax_data_store.current_pipe:
+ raise RelaxNoPipeError
+
+ # Test if sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Extract the data from the file.
- 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][column])
+ int(file_data[i][num_col])
except:
header_lines = header_lines + 1
else:
@@ -62,49 +98,32 @@
file_data = file_data[header_lines:]
# Strip the data.
- file_data = self.relax.IO.strip(file_data)
-
- # Create the list of residues to deselect.
- deselect = []
+ file_data = strip(file_data)
+
+ # Minimum number of columns.
+ min_col_num = max(mol_name_col, res_num_col, res_name_col, spin_num_col,
spin_name_col)
+
+ # First select all spins if desired.
+ if change_all:
+ for spin in spin_loop():
+ spin.select = 1
+
+ # Then deselect the spins in the file.
for i in xrange(len(file_data)):
- try:
- deselect.append(int(file_data[i][column]))
- except:
- raise RelaxError, "Improperly formatted file."
-
- # Create the list of runs.
- self.runs = self.relax.generic.runs.list_of_runs(run)
-
- # Loop over the runs.
- no_match = 1
- for self.run in self.runs:
- # 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 len(relax_data_store.res[self.run]):
- raise RelaxNoSequenceError, self.run
-
- # Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
- # Remap the data structure 'relax_data_store.res[self.run][i]'.
- data = relax_data_store.res[self.run][i]
-
- # Select all residues.
- if change_all:
- data.select = 1
-
- # Deselect the residue if it is in the list deselect.
- if data.num in deselect:
- data.select = 0
-
- # Match flag.
- no_match = 0
-
- # No residue matched.
- if no_match:
- print "No residues match."
+ # 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)
+
+ # Get the corresponding spin container.
+ spin = return_spin(id)
+ if spin == None:
+ raise RelaxNoSpinError, id
+
+ # Deselect the spin.
+ spin.select = 0
def desel_res(self, run=None, num=None, name=None, change_all=None):
@@ -224,7 +243,7 @@
"""
# Extract the data from the file.
- file_data = self.relax.IO.extract_data(file, dir)
+ file_data = extract_data(file, dir)
# Count the number of header lines.
header_lines = 0
@@ -240,7 +259,7 @@
file_data = file_data[header_lines:]
# Strip the data.
- file_data = self.relax.IO.strip(file_data)
+ file_data = strip(file_data)
# Create the list of residues to select.
select = []
r6127 - /1.3/generic_fns/selection.py