Author: bugman
Date: Wed May 7 18:13:52 2008
New Revision: 6138
URL: http://svn.gna.org/viewcvs/relax?rev=6138&view=rev
Log:
Updated sel_read() to the new 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=6138&r1=6137&r2=6138&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Wed May 7 18:13:52 2008
@@ -215,33 +215,57 @@
spin.select = 1
-def sel_read(self, run=None, file=None, dir=None, boolean='OR',
change_all=0, column=None):
- """Select the residues contained in the given file.
-
- @param run: The run name.
- @type run: str
- @param file: The name of the file.
- @type file: str
- @param dir: The directory containing the file.
- @type dir: str
- @param boolean: The boolean operator used to select the spin systems
with. It can be
- one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.
- @type boolean: str
- @param change_all: A flag which if set will set the selection to solely
those of the file.
- @type change_all: int
- @param column: The whitespace separated column in which the residue
numbers are
- located.
- @type column: int
- """
+def sel_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,
boolean='OR', change_all=False):
+ """Select the spins contained in the given 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
+ @param boolean: The boolean operator used to select the
spin systems with. It
+ can be one of 'OR', 'NOR', 'AND',
'NAND', 'XOR', or 'XNOR'.
+ @type boolean: str
+ @keyword change_all: A flag which if True will cause all
spins not specified in the
+ file to be selected.
+ @type change_all: bool
+ @raises RelaxNoPipeError: If the current data pipe does not exist.
+ @raises RelaxNoSequenceError: If no molecule/residue/spins sequence
data exists.
+ """
+
+ # 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 = 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:
@@ -253,18 +277,71 @@
# Strip the data.
file_data = strip(file_data)
- # Create the list of residues to select.
- select = []
- for i in xrange(len(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)
+
+ # Loop over the spins.
+ for spin, mol_name, res_num, res_name in spin_loop(full_info=True)
+ # The spin system is in the file.
+ flag = spin_in_list(file_data, 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, mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin.num, spin_name=spin.name)
+
+ # Skip spins not the file.
+ if not change_all and not flag:
+ continue
+
+ # Boolean selections.
+ if boolean == 'OR':
+ spin.select = spin.select or flag
+ elif boolean == 'NOR':
+ spin.select = not (spin.select or flag)
+ elif boolean == 'AND':
+ spin.select = spin.select and flag
+ elif boolean == 'NAND':
+ spin.select = not (spin.select and flag)
+ elif boolean == 'XOR':
+ spin.select = not (spin.select and flag) and (spin.select or
flag)
+ elif boolean == 'XNOR':
+ spin.select = (spin.select and flag) or not (spin.select or flag)
+ else:
+ raise RelaxError, "Unknown boolean operator " + `boolean`
+
+
+def sel_res(self, run=None, num=None, name=None, boolean='OR', change_all=0):
+ """Select specific residues.
+
+ @param run: The run name.
+ @type run: str
+ @param num: The residue number.
+ @type num: int or regular expression str
+ @param name: The residue name.
+ @type name: regular expression str
+ @param boolean: The boolean operator used to select the spin systems
with. It can be
+ one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.
+ @type boolean: str
+ @param change_all: A flag which if set will set the selection to solely
those residues
+ specified.
+ @type change_all: int
+ """
+
+ # Test if the residue number is a valid regular expression.
+ if type(num) == str:
try:
- select.append(int(file_data[i][column]))
+ compile(num)
except:
- raise RelaxError, "Improperly formatted file."
+ raise RelaxRegExpError, ('residue number', num)
+
+ # Test if the residue name is a valid regular expression.
+ if name:
+ try:
+ compile(name)
+ except:
+ raise RelaxRegExpError, ('residue name', name)
# 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:
@@ -279,13 +356,23 @@
# Remap the data structure 'relax_data_store.res[self.run][i]'.
data = relax_data_store.res[self.run][i]
- # The spin system is in the new selection list.
- if data.num in select:
- new_select = 1
- else:
- new_select = 0
-
- # Select just the residues in the file.
+ # Initialise the new selection flag.
+ new_select = 0
+
+ # Set the new selection flag if the residue matches 'num'.
+ if type(num) == int:
+ if data.num == num:
+ new_select = 1
+ elif type(num) == str:
+ if match(num, `data.num`):
+ new_select = 1
+
+ # Set the new selection flag if the residue matches 'name'.
+ if name != None:
+ if match(name, data.name):
+ new_select = 1
+
+ # Select just the specified residues.
if change_all:
data.select = new_select
@@ -305,93 +392,6 @@
else:
raise RelaxError, "Unknown boolean operator " + `boolean`
-
-def sel_res(self, run=None, num=None, name=None, boolean='OR', change_all=0):
- """Select specific residues.
-
- @param run: The run name.
- @type run: str
- @param num: The residue number.
- @type num: int or regular expression str
- @param name: The residue name.
- @type name: regular expression str
- @param boolean: The boolean operator used to select the spin systems
with. It can be
- one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.
- @type boolean: str
- @param change_all: A flag which if set will set the selection to solely
those residues
- specified.
- @type change_all: int
- """
-
- # Test if the residue number is a valid regular expression.
- if type(num) == str:
- try:
- compile(num)
- except:
- raise RelaxRegExpError, ('residue number', num)
-
- # Test if the residue name is a valid regular expression.
- if name:
- try:
- compile(name)
- except:
- raise RelaxRegExpError, ('residue name', name)
-
- # 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]
-
- # Initialise the new selection flag.
- new_select = 0
-
- # Set the new selection flag if the residue matches 'num'.
- if type(num) == int:
- if data.num == num:
- new_select = 1
- elif type(num) == str:
- if match(num, `data.num`):
- new_select = 1
-
- # Set the new selection flag if the residue matches 'name'.
- if name != None:
- if match(name, data.name):
- new_select = 1
-
- # Select just the specified residues.
- if change_all:
- data.select = new_select
-
- # Boolean selections.
- if boolean == 'OR':
- data.select = data.select or new_select
- elif boolean == 'NOR':
- data.select = not (data.select or new_select)
- elif boolean == 'AND':
- data.select = data.select and new_select
- elif boolean == 'NAND':
- data.select = not (data.select and new_select)
- elif boolean == 'XOR':
- data.select = not (data.select and new_select) and
(data.select or new_select)
- elif boolean == 'XNOR':
- data.select = (data.select and new_select) or not
(data.select or new_select)
- else:
- raise RelaxError, "Unknown boolean operator " + `boolean`
-
# Match flag.
if new_select:
no_match = 0
r6138 - /1.3/generic_fns/selection.py