Author: bugman
Date: Sun Oct 5 17:36:49 2008
New Revision: 7518
URL: http://svn.gna.org/viewcvs/relax?rev=7518&view=rev
Log:
Bug fix for the duplication of sequence data during model selection.
The sequence.copy() function was not preserving the selection flag so that
new option is sent into
the copy() and generate() functions, originating from the duplicate_data()
model-free method.
Modified:
1.3/generic_fns/sequence.py
1.3/specific_fns/model_free/main.py
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=7518&r1=7517&r2=7518&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Sun Oct 5 17:36:49 2008
@@ -35,18 +35,20 @@
-def copy(pipe_from=None, pipe_to=None, verbose=True):
+def copy(pipe_from=None, pipe_to=None, preserve_select=False, verbose=True):
"""Copy the molecule, residue, and spin sequence data from one data pipe
to another.
- @keyword pipe_from: The data pipe to copy the sequence data from. This
defaults to the current
- data pipe.
- @type pipe_from: str
- @keyword pipe_to: The data pipe to copy the sequence data to. This
defaults to the current
- data pipe.
- @type pipe_to: str
- @keyword verbose: A flag which if True will cause info about each spin
to be printed out as
- the sequence is generated.
- @type verbose: bool
+ @keyword pipe_from: The data pipe to copy the sequence data
from. This defaults to the
+ current data pipe.
+ @type pipe_from: str
+ @keyword pipe_to: The data pipe to copy the sequence data to.
This defaults to the
+ current data pipe.
+ @type pipe_to: str
+ @keyword preserve_select: A flag which if True will cause spin
selections to be preserved.
+ @type preserve_select: bool
+ @keyword verbose: A flag which if True will cause info about
each spin to be printed
+ out as the sequence is generated.
+ @type verbose: bool
"""
# Defaults.
@@ -71,8 +73,14 @@
# Loop over the spins of the pipe_from data pipe.
for spin, mol_name, res_num, res_name in spin_loop(pipe=pipe_from,
full_info=True):
+ # Preserve selection.
+ if preserve_select:
+ select = spin.select
+ else:
+ select = True
+
# Generate the new sequence.
- generate(mol_name, res_num, res_name, spin.num, spin.name, pipe_to,
verbose)
+ generate(mol_name, res_num, res_name, spin.num, spin.name, pipe_to,
select=select, verbose=verbose)
def display(sep=None, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, spin_num_flag=False, spin_name_flag=False):
@@ -108,7 +116,7 @@
write_body(file=sys.stdout, sep=sep, mol_name_flag=mol_name_flag,
res_num_flag=res_num_flag, res_name_flag=res_name_flag,
spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
-def generate(mol_name=None, res_num=None, res_name=None, spin_num=None,
spin_name=None, pipe=None, verbose=True):
+def generate(mol_name=None, res_num=None, res_name=None, spin_num=None,
spin_name=None, pipe=None, select=True, verbose=True):
"""Generate the sequence item-by-item by adding a single
molecule/residue/spin container as necessary.
@keyword mol_name: The molecule name.
@@ -124,6 +132,8 @@
@keyword pipe: The data pipe in which to generate the sequence.
This defaults to the
current data pipe.
@type pipe: str
+ @keyword select: The spin selection flag.
+ @type select: bool
@keyword verbose: A flag which if True will cause info about each spin
to be printed out as
the sequence is generated.
@type verbose: bool
@@ -161,6 +171,12 @@
if not curr_spin:
# Add the spin.
curr_res.spin.add_item(spin_name=spin_name, spin_num=spin_num)
+
+ # Get the spin.
+ curr_spin = return_spin(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name),
pipe=pipe)
+
+ # Set the selection flag.
+ curr_spin.select = select
# Print out of all the spins.
if verbose:
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=7518&r1=7517&r2=7518&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/main.py (original)
+++ 1.3/specific_fns/model_free/main.py Sun Oct 5 17:36:49 2008
@@ -1121,7 +1121,7 @@
if model_type == 'mf' or (model_type == 'local_tm' and not
global_stats):
# Duplicate the sequence data if it doesn't exist.
if dp_to.mol.is_empty():
- sequence.copy(pipe_from=pipe_from, pipe_to=pipe_to,
verbose=verbose)
+ sequence.copy(pipe_from=pipe_from, pipe_to=pipe_to,
preserve_select=True, verbose=verbose)
# Get the spin container indices.
mol_index, res_index, spin_index =
convert_from_global_index(global_index=model_index, pipe=pipe_from)
r7518 - in /1.3: generic_fns/sequence.py specific_fns/model_free/main.py