Author: bugman
Date: Tue Jan 15 12:46:17 2013
New Revision: 18202
URL: http://svn.gna.org/viewcvs/relax?rev=18202&view=rev
Log:
Added the 'empty' flag to the sequence.copy user function to allow all the
spin contents to be copied.
The user function was only copying the basic empty molecule, residue and spin
containers, in contrast
to the interatomic.copy user function which copies all of the container
contents as well. This new
flag is for backwards compatibility - it allows old scripts to operate as
before while enabling the
new functionality.
Modified:
trunk/generic_fns/sequence.py
trunk/user_functions/sequence.py
Modified: trunk/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/sequence.py?rev=18202&r1=18201&r2=18202&view=diff
==============================================================================
--- trunk/generic_fns/sequence.py (original)
+++ trunk/generic_fns/sequence.py Tue Jan 15 12:46:17 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2012 Edward d'Auvergne
#
+# Copyright (C) 2003-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -21,6 +21,11 @@
# Module docstring.
"""Module for handling the molecule, residue, and spin sequence."""
+
+# Python module imports.
+from copy import deepcopy
+from re import search
+import sys
# relax module imports.
from arg_check import is_int
@@ -29,7 +34,6 @@
from generic_fns import pipes
from relax_errors import RelaxError, RelaxDiffMolNumError,
RelaxDiffResNumError, RelaxDiffSeqError, RelaxDiffSpinNumError,
RelaxFileEmptyError, RelaxInvalidSeqError, RelaxNoSequenceError,
RelaxSequenceError
from relax_io import open_write_file, read_spin_data, write_spin_data
-import sys
@@ -79,19 +83,17 @@
set_spin_isotope(spin_id='@H', isotope='1H')
-def copy(pipe_from=None, pipe_to=None, preserve_select=False, verbose=True):
+def copy(pipe_from=None, pipe_to=None, preserve_select=False, empty=True,
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.
+ @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.
+ @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.
+ @keyword empty: A flag which if True will create a molecule,
residue, and spin sequence in the target pipe lacking all of the spin data of
the source pipe. If False, then the spin data will also be copied.
+ @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
"""
@@ -117,14 +119,38 @@
# 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):
+ # Generate the new sequence.
+ new_spin = create_spin(spin_num=spin.num, spin_name=spin.name,
res_num=res_num, res_name=res_name, mol_name=mol_name, pipe=pipe_to)
+
# Preserve selection.
if preserve_select:
- select = spin.select
+ new_spin.select = spin.select
else:
select = True
- # Generate the new sequence.
- generate(mol_name, res_num, res_name, spin.num, spin.name, pipe_to,
select=select, verbose=verbose)
+ # Copy all the spin data.
+ if not empty:
+ # Duplicate all the objects of the container.
+ for name in dir(spin):
+ # Skip special objects.
+ if search('^_', name):
+ continue
+
+ # Skip the spin ID.
+ #if name in ['spin_id']:
+ # continue
+
+ # Skip class methods.
+ if name in list(spin.__class__.__dict__.keys()):
+ continue
+
+ # Duplicate all other objects.
+ obj = deepcopy(getattr(spin, name))
+ setattr(new_spin, name, obj)
+
+ # Print out.
+ if verbose:
+ display(mol_name_flag=True, res_num_flag=True, res_name_flag=True,
spin_num_flag=True, spin_name_flag=True)
def compare_sequence(pipe1=None, pipe2=None, fail=True):
Modified: trunk/user_functions/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/sequence.py?rev=18202&r1=18201&r2=18202&view=diff
==============================================================================
--- trunk/user_functions/sequence.py (original)
+++ trunk/user_functions/sequence.py Tue Jan 15 12:46:17 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2012 Edward d'Auvergne
#
+# Copyright (C) 2003-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -85,6 +85,13 @@
wiz_combo_iter = pipes.pipe_names,
wiz_read_only = True,
can_be_none = True
+)
+uf.add_keyarg(
+ name = "empty",
+ default = True,
+ py_type = "bool",
+ desc_short = "empty sequence flag",
+ desc = "A flag which if True will create a molecule, residue, and spin
sequence in the target pipe lacking all of the spin data of the source pipe.
If False, then the spin data will also be copied."
)
# Description.
uf.desc.append(Desc_container())
r18202 - in /trunk: generic_fns/sequence.py user_functions/sequence.py