Author: bugman
Date: Tue Jun 19 14:12:23 2012
New Revision: 16955
URL: http://svn.gna.org/viewcvs/relax?rev=16955&view=rev
Log:
Expanded the functionality of the generic_fns.interatomic module.
The copy() and exists_data() functions have been added to copy all
interatomic data from one data
pipe to another and to check if interatomic data exists within a data pipe
respectively. The
create_interatom() function now also accepts a 'pipe' argument so that
non-current pipes can be
used.
Modified:
branches/interatomic/generic_fns/interatomic.py
Modified: branches/interatomic/generic_fns/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/interatomic.py?rev=16955&r1=16954&r2=16955&view=diff
==============================================================================
--- branches/interatomic/generic_fns/interatomic.py (original)
+++ branches/interatomic/generic_fns/interatomic.py Tue Jun 19 14:12:23 2012
@@ -23,34 +23,138 @@
# Module docstring.
"""Module for the manipulation of the interatomic data structures in the
relax data store."""
+# Python module imports.
+from copy import deepcopy
+from re import search
+
# relax module imports.
from generic_fns import pipes
from generic_fns.mol_res_spin import return_spin
-from relax_errors import RelaxError
+from relax_errors import RelaxError, RelaxInteratomError,
RelaxNoInteratomError
+from relax_io import write_data
from relax_warnings import RelaxNoSpinWarning
-def create_interatom(spin_id1=None, spin_id2=None):
+def copy(pipe_from=None, pipe_to=None, verbose=True):
+ """Copy the interatomic data from one data pipe to another.
+
+ @keyword pipe_from: The data pipe to copy the interatomic data
from. This defaults to the current data pipe.
+ @type pipe_from: str
+ @keyword pipe_to: The data pipe to copy the interatomic 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 pair to be printed out.
+ @type verbose: bool
+ """
+
+ # Defaults.
+ if pipe_from == None and pipe_to == None:
+ raise RelaxError("The pipe_from and pipe_to arguments cannot both be
set to None.")
+ elif pipe_from == None:
+ pipe_from = pipes.cdp_name()
+ elif pipe_to == None:
+ pipe_to = pipes.cdp_name()
+
+ # Test if the pipe_from and pipe_to data pipes exist.
+ pipes.test(pipe_from)
+ pipes.test(pipe_to)
+
+ # Test if pipe_from contains interatomic data.
+ if not exists_data(pipe_from):
+ raise RelaxNoInteratomError
+
+ # Test if pipe_to contains interatomic data.
+ if exists_data(pipe_to):
+ raise RelaxInteratomError
+
+ # Loop over the interatomic data of the pipe_from data pipe.
+ ids = []
+ for interatom in interatomic_loop(pipe=pipe_from):
+ # Create a new container.
+ new_interatom = create_interatom(spin_id1=interatom.spin_id1,
spin_id2=interatom.spin_id2, pipe=pipe_to)
+
+ # Duplicate all the objects of the container.
+ for name in dir(interatom):
+ # Skip special objects.
+ if search('^_', name):
+ continue
+
+ # Skip the spin IDs.
+ if name in ['spin_id1', 'spin_id2']:
+ continue
+
+ # Skip class methods.
+ if name in list(interatom.__class__.__dict__.keys()):
+ continue
+
+ # Duplicate all other objects.
+ obj = deepcopy(getattr(interatom, name))
+ setattr(new_interatom, name, obj)
+
+ # Store the IDs for the print out.
+ ids.append([repr(interatom.spin_id1), repr(interatom.spin_id2)])
+
+ # Print out.
+ if verbose:
+ write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2"],
data=ids)
+
+
+def create_interatom(spin_id1=None, spin_id2=None, pipe=None):
"""Create and return the interatomic data container for the two spins.
@keyword spin_id1: The spin ID string of the first atom.
@type spin_id1: str
@keyword spin_id2: The spin ID string of the first atom.
@type spin_id2: str
+ @keyword pipe: The data pipe to create the interatomic data
container for. This defaults to the current data pipe if not supplied.
+ @type pipe: str or None
@return: The newly created interatomic data container.
@rtype: data.interatomic.InteratomContainer instance
"""
+ # The data pipe.
+ if pipe == None:
+ pipe = pipes.cdp_name()
+
+ # Get the data pipe.
+ dp = pipes.get_pipe(pipe)
+
# Check that the spin IDs exist.
- spin = return_spin(spin_id1)
+ spin = return_spin(spin_id1, pipe)
if spin == None:
raise RelaxNoSpinWarning(spin_id1)
- spin = return_spin(spin_id2)
+ spin = return_spin(spin_id2, pipe)
if spin == None:
raise RelaxNoSpinWarning(spin_id2)
# Add and return the data.
- return cdp.interatomic.add_item(spin_id1=spin_id1, spin_id2=spin_id2)
+ return dp.interatomic.add_item(spin_id1=spin_id1, spin_id2=spin_id2)
+
+
+def exists_data(pipe=None):
+ """Determine if any interatomic data exists.
+
+ @keyword pipe: The data pipe in which the interatomic data will be
checked for.
+ @type pipe: str
+ @return: The answer to the question about the existence of
data.
+ @rtype: bool
+ """
+
+ # The current data pipe.
+ if pipe == None:
+ pipe = pipes.cdp_name()
+
+ # Test the data pipe.
+ pipes.test(pipe)
+
+ # Get the data pipe.
+ dp = pipes.get_pipe(pipe)
+
+ # The interatomic data structure is empty.
+ if dp.interatomic.is_empty():
+ return False
+
+ # Otherwise.
+ return True
def interatomic_loop(pipe=None):
@@ -108,7 +212,7 @@
# Single spin.
else:
for i in range(len(dp.interatomic)):
- if dp.interatomic[i].spin_id1 == spin_id1 or
dp.interatomic[i].spin_id2 == spin_id1:
+ if dp.interatomic[i].spin_id1 == spin_id1 or
dp.interatomic[i].spin_id2 == spin_id1:
interatoms.append(dp.interatomic[i])
# Return the list of containers.
r16955 - /branches/interatomic/generic_fns/interatomic.py