Author: bugman
Date: Sun Aug 7 22:04:16 2011
New Revision: 14241
URL: http://svn.gna.org/viewcvs/relax?rev=14241&view=rev
Log:
All of the generic_fns.mol_res_spin fns which modify the data structure are
now using the new lock.
Modified:
branches/gui_testing/generic_fns/mol_res_spin.py
Modified: branches/gui_testing/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/generic_fns/mol_res_spin.py?rev=14241&r1=14240&r2=14241&view=diff
==============================================================================
--- branches/gui_testing/generic_fns/mol_res_spin.py (original)
+++ branches/gui_testing/generic_fns/mol_res_spin.py Sun Aug 7 22:04:16 2011
@@ -48,6 +48,7 @@
from generic_fns import relax_re
from relax_errors import RelaxError, RelaxNoSpinError,
RelaxResSelectDisallowError, RelaxSpinSelectDisallowError
from relax_warnings import RelaxWarning
+from status import Status; status = Status()
ALLOWED_MOL_TYPES = ['protein',
@@ -601,6 +602,9 @@
@type mol_to: str
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# The current data pipe.
if pipe_from == None:
pipe_from = pipes.cdp_name()
@@ -616,10 +620,12 @@
# Disallow spin selections.
if spin_from_token != None or spin_to_token != None:
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Disallow residue selections.
if res_from_token != None or res_to_token != None:
+ status.spin_lock.release()
raise RelaxResSelectDisallowError
# Parse the molecule token for renaming.
@@ -628,6 +634,7 @@
# Test if the molecule name already exists.
mol_to_cont = return_molecule(mol_to, pipe_to)
if mol_to_cont and not mol_to_cont.is_empty():
+ status.spin_lock.release()
raise RelaxError("The molecule " + repr(mol_to) + " already exists
in the " + repr(pipe_to) + " data pipe.")
# Get the single molecule data container.
@@ -635,6 +642,7 @@
# No molecule to copy data from.
if mol_from_cont == None:
+ status.spin_lock.release()
raise RelaxError("The molecule " + repr(mol_from) + " does not exist
in the " + repr(pipe_from) + " data pipe.")
# Get the target pipe.
@@ -649,6 +657,9 @@
# Change the new molecule name.
if mol_name_to != None:
pipe.mol[-1].name = mol_name_to
+
+ # Release the lock.
+ status.spin_lock.release()
def copy_residue(pipe_from=None, res_from=None, pipe_to=None, res_to=None):
@@ -669,6 +680,9 @@
@type res_to: str
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# The current data pipe.
if pipe_from == None:
pipe_from = pipes.cdp_name()
@@ -687,6 +701,7 @@
# Disallow spin selections.
if spin_from_token != None or spin_to_token != None:
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Parse the residue token for renaming and renumbering.
@@ -695,6 +710,7 @@
# Test if the residue number already exists.
res_to_cont = return_residue(res_to, pipe_to)
if res_to_cont and not res_to_cont.is_empty():
+ status.spin_lock.release()
raise RelaxError("The residue " + repr(res_to) + " already exists in
the " + repr(pipe_to) + " data pipe.")
# Get the single residue data container.
@@ -702,6 +718,7 @@
# No residue to copy data from.
if res_from_cont == None:
+ status.spin_lock.release()
raise RelaxError("The residue " + repr(res_from) + " does not exist
in the " + repr(pipe_from) + " data pipe.")
# Get the single molecule data container to copy the residue to (default
to the first molecule).
@@ -720,6 +737,9 @@
mol_to_container.res[-1].num = res_num_to
if res_name_to != None:
mol_to_container.res[-1].name = res_name_to
+
+ # Release the lock.
+ status.spin_lock.release()
def copy_spin(pipe_from=None, spin_from=None, pipe_to=None, spin_to=None):
@@ -740,6 +760,9 @@
@type spin_to: str
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# The current data pipe.
if pipe_from == None:
pipe_from = pipes.cdp_name()
@@ -759,21 +782,25 @@
if spin_to_token:
spin_to_cont = return_spin(spin_to, pipe_to)
if spin_to_cont and not spin_to_cont.is_empty():
+ status.spin_lock.release()
raise RelaxError("The spin " + repr(spin_to) + " already exists
in the " + repr(pipe_from) + " data pipe.")
# No residue to copy data from.
if not return_residue(spin_from, pipe_from):
+ status.spin_lock.release()
raise RelaxError("The residue in " + repr(spin_from) + " does not
exist in the " + repr(pipe_from) + " data pipe.")
# No spin to copy data from.
spin_from_cont = return_spin(spin_from, pipe_from)
if spin_from_cont == None:
+ status.spin_lock.release()
raise RelaxError("The spin " + repr(spin_from) + " does not exist in
the " + repr(pipe_from) + " data pipe.")
# Get the single residue data container to copy the spin to (default to
the first molecule, first residue).
res_to_cont = return_residue(spin_to, pipe_to)
if res_to_cont == None and spin_to:
# No residue to copy data to.
+ status.spin_lock.release()
raise RelaxError("The residue in " + repr(spin_to) + " does not
exist in the " + repr(pipe_from) + " data pipe.")
if res_to_cont == None:
res_to_cont = pipe.mol[0].res[0]
@@ -792,6 +819,9 @@
res_to_cont.spin[-1].num = spin_num_to
if spin_name_to != None:
res_to_cont.spin[-1].name = spin_name_to
+
+ # Release the lock.
+ status.spin_lock.release()
def count_molecules(selection=None, pipe=None):
@@ -914,20 +944,31 @@
# Test if the current data pipe exists.
pipes.test()
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Test the molecule type.
if mol_type and mol_type not in ALLOWED_MOL_TYPES:
+ status.spin_lock.release()
raise RelaxError("The molecule type '%s' must be one of %s" %
(mol_type, ALLOWED_MOL_TYPES))
# Test if the molecule name already exists.
for i in xrange(len(cdp.mol)):
if cdp.mol[i].name == mol_name:
+ status.spin_lock.release()
raise RelaxError("The molecule '" + repr(mol_name) + "' already
exists in the relax data store.")
# Append the molecule.
cdp.mol.add_item(mol_name=mol_name, mol_type=mol_type)
+ # Alias the molecule.
+ mol = cdp.mol[-1]
+
+ # Release the lock.
+ status.spin_lock.release()
+
# Return the molecule.
- return cdp.mol[-1]
+ return mol
def create_residue(res_num=None, res_name=None, mol_name=None):
@@ -950,6 +991,9 @@
if not return_molecule(generate_spin_id(mol_name=mol_name)):
create_molecule(mol_name=mol_name)
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Get the molecule container to add the residue to.
mol_cont = return_molecule(generate_spin_id(mol_name=mol_name))
if not mol_cont:
@@ -958,8 +1002,14 @@
# Add the residue.
mol_cont.res.add_item(res_num=res_num, res_name=res_name)
+ # Alias the residue.
+ res = mol_cont.res[-1]
+
+ # Release the lock.
+ status.spin_lock.release()
+
# Return the residue.
- return mol_cont.res[-1]
+ return res
def create_pseudo_spin(spin_name=None, spin_num=None, res_id=None,
members=None, averaging=None):
@@ -976,23 +1026,29 @@
# Test if the current data pipe exists.
pipes.test()
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Split up the selection string.
mol_token, res_token, spin_token = tokenise(res_id)
# Disallow spin selections.
if spin_token != None:
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Get the residue container to add the spin to.
if res_id:
res_to_cont = return_residue(res_id)
if res_to_cont == None:
+ status.spin_lock.release()
raise RelaxError("The residue in " + repr(res_id) + " does not
exist in the current data pipe.")
else:
res_to_cont = cdp.mol[0].res[0]
# Check the averaging technique.
if averaging not in ['linear']:
+ status.spin_lock.release()
raise RelaxError("The '%s' averaging technique is unknown." %
averaging)
# Get the spin positions.
@@ -1003,6 +1059,7 @@
# Test that the spin exists.
if spin == None:
+ status.spin_lock.release()
raise RelaxNoSpinError(atom)
# Test the position.
@@ -1051,6 +1108,9 @@
spin.pos = ave
else:
spin.pos = ave[0]
+
+ # Release the lock.
+ status.spin_lock.release()
def create_spin(spin_num=None, spin_name=None, res_num=None, res_name=None,
mol_name=None):
@@ -1079,6 +1139,9 @@
if not return_residue(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name)):
create_residue(mol_name=mol_name, res_num=res_num, res_name=res_name)
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Get the residue container to add the spin to.
res_cont = return_residue(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name))
if not res_cont:
@@ -1094,6 +1157,9 @@
else:
res_cont.spin.add_item(spin_num=spin_num, spin_name=spin_name)
spin_cont = res_cont.spin[-1]
+
+ # Release the lock.
+ status.spin_lock.release()
# Return the spin.
return spin_cont
@@ -1136,15 +1202,20 @@
@type mol_id: str
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Split up the selection string.
mol_token, res_token, spin_token = tokenise(mol_id)
# Disallow spin selections.
if spin_token != None:
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Disallow residue selections.
if res_token != None:
+ status.spin_lock.release()
raise RelaxResSelectDisallowError
# Parse the token.
@@ -1170,6 +1241,9 @@
if len(cdp.mol) == 0:
cdp.mol.add_item()
+ # Release the lock.
+ status.spin_lock.release()
+
def delete_residue(res_id=None):
"""Function for deleting residues from the current data pipe.
@@ -1178,11 +1252,15 @@
@type res_id: str
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Split up the selection string.
mol_token, res_token, spin_token = tokenise(res_id)
# Disallow spin selections.
if spin_token != None:
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Parse the tokens.
@@ -1210,6 +1288,9 @@
if len(mol.res) == 0:
mol.res.add_item()
+ # Release the lock.
+ status.spin_lock.release()
+
def delete_spin(spin_id=None):
"""Function for deleting spins from the current data pipe.
@@ -1217,6 +1298,9 @@
@param spin_id: The molecule, residue, and spin identifier string.
@type spin_id: str
"""
+
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
# Split up the selection string.
mol_token, res_token, spin_token = tokenise(spin_id)
@@ -1245,6 +1329,9 @@
# Create an empty spin container if no spins remain.
if len(res.spin) == 0:
res.spin.add_item()
+
+ # Release the lock.
+ status.spin_lock.release()
def display_molecule(mol_id=None):
@@ -1719,14 +1806,19 @@
@type force: bool
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Get the single molecule data container.
mol = return_molecule(mol_id)
# Disallow residue and spin selections.
select_obj = Selection(mol_id)
if select_obj.has_residues():
+ status.spin_lock.release()
raise RelaxResSelectDisallowError
if select_obj.has_spins():
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Name the molecule is there is a single match.
@@ -1736,6 +1828,9 @@
else:
mol.name = name
+ # Release the lock.
+ status.spin_lock.release()
+
def name_residue(res_id, name=None, force=False):
"""Name the residues.
@@ -1748,9 +1843,13 @@
@type force: bool
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Disallow spin selections.
select_obj = Selection(res_id)
if select_obj.has_spins():
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Rename the matching residues.
@@ -1760,6 +1859,9 @@
else:
res.name = name
+ # Release the lock.
+ status.spin_lock.release()
+
def name_spin(spin_id=None, name=None, force=False):
"""Name the spins.
@@ -1772,6 +1874,9 @@
@type force: bool
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Rename the matching spins.
for spin, id in spin_loop(spin_id, return_id=True):
if spin.name and not force:
@@ -1779,6 +1884,9 @@
else:
spin.name = name
+ # Release the lock.
+ status.spin_lock.release()
+
def number_residue(res_id, number=None, force=False):
"""Number the residues.
@@ -1791,6 +1899,9 @@
@type force: bool
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Catch multiple numberings!
i = 0
for res in residue_loop(res_id):
@@ -1798,11 +1909,13 @@
# Fail if multiple residues are numbered.
if i > 1:
+ status.spin_lock.release()
raise RelaxError("The numbering of multiple residues is disallowed,
each residue requires a unique number.")
# Disallow spin selections.
select_obj = Selection(res_id)
if select_obj.has_spins():
+ status.spin_lock.release()
raise RelaxSpinSelectDisallowError
# Rename the residue.
@@ -1812,6 +1925,9 @@
else:
res.num = number
+ # Release the lock.
+ status.spin_lock.release()
+
def number_spin(spin_id=None, number=None, force=False):
"""Number the spins.
@@ -1824,6 +1940,9 @@
@type force: bool
"""
+ # Acquire the spin lock (data modifying function).
+ status.spin_lock.acquire()
+
# Catch multiple renumberings!
i = 0
for spin in spin_loop(spin_id):
@@ -1831,6 +1950,7 @@
# Fail if multiple spins are numbered.
if number != None and i > 1:
+ status.spin_lock.release()
raise RelaxError("The numbering of multiple spins is disallowed, as
each spin requires a unique number.")
# Rename the spin.
@@ -1839,6 +1959,9 @@
warn(RelaxWarning("The spin '%s' is already numbered. Set the
force flag to renumber." % id))
else:
spin.num = number
+
+ # Release the lock.
+ status.spin_lock.release()
def one_letter_code(res_names):
@@ -2853,6 +2976,3 @@
warn(RelaxWarning("The molecule '%s' already has its type set.
Set the force flag to change." % mol_id))
else:
mol.type = type
-
-
-
r14241 - /branches/gui_testing/generic_fns/mol_res_spin.py