Author: bugman
Date: Sun Mar 10 14:48:54 2013
New Revision: 18734
URL: http://svn.gna.org/viewcvs/relax?rev=18734&view=rev
Log:
Redesign of the generic_fns.mol_res_spin.generate_spin_id() function.
The function now tries to generate a unique ID based on the spin information
in the specified data
pipe. This is to attempt to fix a bug uncovered by the
Structure.test_read_xyz_internal2 system
test. Defaulting in all cases to the spin name rather than spin number will
often fail for a small
organic molecule, as the name in XYZ files is the atomic symbol and hence
will almost never be
unique.
Modified:
trunk/generic_fns/angles.py
trunk/generic_fns/mol_res_spin.py
trunk/generic_fns/structure/scientific.py
trunk/specific_fns/model_free/results.py
trunk/specific_fns/relax_fit.py
Modified: trunk/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/angles.py?rev=18734&r1=18733&r2=18734&view=diff
==============================================================================
--- trunk/generic_fns/angles.py (original)
+++ trunk/generic_fns/angles.py Sun Mar 10 14:48:54 2013
@@ -77,7 +77,7 @@
# Test if the vector exists.
if not hasattr(spin, 'xh_vect'):
# Get the spin id string.
- spin_id = generate_spin_id(mol_name, res_num, res_name,
spin.num, spin.name)
+ spin_id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin.num, spin_name=spin.name)
# Throw a warning.
warn(RelaxWarning("No angles could be calculated for the spin "
+ repr(spin_id) + "."))
Modified: trunk/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/mol_res_spin.py?rev=18734&r1=18733&r2=18734&view=diff
==============================================================================
--- trunk/generic_fns/mol_res_spin.py (original)
+++ trunk/generic_fns/mol_res_spin.py Sun Mar 10 14:48:54 2013
@@ -1026,7 +1026,7 @@
status.spin_lock.acquire(sys._getframe().f_code.co_name)
try:
# Create the molecule if it does not exist.
- mol_cont = return_molecule(generate_spin_id(mol_name=mol_name),
pipe=pipe)
+ mol_cont = return_molecule(generate_spin_id(pipe_name=pipe,
mol_name=mol_name), pipe=pipe)
if mol_cont == None:
mol_cont = create_molecule(mol_name=mol_name, pipe=pipe)
@@ -1226,7 +1226,7 @@
# The spin index and id.
spin_index = len(res_cont.spin) - 1
- spin_id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
+ spin_id = generate_spin_id(pipe_cont=dp, mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name)
# Update the private metadata.
if len(res_cont.spin) == 2:
@@ -1596,43 +1596,99 @@
return mol.res[0].num
-def generate_spin_id(mol_name=None, res_num=None, res_name=None,
spin_num=None, spin_name=None):
+def generate_spin_id(pipe_cont=None, pipe_name=None, mol_name=None,
res_num=None, res_name=None, spin_num=None, spin_name=None):
"""Generate the spin selection string.
- @param mol_name: The molecule name.
+ @keyword pipe_cont: The data pipe object.
+ @type pipe_cont: PipeContainer instance
+ @keyword pipe_name: The data pipe name.
+ @type pipe_name: str
+ @keyword mol_name: The molecule name.
@type mol_name: str or None
- @param res_num: The residue number.
+ @keyword res_num: The residue number.
@type res_num: int or None
- @param res_name: The residue name.
+ @keyword res_name: The residue name.
@type res_name: str or None
- @param spin_num: The spin number.
+ @keyword spin_num: The spin number.
@type spin_num: int or None
- @param spin_name: The spin name.
+ @keyword spin_name: The spin name.
@type spin_name: str or None
@return: The spin identification string.
@rtype: str
"""
+ # The data pipe.
+ if pipe_cont == None:
+ pipe_cont = pipes.get_pipe(pipe_name)
+
# Init.
id = ""
- # Molecule name.
+ # Molecule name and container.
if mol_name != None:
id = id + "#" + mol_name
# Residue data.
+ res_num_id = ''
+ res_name_id = ''
if res_num != None:
- id = id + ":" + str(res_num)
+ res_num_id = id + ":" + str(res_num)
+ res_num_exists = res_num_id in pipe_cont.mol._spin_id_lookup
+ if res_name != None:
+ res_name_id = id + ":" + res_name
+ res_name_exists = res_name_id in pipe_cont.mol._spin_id_lookup
+
+ # Select between the name and number, defaulting to the residue number
if needed.
+ if res_name != None and res_num != None:
+ if res_num_exists and res_name_exists:
+ id = res_num_id
+ elif not res_num_exists or not res_name_exists:
+ id = res_num_id
+ elif res_num_exists:
+ id = res_num_id
+ elif res_name_exists:
+ id = res_name_id
+ elif res_num != None:
+ id = res_num_id
+ elif res_name != None:
+ id = res_name_id
+ elif res_num != None:
+ id = res_num_id
elif res_name != None:
- id = id + ":" + res_name
+ id = res_name_id
# Spin data.
+ spin_num_id = ''
+ spin_name_id = ''
+ spin_num_exists = False
+ spin_name_exists = False
+ if spin_num != None:
+ spin_num_id = id + "@" + str(spin_num)
+ spin_num_exists = spin_num_id in pipe_cont.mol._spin_id_lookup
if spin_name != None:
- id = id + "@" + spin_name
+ spin_name_id = id + "@" + spin_name
+ spin_name_exists = spin_name_id in pipe_cont.mol._spin_id_lookup
+
+ # Select between the name and number, defaulting to the spin name if
needed.
+ if spin_name != None and spin_num != None:
+ if spin_num_exists and spin_name_exists:
+ id = spin_name_id
+ elif not spin_num_exists or not spin_name_exists:
+ id = spin_name_id
+ elif spin_name_exists:
+ id = spin_name_id
+ elif spin_num_exists:
+ id = spin_num_id
+ elif spin_name != None:
+ id = spin_name_id
+ elif spin_num != None:
+ id = spin_num_id
+ elif spin_name != None:
+ id = spin_name_id
elif spin_num != None:
- id = id + "@" + str(spin_num)
-
- # Return the spin id string.
+ id = spin_num_id
+
+ # Return the full spin ID string.
return id
@@ -2041,7 +2097,7 @@
# Alias.
mol = dp.mol[i]
- # Update the residue metadata.
+ # Update the molecule metadata.
mol._mol_index = i
# Loop over the residues.
@@ -2130,7 +2186,7 @@
# Generate the spin id.
if return_id:
- mol_id = generate_spin_id(mol.name)
+ mol_id = generate_spin_id(pipe_cont=dp, mol_name=mol.name)
# Yield the molecule data container.
if return_id:
@@ -2202,7 +2258,7 @@
# Rename the matching residues.
for res, mol_name in residue_loop(res_id, full_info=True):
if res.name and not force:
- warn(RelaxWarning("The residue '%s' is already named. Set
the force flag to rename." % generate_spin_id(mol_name, res.num, res.name)))
+ warn(RelaxWarning("The residue '%s' is already named. Set
the force flag to rename." % generate_spin_id(mol_name=mol_name,
res_num=res.num, res_name=res.name)))
else:
res.name = name
@@ -2288,7 +2344,7 @@
# Rename the residue.
for res, mol_name in residue_loop(res_id, full_info=True):
if res.num and not force:
- warn(RelaxWarning("The residue '%s' is already numbered.
Set the force flag to renumber." % generate_spin_id(mol_name, res.num,
res.name)))
+ warn(RelaxWarning("The residue '%s' is already numbered.
Set the force flag to renumber." % generate_spin_id(mol_name=mol_name,
res_num=res.num, res_name=res.name)))
else:
res.num = number
@@ -2526,7 +2582,7 @@
# Generate the spin id.
if return_id:
- res_id = generate_spin_id(mol.name, res.num, res.name)
+ res_id = generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name)
# Yield the residue data container.
if full_info and return_id:
@@ -2756,7 +2812,7 @@
spin_num = spin_num + 1
# Generate as store the spin ID.
- spin_ids.append(generate_spin_id(mol_name=mol.name,
res_num=res.num, res_name=res.name, spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_num=res.num, res_name=res.name, spin_num=spin.num,
spin_name=spin.name))
# No unique identifier.
if not multi and spin_num > 1:
@@ -2803,7 +2859,7 @@
# Return the spin and the spin_id string.
if return_spin_id:
# The spin identification string.
- spin_id = generate_spin_id(mol_name, res_num, res_name,
spin.num, spin.name)
+ spin_id = generate_spin_id(pipe_name=pipe,
mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin.num,
spin_name=spin.name)
# Return both objects.
return spin, spin_id
@@ -3212,34 +3268,58 @@
spin_count = len(res.spin)
# The spin ID.
- spin_ids.append(generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name, spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name, spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name, spin_num=spin.num))
# The spin IDs without spin info.
if spin_count == 1:
- spin_ids.append(generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num))
# The spin IDs without residue info.
if res_count == 1:
- spin_ids.append(generate_spin_id(mol_name=mol.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
spin_num=spin.num))
# The spin IDs without molecule info.
if mol_count == 1:
- spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name, spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_name=res.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name, spin_num=spin.num))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_name=res.name,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_name=res.name,
spin_num=spin.num))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
spin_num=spin.num))
# The spin IDs without spin or residue info.
if spin_count == 1 and res_count == 1:
- spin_ids.append(generate_spin_id(mol_name=mol.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name))
# The spin IDs without spin or molecule info.
if spin_count == 1 and mol_count == 1:
- spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num))
# The spin IDs without residue or molecule info.
if res_count == 1 and mol_count == 1:
- spin_ids.append(generate_spin_id(spin_num=spin.num,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, spin_num=spin.num,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, spin_num=spin.num))
+
+ # Collect the unique IDs.
+ unique = []
+ for id in spin_ids:
+ if id not in unique:
+ unique.append(id)
# Return the IDs.
- return spin_ids
+ return unique
def spin_id_variants_elim(dp=None, mol_index=None, res_index=None,
spin_index=None):
@@ -3267,36 +3347,36 @@
spin_count = len(res.spin)
# The spin ID.
- spin_ids.append(generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name, spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name, spin_num=spin.num, spin_name=spin.name))
# The spin IDs without spin info.
if spin_count > 1:
- spin_ids.append(generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name))
- spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name))
- spin_ids.append(generate_spin_id(mol_name=mol.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name))
# The spin IDs without residue info.
if res_count > 1:
- spin_ids.append(generate_spin_id(mol_name=mol.name,
spin_num=spin.num, spin_name=spin.name))
- spin_ids.append(generate_spin_id(spin_num=spin.num,
spin_name=spin.name))
- spin_ids.append(generate_spin_id(mol_name=mol.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, spin_num=spin.num,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name))
# The spin IDs without molecule info.
if mol_count > 1:
- spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name))
- spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name, spin_num=spin.num, spin_name=spin.name))
# The spin IDs without spin or residue info.
if spin_count > 1 and res_count > 1:
- spin_ids.append(generate_spin_id(mol_name=mol.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name))
# The spin IDs without spin or molecule info.
if spin_count > 1 and mol_count > 1:
- spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, res_num=res.num,
res_name=res.name))
# The spin IDs without residue or molecule info.
if res_count > 1 and mol_count > 1:
- spin_ids.append(generate_spin_id(spin_num=spin.num,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(pipe_cont=dp, spin_num=spin.num,
spin_name=spin.name))
# Return the IDs.
return spin_ids
@@ -3442,7 +3522,7 @@
# Generate the spin id.
if return_id:
- spin_id = generate_spin_id(mol.name, res.num, res.name,
spin.num, spin.name)
+ spin_id = generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_num=res.num, res_name=res.name, spin_num=spin.num,
spin_name=spin.name)
# Yield the data.
if full_info and return_id:
Modified: trunk/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/scientific.py?rev=18734&r1=18733&r2=18734&view=diff
==============================================================================
--- trunk/generic_fns/structure/scientific.py (original)
+++ trunk/generic_fns/structure/scientific.py Sun Mar 10 14:48:54 2013
@@ -431,7 +431,7 @@
"""
# Generate the selection object.
- sel_obj = Selection(generate_spin_id(mol_name, res_num, res_name,
spin_num, spin_name))
+ sel_obj = Selection(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name))
# Initialise some objects.
vectors = []
Modified: trunk/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/model_free/results.py?rev=18734&r1=18733&r2=18734&view=diff
==============================================================================
--- trunk/specific_fns/model_free/results.py (original)
+++ trunk/specific_fns/model_free/results.py Sun Mar 10 14:48:54 2013
@@ -166,7 +166,7 @@
generic_fns.sequence.generate(mol_name, res_num, res_name, spin_num,
spin_name, verbose=False)
# Get the spin identification string.
- spin_id = generate_spin_id(mol_name, res_num, res_name, spin_num,
spin_name)
+ spin_id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
# Set the selection status.
select = bool(int(spin_line[col['select']]))
@@ -701,7 +701,7 @@
spin_name = file_line[col['spin_name']]
# Create the spin ID.
- spin_id = generate_spin_id(mol_name, res_num, res_name,
spin_num, spin_name)
+ spin_id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
# Get the spin container.
spin = return_spin(spin_id)
Modified: trunk/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/relax_fit.py?rev=18734&r1=18733&r2=18734&view=diff
==============================================================================
--- trunk/specific_fns/relax_fit.py (original)
+++ trunk/specific_fns/relax_fit.py Sun Mar 10 14:48:54 2013
@@ -672,7 +672,7 @@
# Print out.
if verbosity >= 1:
# Get the spin id string.
- spin_id = generate_spin_id(mol_name, res_num, res_name,
spin.num, spin.name)
+ spin_id = generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name, spin_num=spin.num, spin_name=spin.name)
# Individual spin printout.
if verbosity >= 2:
r18734 - in /trunk: generic_fns/ generic_fns/structure/ specific_fns/ specific_fns/model_free/