Author: bugman
Date: Sun Mar 10 15:40:50 2013
New Revision: 18736
URL: http://svn.gna.org/viewcvs/relax?rev=18736&view=rev
Log:
Bug fix for the maintenance of the spin ID lookup table metadata.
This is important for small molecules. Non-unique IDs were being placed into
the lookup table,
resulting in incorrect spin containers being sometimes used. Now the
molecule container has the
_res_name_count and _res_num_count metadata and the residue container the
_spin_name_count and
_spin_num_count structures. These are updated via metadata_update() and are
used by the
spin_id_variants() function to create a list of purely unique spin IDs.
Modified:
trunk/generic_fns/mol_res_spin.py
Modified: trunk/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/mol_res_spin.py?rev=18736&r1=18735&r2=18736&view=diff
==============================================================================
--- trunk/generic_fns/mol_res_spin.py (original)
+++ trunk/generic_fns/mol_res_spin.py Sun Mar 10 15:40:50 2013
@@ -2087,6 +2087,57 @@
# Get the data pipe.
dp = pipes.get_pipe(pipe)
+
+ # Pre-parse: Update the metadata for determining if names and numbers
already exist.
+ for i in range(len(dp.mol)):
+ # Alias.
+ mol = dp.mol[i]
+
+ # The residue counts.
+ mol._res_name_count = {}
+ mol._res_num_count = {}
+
+ # Loop over the residues.
+ for j in range(len(mol.res)):
+ # Alias.
+ res = mol.res[j]
+
+ # Count the residue names.
+ if res.name != None:
+ if res.name not in mol._res_names:
+ mol._res_name_count[res.name] = 1
+ else:
+ mol._res_name_count[res.name] += 1
+
+ # Count the residue numbers.
+ if res.num != None:
+ if res.num not in mol._res_num_count:
+ mol._res_num_count[res.num] = 1
+ else:
+ mol._res_num_count[res.num] += 1
+
+ # The spin counts.
+ res._spin_name_count = {}
+ res._spin_num_count = {}
+
+ # Loop over the spins.
+ for k in range(len(res.spin)):
+ # Alias.
+ spin = res.spin[k]
+
+ # Count the spin names.
+ if spin.name != None:
+ if spin.name not in res._spin_name_count:
+ res._spin_name_count[spin.name] = 10
+ else:
+ res._spin_name_count[spin.name] += 1
+
+ # Count the spin numbers.
+ if spin.num != None:
+ if spin.num not in res._spin_num_count:
+ res._spin_num_count[spin.num] = 1
+ else:
+ res._spin_num_count[spin.num] += 1
# Loop over the molecules.
for i in range(len(dp.mol)):
@@ -3300,34 +3351,62 @@
res_count = len(mol.res)
spin_count = len(res.spin)
+ # Unique info.
+ unique_res_name = True
+ if res.name != None and mol._res_name_count[res.name] > 1:
+ unique_res_name = False
+ unique_res_num = True
+ if res.num != None and mol._res_num_count[res.num] > 1:
+ unique_res_num = False
+ unique_spin_name = True
+ if spin.name != None and res._spin_name_count[spin.name] > 1:
+ unique_spin_name = False
+ unique_spin_num = True
+ if spin.num != None and res._spin_num_count[spin.num] > 1:
+ unique_spin_num = False
+
# The spin ID.
- 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))
+ if unique_res_name and unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_name=res.name, spin_name=spin.name))
+ if unique_res_name and unique_spin_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_name=res.name, spin_num=spin.num))
+ if unique_res_num and unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, spin_name=spin.name))
+ if unique_res_num and unique_spin_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp, mol_name=mol.name,
res_num=res.num, spin_num=spin.num))
# The spin IDs without spin info.
if spin_count == 1:
- 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))
+ if unique_res_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_name=res.name))
+ if unique_res_num:
+ 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(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))
+ if unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, spin_name=spin.name))
+ if unique_spin_num:
+ 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(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))
+ if unique_res_name and unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_name=res.name, spin_name=spin.name))
+ if unique_res_name and unique_spin_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_name=res.name, spin_num=spin.num))
+ if unique_res_num and unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_num=res.num, spin_name=spin.name))
+ if unique_res_num and unique_spin_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_num=res.num, spin_num=spin.num))
+ if unique_res_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_name=res.name))
+ if unique_res_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, res_num=res.num))
+ if unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, spin_name=spin.name))
+ if unique_spin_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
mol_name=mol.name, spin_num=spin.num))
# The spin IDs without spin or residue info.
if spin_count == 1 and res_count == 1:
@@ -3335,15 +3414,17 @@
# The spin IDs without spin or molecule info.
if spin_count == 1 and mol_count == 1:
- 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))
+ if unique_res_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
res_name=res.name))
+ if unique_res_num:
+ 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(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))
+ if unique_spin_name:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
spin_name=spin.name))
+ if unique_spin_num:
+ spin_ids.append(generate_spin_id(pipe_cont=dp,
spin_num=spin.num))
# Collect the unique IDs.
unique = []
r18736 - /trunk/generic_fns/mol_res_spin.py