Author: bugman
Date: Thu Jun 14 14:54:56 2012
New Revision: 16909
URL: http://svn.gna.org/viewcvs/relax?rev=16909&view=rev
Log:
Started to fill up the spin ID look up table.
The index_molecule() and index_residue() functions have been added to
determine the MoleculeList and
ResidueList indices of given molecules and residues. These are used by the
create_spin for
efficiency and to allow the indices (together with the spin index and spin ID
string) to be
assembled into the look up table. This table is not used anywhere yet.
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=16909&r1=16908&r2=16909&view=diff
==============================================================================
--- trunk/generic_fns/mol_res_spin.py (original)
+++ trunk/generic_fns/mol_res_spin.py Thu Jun 14 14:54:56 2012
@@ -1150,12 +1150,20 @@
# Acquire the spin lock (data modifying function), and make sure it is
finally released.
status.spin_lock.acquire(sys._getframe().f_code.co_name)
try:
- # Create the molecule and residue if they do not exist.
- if not return_molecule(generate_spin_id(mol_name=mol_name)):
+ # Create the molecule if it does not exist.
+ mol_index = index_molecule(mol_name)
+ if mol_index == None:
create_molecule(mol_name=mol_name)
- res_cont = return_residue(generate_spin_id(mol_name=mol_name,
res_num=res_num, res_name=res_name))
- if res_cont == None:
- res_cont = create_residue(mol_name=mol_name, res_num=res_num,
res_name=res_name)
+ mol_index = len(cdp.mol) - 1
+
+ # Create the residue if it does not exist.
+ res_index = index_residue(res_num=res_num, res_name=res_name,
mol_index=mol_index)
+ if res_index == None:
+ create_residue(mol_name=mol_name, res_num=res_num,
res_name=res_name)
+ res_index = len(cdp.mol[mol_index].res) - 1
+
+ # Alias the residue.
+ res_cont = cdp.mol[mol_index].res[res_index]
# Rename the spin, if only a single one exists and it is empty.
if len(res_cont.spin) == 1 and res_cont.spin[0].is_empty():
@@ -1167,6 +1175,13 @@
else:
res_cont.spin.add_item(spin_num=spin_num, spin_name=spin_name)
spin_cont = res_cont.spin[-1]
+
+ # 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)
+
+ # Add the spin ID and indices to the lookup table.
+ cdp.mol.lookup_table[spin_id] = [mol_index, res_index, spin_index]
# Release the lock.
finally:
@@ -1706,6 +1721,64 @@
# Return the IDs.
return spin_ids
+
+
+def index_molecule(mol_name=None):
+ """Return the index of the molecule of the given name.
+
+ @keyword mol_name: The name of the molecule.
+ @type mol_name: str
+ @return: The index of the molecule, if it exists.
+ @rtype: int or None
+ """
+
+ # Loop over the molecules.
+ i = 0
+ for mol in cdp.mol:
+ # A match.
+ if mol.name == mol_name:
+ return i
+
+ # Increment the index.
+ i += 1
+
+ # Nothing found.
+ return None
+
+
+def index_residue(res_num=None, res_name=None, mol_index=None):
+ """Return the index of the residue.
+
+ @keyword res_num: The number of the residue.
+ @type res_num: int
+ @keyword res_name: The name of the residue.
+ @type res_name: str
+ @keyword mol_index: The index of the molecule.
+ @type mol_index: str
+ @return: The index of the residue, if it exists.
+ @rtype: int or None
+ """
+
+ # Single unnamed residue.
+ if len(cdp.mol[mol_index].res) == 1 and res_num ==
cdp.mol[mol_index].res[0].num and res_name == cdp.mol[mol_index].res[0].name:
+ return 0
+
+ # Loop over the residues.
+ i = 0
+ for res in cdp.mol[mol_index].res:
+ # A unique number match.
+ if res_num != None and res.num == res_num:
+ return i
+
+ # Match names, if no number is given.
+ if res_num == None and res_name != None and res.name == res_name:
+ return i
+
+ # Increment the index.
+ i += 1
+
+ # Nothing found.
+ return None
def last_residue_num(selection=None):
r16909 - /trunk/generic_fns/mol_res_spin.py