Author: bugman
Date: Sun Mar 10 17:01:34 2013
New Revision: 18745
URL: http://svn.gna.org/viewcvs/relax?rev=18745&view=rev
Log:
Improved the generic_fns.mol_res_spin.generate_spin_id_unique() function.
This can now work with molecule, residue, and spin names and numbers
alternatively to the containers
supplied as arguments. For this to work, the return_molecule_by_name()
function has been improved
and the functions return_residue_by_info() and return_spin_by_info() have
been added.
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=18745&r1=18744&r2=18745&view=diff
==============================================================================
--- trunk/generic_fns/mol_res_spin.py (original)
+++ trunk/generic_fns/mol_res_spin.py Sun Mar 10 17:01:34 2013
@@ -1734,7 +1734,7 @@
return id
-def generate_spin_id_unique(pipe_cont=None, pipe_name=None, mol=None,
res=None, spin=None):
+def generate_spin_id_unique(pipe_cont=None, pipe_name=None, mol=None,
res=None, spin=None, mol_name=None, res_num=None, res_name=None,
spin_num=None, spin_name=None):
"""Generate a list of spin ID variants for the given set of molecule,
residue and spin indices.
@keyword pipe_cont: The data pipe object.
@@ -1747,6 +1747,16 @@
@type res: ResidueContainer instance
@keyword spin: The spin container.
@type spin: SpinContainer instance
+ @keyword mol_name: The molecule name (an alternative to the molecule
container).
+ @type mol_name: str or None
+ @keyword res_num: The residue number (an alternative to the residue
container).
+ @type res_num: int or None
+ @keyword res_name: The residue name (an alternative to the residue
container).
+ @type res_name: str or None
+ @keyword spin_num: The spin number (an alternative to the spin
container).
+ @type spin_num: int or None
+ @keyword spin_name: The spin name (an alternative to the spin container).
+ @type spin_name: str or None
@return: The unique spin ID.
@rtype: str
"""
@@ -1755,29 +1765,47 @@
if pipe_cont == None:
pipe_cont = pipes.get_pipe(pipe_name)
+ # Get the containers if needed.
+ if mol == None:
+ mol = return_molecule_by_name(pipe_cont=pipe_cont, mol_name=mol_name)
+ if res == None and (res_name != None or res_num != None):
+ res = return_residue_by_info(mol=mol, res_name=res_name,
res_num=res_num)
+ if spin == None and (spin_name != None or spin_num != None):
+ spin = return_spin_by_info(res=res, spin_name=spin_name,
spin_num=spin_num)
+
+ # The info.
+ if mol:
+ mol_name = mol.name
+ if res:
+ res_name = res.name
+ res_num = res.num
+ if spin:
+ spin_name = spin.name
+ spin_num = spin.num
+
# Unique info.
unique_res_name = True
- if res.name != None and mol._res_name_count[res.name] > 1:
+ if res and 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:
+ if res and 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:
+ if spin and 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:
+ if spin and spin.num != None and res._spin_num_count[spin.num] > 1:
unique_spin_num = False
# The unique ID.
if unique_res_num and unique_spin_name:
- return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol.name,
res_num=res.num, spin_name=spin.name)
+ return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol_name,
res_num=res_num, spin_name=spin_name)
if unique_res_num and unique_spin_num:
- return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol.name,
res_num=res.num, spin_num=spin.num)
+ return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol_name,
res_num=res_num, spin_num=spin_num)
if unique_res_name and unique_spin_num:
- return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol.name,
res_name=res.name, spin_num=spin.num)
+ return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol_name,
res_name=res_name, spin_num=spin_num)
if unique_res_name and unique_spin_name:
- return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol.name,
res_name=res.name, spin_name=spin.name)
+ return generate_spin_id(pipe_cont=pipe_cont, mol_name=mol_name,
res_name=res_name, spin_name=spin_name)
def get_molecule_ids(selection=None):
@@ -2742,15 +2770,15 @@
return mol_container
-def return_molecule_by_name(name=None, pipe_cont=None, pipe_name=None):
+def return_molecule_by_name(pipe_cont=None, pipe_name=None, mol_name=None):
"""Return the molecule container matching the given name.
- @keyword name: The molecule name. If not supplied and only a
single molecule container exists, then that container will be returned.
- @type name: str
@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. If not supplied and only a
single molecule container exists, then that container will be returned.
+ @type mol_name: str
@return: The molecule container object.
@rtype: MoleculeContainer instance
"""
@@ -2760,7 +2788,7 @@
pipe_cont = pipes.get_pipe(pipe)
# No molecule name specified, so assume a single molecule.
- if name == None:
+ if mol_name == None:
# More than one molecule.
if len(pipe_cont.mol) > 1:
raise RelaxError("Cannot return the molecule with no name as
more than one molecule exists.")
@@ -2771,7 +2799,7 @@
# Loop over the molecules.
for mol in pipe_cont.mol:
# Return the matching molecule.
- if mol.name == name:
+ if mol.name == mol_name:
return mol
@@ -2833,6 +2861,42 @@
return res_container, mol_index, res_index
else:
return res_container
+
+
+def return_residue_by_info(mol=None, res_name=None, res_num=None):
+ """Return the residue container matching the given name.
+
+ @keyword mol: The molecule container.
+ @type mol: MoleculeContainer instance
+ @keyword res_name: The residue name. If not supplied and only a single
residue container exists, then that container will be returned.
+ @type res_name: str
+ @keyword res_num: The residue number. If not supplied and only a
single residue container exists, then that container will be returned.
+ @type res_num: str
+ @return: The residue container object.
+ @rtype: ResidueContainer instance
+ """
+
+ # No residue name or number specified, so assume a single residue.
+ if res_name == None and res_num == None:
+ # More than one residue.
+ if len(mol.res) > 1:
+ raise RelaxError("Cannot return the residue with no name or
number as more than one residue exists.")
+
+ # Return the residue.
+ return mol.res[0]
+
+ # Loop over the residues.
+ for res in mol.res:
+ # Return the matching residue.
+ if res_name != None and res_num != None:
+ if res.name == res_name and res.num == res_num:
+ return res
+ elif res_name != None:
+ if res.name == res_name:
+ return res
+ elif res_num != None:
+ if res.num == res_num:
+ return res
def return_spin(spin_id=None, pipe=None, full_info=False, multi=False):
@@ -2874,6 +2938,42 @@
return [dp.mol[mol_index].res[res_index].spin[spin_index]]
else:
return dp.mol[mol_index].res[res_index].spin[spin_index]
+
+
+def return_spin_by_info(res=None, spin_name=None, spin_num=None):
+ """Return the spin container matching the given name.
+
+ @keyword res: The residue container.
+ @type res: ResidueContainer instance
+ @keyword spin_name: The spin name. If not supplied and only a single
spin container exists, then that container will be returned.
+ @type spin_name: str
+ @keyword spin_num: The spin number. If not supplied and only a single
spin container exists, then that container will be returned.
+ @type spin_num: str
+ @return: The spin container object.
+ @rtype: SpinContainer instance
+ """
+
+ # No spin name or number specified, so assume a single spin.
+ if spin_name == None and spin_num == None:
+ # More than one spin.
+ if len(res.spin) > 1:
+ raise RelaxError("Cannot return the spin with no name or number
as more than one spin exists.")
+
+ # Return the spin.
+ return res.spin[0]
+
+ # Loop over the spins.
+ for spin in res.spin:
+ # Return the matching spin.
+ if spin_name != None and spin_num != None:
+ if spin.name == spin_name and spin.num == spin_num:
+ return spin
+ elif spin_name != None:
+ if spin.name == spin_name:
+ return spin
+ elif spin_num != None:
+ if spin.num == spin_num:
+ return spin
def return_spin_from_selection(selection=None, pipe=None, full_info=False,
multi=False):
r18745 - /trunk/generic_fns/mol_res_spin.py