Author: bugman
Date: Sun Mar 24 18:58:47 2013
New Revision: 19137
URL: http://svn.gna.org/viewcvs/relax?rev=19137&view=rev
Log:
The pipe_control.mol_res_spin functions no longer use the selection object
__contains__() method.
All functions now use the contains_*() methods of the lib.selection.Selection
object.
Modified:
trunk/pipe_control/mol_res_spin.py
Modified: trunk/pipe_control/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/mol_res_spin.py?rev=19137&r1=19136&r2=19137&view=diff
==============================================================================
--- trunk/pipe_control/mol_res_spin.py (original)
+++ trunk/pipe_control/mol_res_spin.py Sun Mar 24 18:58:47 2013
@@ -1150,7 +1150,7 @@
global_i = global_i + 1
# Stop if the spin matches the selection.
- if (mol, res, spin) in select_obj:
+ if select_obj.contains_spin(spin_num=spin.num,
spin_name=spin.name, res_num=res.num, res_name=res.name, mol=mol.name):
# Return the indices.
if global_index:
return global_i
@@ -2022,7 +2022,7 @@
# Loop over the molecules.
for mol in dp.mol:
# Skip the molecule if there is no match to the selection.
- if mol not in select_obj:
+ if not select_obj.contains_mol(mol.name):
continue
# Generate the spin id.
@@ -2418,7 +2418,7 @@
# Loop over the residues.
for res in mol.res:
# Skip the residue if there is no match to the selection.
- if (mol, res) not in select_obj:
+ if not select_obj.contains_res(res_num=res.num,
res_name=res.name, mol=mol.name):
continue
# Generate the spin id.
@@ -2465,7 +2465,7 @@
mol_container = None
for mol in dp.mol:
# Skip the molecule if there is no match to the selection.
- if mol not in select_obj:
+ if not select_obj.contains_mol(mol=mol.name):
continue
# Skip named molecules if the selection is None.
@@ -2549,7 +2549,7 @@
res_container = None
for i in range(len(dp.mol)):
# Skip the molecule if there is no match to the selection.
- if dp.mol[i] not in select_obj:
+ if not select_obj.contains_mol(mol=dp.mol[i].name):
continue
# Store the molecule index.
@@ -2558,7 +2558,7 @@
# Loop over the residues.
for j in range(len(dp.mol[i].res)):
# Skip the residue if there is no match to the selection.
- if dp.mol[i].res[j] not in select_obj:
+ if not select_obj.contains_res(res_num=dp.mol[i].res[j].num,
res_name=dp.mol[i].res[j].name, mol=dp.mol[i].name):
continue
# Store the residue container and index.
@@ -2733,19 +2733,19 @@
spin_ids = []
for mol in dp.mol:
# Skip the molecule if there is no match to the selection.
- if mol not in select_obj:
+ if not select_obj.contains_mol(mol=mol.name):
continue
# Loop over the residues.
for res in mol.res:
# Skip the residue if there is no match to the selection.
- if res not in select_obj:
+ if not select_obj.contains_res(res_num=res.num,
res_name=res.name, mol=mol.name):
continue
# Loop over the spins.
for spin in res.spin:
# Skip the spin if there is no match to the selection.
- if spin not in select_obj:
+ if not select_obj.contains_spin(spin_num=spin.num,
spin_name=spin.name, res_num=res.num, res_name=res.name, mol=mol.name):
continue
# Store all data.
@@ -2844,7 +2844,7 @@
# Loop over the molecules.
for i in range(len(dp.mol)):
# Skip the molecule if there is no match to the selection.
- if dp.mol[i] not in select_obj:
+ if not select_obj.contains_mol(mol=dp.mol[i].name):
continue
# The molecule index.
@@ -2853,7 +2853,7 @@
# Loop over the residues.
for j in range(len(dp.mol[i].res)):
# Skip the residue if there is no match to the selection.
- if dp.mol[i].res[j] not in select_obj:
+ if not select_obj.contains_res(res_num=dp.mol[i].res[j].num,
res_name=dp.mol[i].res[j].name, mol=dp.mol[i].name):
continue
# The residue index.
@@ -2862,7 +2862,7 @@
# Loop over the spins.
for k in range(len(dp.mol[i].res[j].spin)):
# Skip the spin if there is no match to the selection.
- if dp.mol[i].res[j].spin[k] not in select_obj:
+ if not
select_obj.contains_spin(spin_num=dp.mol[i].res[j].spin[k].num,
spin_name=dp.mol[i].res[j].spin[k].name, res_num=dp.mol[i].res[j].num,
res_name=dp.mol[i].res[j].name, mol=dp.mol[i].name):
continue
# The spin index.
@@ -3579,51 +3579,6 @@
return spin_ids
-def spin_in_list(spin_list, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, mol_name=None,
res_num=None, res_name=None, spin_num=None, spin_name=None):
- """Function for determining if the spin is located within the list of
spins.
-
- @param spin_list: The list of spins. The first dimension
corresponds to different spins, the second corresponds to the spin
information columns.
- @type spin_list: list of lists of str
- @keyword mol_name_col: The column containing the molecule name
information.
- @type mol_name_col: int or None
- @keyword res_num_col: The column containing the residue number
information.
- @type res_num_col: int or None
- @keyword res_name_col: The column containing the residue name
information.
- @type res_name_col: int or None
- @keyword spin_num_col: The column containing the spin number
information.
- @type spin_num_col: int or None
- @keyword spin_name_col: The column containing the spin name information.
- @type spin_name_col: int or None
- @keyword mol_name: The molecule name.
- @type mol_name: str or None
- @keyword res_num: The residue number.
- @type res_num: int or None
- @keyword res_name: The residue name.
- @type res_name: str or None
- @keyword spin_num: The spin number.
- @type spin_num: int or None
- @keyword spin_name: The spin name.
- @type spin_name: str or None
- @return: The answer of whether the spin is within the
list.
- @rtype: bool
- """
-
- # Create a selection object based on the spin.
- select_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))
-
- # Loop over the spins.
- for spin in spin_list:
- # Generate the spin identification string.
- spin_id = generate_spin_id_data_array(data=file_data[i],
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
-
- # There is a hit.
- if spin_id in select_obj:
- return True
-
- # Not in the list.
- return False
-
-
def spin_index_loop(selection=None, pipe=None):
"""Generator function for looping over all selected spins, returning the
mol-res-spin indices.
@@ -3668,7 +3623,7 @@
spin = dp.mol[mol_index].res[res_index].spin[spin_index]
# Skip the spin if there is no match to the selection.
- if (mol, res, spin) not in select_obj:
+ if not select_obj.contains_spin(spin_num=spin.num,
spin_name=spin.name, res_num=res.num, res_name=res.name, mol=mol.name):
continue
# Yield the spin system specific indices.
@@ -3714,7 +3669,7 @@
# Loop over the spins.
for spin in res.spin:
# Skip the spin if there is no match to the selection.
- if (mol, res, spin) not in select_obj:
+ if not select_obj.contains_spin(spin_num=spin.num,
spin_name=spin.name, res_num=res.num, res_name=res.name, mol=mol.name):
continue
# Generate the spin id.
r19137 - /trunk/pipe_control/mol_res_spin.py