Author: bugman
Date: Wed Jun 20 15:35:50 2012
New Revision: 17005
URL: http://svn.gna.org/viewcvs/relax?rev=17005&view=rev
Log:
Bug fix - the spin_id arg for the relax_data.read user function now actually
does something.
This argument is passed into the pack_data() function, where it is used to
match against the spins
matching each file line. Only if there is a match, is the relaxation data
loaded for that spin.
Modified:
branches/interatomic/generic_fns/relax_data.py
Modified: branches/interatomic/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/relax_data.py?rev=17005&r1=17004&r2=17005&view=diff
==============================================================================
--- branches/interatomic/generic_fns/relax_data.py (original)
+++ branches/interatomic/generic_fns/relax_data.py Wed Jun 20 15:35:50 2012
@@ -36,11 +36,11 @@
from data.exp_info import ExpInfo
from generic_fns import bmrb
from generic_fns.interatomic import create_interatom, return_interatom
-from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data,
find_index, generate_spin_id, get_molecule_names, return_spin,
spin_index_loop, spin_loop
+from generic_fns.mol_res_spin import Selection, create_spin,
exists_mol_res_spin_data, find_index, generate_spin_id, get_molecule_names,
return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
from generic_fns import value
from physical_constants import element_from_isotope, number_from_isotope
-from relax_errors import RelaxError, RelaxNoRiError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxRiError
+from relax_errors import RelaxError, RelaxMultiSpinIDError, RelaxNoRiError,
RelaxNoSequenceError, RelaxNoSpinError, RelaxRiError
from relax_io import read_spin_data
from relax_warnings import RelaxWarning
import specific_fns
@@ -735,7 +735,7 @@
return count
-def pack_data(ri_id, ri_type, frq, values, errors, spin_ids=None,
mol_names=None, res_nums=None, res_names=None, spin_nums=None,
spin_names=None, gen_seq=False):
+def pack_data(ri_id, ri_type, frq, values, errors, spin_ids=None,
mol_names=None, res_nums=None, res_names=None, spin_nums=None,
spin_names=None, spin_id=None, gen_seq=False):
"""Pack the relaxation data into the data pipe and spin containers.
The values, errors, and spin_ids arguments must be lists of equal length
or None. Each element i corresponds to a unique spin.
@@ -822,22 +822,49 @@
if gen_seq:
bmrb.generate_sequence(N, spin_ids=spin_ids, spin_nums=spin_nums,
spin_names=spin_names, res_nums=res_nums, res_names=res_names,
mol_names=mol_names)
+ # The selection object.
+ select_obj = None
+ if spin_id:
+ select_obj = Selection(spin_id)
+
# Loop over the spin data.
for i in range(N):
# Get the corresponding spin container.
- spin = return_spin(spin_ids[i])
- if spin == None:
+ mol_names, res_nums, res_names, spins = return_spin(spin_ids[i],
full_info=True, multi=True)
+ if spins in [None, []]:
raise RelaxNoSpinError(spin_ids[i])
- # Initialise the spin data if necessary.
- if not hasattr(spin, 'ri_data') or spin.ri_data == None:
- spin.ri_data = {}
- if not hasattr(spin, 'ri_data_err') or spin.ri_data_err == None:
- spin.ri_data_err = {}
-
- # Update all data structures.
- spin.ri_data[ri_id] = values[i]
- spin.ri_data_err[ri_id] = errors[i]
+ # Remove non-matching spins.
+ if select_obj:
+ new_spins = []
+ for spin in spins:
+ if spin in select_obj:
+ new_spins.append(spin)
+ spins = new_spins
+
+ # Create spin IDs for all remaining spins (for the error message).
+
+ # Check that only a singe spin is present.
+ if len(spins) > 1:
+ raise RelaxMultiSpinIDError(spin_ids[i])
+ if len(spins) == 0:
+ raise RelaxNoSpinError(spin_ids[i])
+
+ # Loop over the spins.
+ for spin in spins:
+ # No match to the selection.
+ if select_obj and spin not in select_obj:
+ continue
+
+ # Initialise the spin data if necessary.
+ if not hasattr(spin, 'ri_data') or spin.ri_data == None:
+ spin.ri_data = {}
+ if not hasattr(spin, 'ri_data_err') or spin.ri_data_err == None:
+ spin.ri_data_err = {}
+
+ # Update all data structures.
+ spin.ri_data[ri_id] = values[i]
+ spin.ri_data_err[ri_id] = errors[i]
def peak_intensity_type(ri_id=None, type=None):
@@ -936,7 +963,7 @@
res_names = []
spin_nums = []
spin_names = []
- for data in read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, 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, data_col=data_col, error_col=error_col, sep=sep,
spin_id=spin_id):
+ for data in read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, 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, data_col=data_col, error_col=error_col, sep=sep):
# Unpack.
if data_col and error_col:
mol_name, res_num, res_name, spin_num, spin_name, value, error =
data
@@ -957,7 +984,7 @@
errors.append(error)
# Pack the data.
- pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names)
+ pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names, spin_id=spin_id)
def return_data_desc(name):
r17005 - /branches/interatomic/generic_fns/relax_data.py