Author: bugman
Date: Wed Oct 7 14:41:02 2009
New Revision: 9630
URL: http://svn.gna.org/viewcvs/relax?rev=9630&view=rev
Log:
Renamed read_spin_data_file() to read_spin_data() and write_spin_data_file()
to write_spin_data().
Modified:
1.3/generic_fns/pcs.py
1.3/generic_fns/rdc.py
1.3/generic_fns/relax_data.py
1.3/generic_fns/selection.py
1.3/generic_fns/sequence.py
1.3/generic_fns/spectrum.py
1.3/generic_fns/structure/main.py
1.3/generic_fns/value.py
1.3/relax_io.py
Modified: 1.3/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pcs.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/pcs.py (original)
+++ 1.3/generic_fns/pcs.py Wed Oct 7 14:41:02 2009
@@ -31,7 +31,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxPCSError
-from relax_io import read_spin_data_file
+from relax_io import read_spin_data
def add_data_to_spin(spin=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, values=None, errors=None, sim=False):
@@ -500,7 +500,7 @@
# Loop over the PCS data.
print(("\n%-50s %-15s %-15s" % ("spin_id", "value", "error")))
- for data in read_spin_data_file(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,
spin_id=spin_id):
# Unpack.
if data_col and error_col:
id, value, error = data
Modified: 1.3/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/rdc.py (original)
+++ 1.3/generic_fns/rdc.py Wed Oct 7 14:41:02 2009
@@ -30,7 +30,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxRDCError
-from relax_io import read_spin_data_file, write_spin_data_file
+from relax_io import read_spin_data, write_spin_data
def add_data_to_spin(spin=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, values=None, errors=None, sim=False):
@@ -425,7 +425,7 @@
spin_ids = []
values = []
errors = []
- for data in read_spin_data_file(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,
spin_id=spin_id):
# Unpack.
if data_col and error_col:
id, value, error = data
@@ -469,7 +469,7 @@
errors.append(error)
# Print out.
- write_spin_data_file(spin_ids=spin_ids, data=values, data_name='RDCs',
error=errors, error_name='RDC_error')
+ write_spin_data(spin_ids=spin_ids, data=values, data_name='RDCs',
error=errors, error_name='RDC_error')
# Global (non-spin specific) data.
Modified: 1.3/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/relax_data.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/relax_data.py (original)
+++ 1.3/generic_fns/relax_data.py Wed Oct 7 14:41:02 2009
@@ -33,7 +33,7 @@
from generic_fns import pipes
from generic_fns import value
from relax_errors import RelaxError, RelaxNoRiError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxRiError
-from relax_io import read_spin_data_file
+from relax_io import read_spin_data
import specific_fns
@@ -631,7 +631,7 @@
values = []
errors = []
ids = []
- for data in read_spin_data_file(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,
spin_id=spin_id):
# Unpack.
if data_col and error_col:
id, value, error = data
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Wed Oct 7 14:41:02 2009
@@ -30,7 +30,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoSequenceError
-from relax_io import read_spin_data_file
+from relax_io import read_spin_data
from relax_warnings import RelaxNoSpinWarning
@@ -114,7 +114,7 @@
spin.select = True
# Then deselect the spins in the file.
- for id in read_spin_data_file(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, sep=sep, spin_id=spin_id):
+ for id 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, sep=sep, spin_id=spin_id):
# Get the corresponding spin container.
spin = return_spin(id)
@@ -304,7 +304,7 @@
spin.select = False
# Then deselect the spins in the file.
- for id in read_spin_data_file(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, sep=sep, spin_id=spin_id):
+ for id 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, sep=sep, spin_id=spin_id):
# Get the corresponding spin container.
spin = return_spin(id)
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Wed Oct 7 14:41:02 2009
@@ -27,7 +27,7 @@
from generic_fns.mol_res_spin import count_molecules, count_residues,
count_spins, exists_mol_res_spin_data, generate_spin_id, return_molecule,
return_residue, return_spin, spin_id_to_data_list, spin_loop
import pipes
from relax_errors import RelaxError, RelaxDiffMolNumError,
RelaxDiffResNumError, RelaxDiffSeqError, RelaxDiffSpinNumError,
RelaxFileEmptyError, RelaxInvalidSeqError, RelaxNoSequenceError,
RelaxSequenceError
-from relax_io import open_write_file, read_spin_data_file
+from relax_io import open_write_file, read_spin_data
import sys
@@ -282,7 +282,7 @@
write_header(sys.stdout, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, spin_num_flag=True, spin_name_flag=True)
# Generate the sequence.
- for id in read_spin_data_file(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, sep=sep, spin_id=spin_id):
+ for id 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, sep=sep, spin_id=spin_id):
# Add the spin.
generate(*spin_id_to_data_list(id))
Modified: 1.3/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/spectrum.py (original)
+++ 1.3/generic_fns/spectrum.py Wed Oct 7 14:41:02 2009
@@ -35,7 +35,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, generate_spin_id_data_array, return_spin, spin_loop
from generic_fns import pipes
from relax_errors import RelaxArgNotNoneError, RelaxError,
RelaxImplementError, RelaxNoSequenceError
-from relax_io import extract_data, read_spin_data_file, strip
+from relax_io import extract_data, read_spin_data, strip
from relax_warnings import RelaxWarning, RelaxNoSpinWarning
@@ -467,7 +467,7 @@
# Loop over the data.
data = []
- for id, value in read_spin_data_file(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, sep=sep, spin_id=spin_id):
+ for id, value in read_spin_data(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, sep=sep, spin_id=spin_id):
data.append([None, None, id, value])
# Return the data.
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Oct 7 14:41:02 2009
@@ -36,7 +36,7 @@
from generic_fns.structure.internal import Internal
from generic_fns.structure.scientific import Scientific_data
from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoSequenceError, RelaxPdbError
-from relax_io import get_file_path, open_write_file, write_spin_data_file
+from relax_io import get_file_path, open_write_file, write_spin_data
from relax_warnings import RelaxWarning, RelaxNoPDBFileWarning,
RelaxZeroVectorWarning
Modified: 1.3/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/value.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/generic_fns/value.py (original)
+++ 1.3/generic_fns/value.py Wed Oct 7 14:41:02 2009
@@ -31,7 +31,7 @@
from generic_fns import minimise, pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_loop
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxParamSetError, RelaxValueError
-from relax_io import open_write_file, read_spin_data_file,
write_spin_data_file
+from relax_io import open_write_file, read_spin_data, write_spin_data
import specific_fns
@@ -278,7 +278,7 @@
raise RelaxValueError(param)
# Loop over the data.
- for data in read_spin_data_file(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,
spin_id=spin_id):
# Unpack.
if data_col and error_col:
id, value, error = data
Modified: 1.3/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_io.py?rev=9630&r1=9629&r2=9630&view=diff
==============================================================================
--- 1.3/relax_io.py (original)
+++ 1.3/relax_io.py Wed Oct 7 14:41:02 2009
@@ -462,7 +462,7 @@
return file_obj
-def read_spin_data_file(file=None, dir=None, file_data=None,
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=None, error_col=None,
sep=None, spin_id=None):
+def read_spin_data(file=None, dir=None, file_data=None, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None):
"""Generator function for reading the spin specific data from file.
Description
@@ -664,7 +664,7 @@
raise RelaxNoInPathError(binary)
-def write_spin_data_file(file=sys.stdout, dir=None, sep=None, spin_ids=None,
mol_names=None, res_nums=None, res_names=None, spin_nums=None,
spin_names=None, force=False, data=None, data_name=None, data_length=20,
data_format=None, error=None, error_name=None, error_length=20,
error_format=None):
+def write_spin_data(file=sys.stdout, dir=None, sep=None, spin_ids=None,
mol_names=None, res_nums=None, res_names=None, spin_nums=None,
spin_names=None, force=False, data=None, data_name=None, data_length=20,
data_format=None, error=None, error_name=None, error_length=20,
error_format=None):
"""Generator function for reading the spin specific data from file.
Description
r9630 - in /1.3: ./ generic_fns/ generic_fns/structure/