Author: bugman
Date: Wed Sep 4 18:08:18 2013
New Revision: 20812
URL: http://svn.gna.org/viewcvs/relax?rev=20812&view=rev
Log:
Merged revisions 20809-20811 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20809 | bugman | 2013-09-04 17:59:10 +0200 (Wed, 04 Sep 2013) | 5 lines
Renamed pipe_control.spectrum.test_spectrum_id() to check_spectrum_id().
A bug in the function was also removed, and the other code in the module
now uses this function.
........
r20810 | bugman | 2013-09-04 18:05:59 +0200 (Wed, 04 Sep 2013) | 6 lines
Created the pipe_control.mol_res_spin.check_mol_res_spin_data() function.
This will check for the existence of molecule, residue and spin data and
raise a RelaxError if none
exists.
........
r20811 | bugman | 2013-09-04 18:07:14 +0200 (Wed, 04 Sep 2013) | 5 lines
Simplification of the data checks in the pipe_control.spectrum module.
This is using the new pipe_control.*.check*() functions.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/pipe_control/mol_res_spin.py
branches/relax_disp/pipe_control/spectrum.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Sep 4 18:08:18 2013
@@ -1,1 +1,1 @@
-/trunk:1-20807
+/trunk:1-20811
Modified: branches/relax_disp/pipe_control/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/mol_res_spin.py?rev=20812&r1=20811&r2=20812&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/mol_res_spin.py (original)
+++ branches/relax_disp/pipe_control/mol_res_spin.py Wed Sep 4 18:08:18 2013
@@ -39,7 +39,7 @@
# relax module imports.
from lib.check_types import is_unicode
-from lib.errors import RelaxError, RelaxNoSpinError, RelaxMultiMolIDError,
RelaxMultiResIDError, RelaxMultiSpinIDError, RelaxResSelectDisallowError,
RelaxSpinSelectDisallowError
+from lib.errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxMultiMolIDError, RelaxMultiResIDError, RelaxMultiSpinIDError,
RelaxResSelectDisallowError, RelaxSpinSelectDisallowError
from lib.selection import Selection, parse_token, tokenise
from lib.warnings import RelaxWarning
from pipe_control import exp_info, pipes
@@ -180,6 +180,17 @@
# Add the entity.
star.entity.add(mol_name=mol.name, mol_type=mol_type,
polymer_type=polymer_type, polymer_seq_code=polymer_seq_code,
thiol_state=cdp.exp_info.thiol_state, res_nums=res_nums, res_names=res_names)
+
+
+def check_mol_res_spin_data():
+ """Check for the presence of molecule, residue, and spin data.
+
+ @raises: RelaxNoSequenceError if no data is present.
+ """
+
+ # Check that the spectrum ID structure exists.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
def copy_molecule(pipe_from=None, mol_from=None, pipe_to=None, mol_to=None):
Modified: branches/relax_disp/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/spectrum.py?rev=20812&r1=20811&r2=20812&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/spectrum.py (original)
+++ branches/relax_disp/pipe_control/spectrum.py Wed Sep 4 18:08:18 2013
@@ -31,12 +31,12 @@
from warnings import warn
# relax module imports.
-from lib.errors import RelaxError, RelaxImplementError,
RelaxNoSequenceError, RelaxNoSpectraError
+from lib.errors import RelaxError, RelaxImplementError, RelaxNoSpectraError
from lib.io import write_data
from lib.spectrum.peak_list import read_peak_list
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control import pipes
-from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
+from pipe_control.mol_res_spin import check_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
def __errors_height_no_repl():
@@ -264,16 +264,10 @@
@type spin_id: str
"""
- # Test if the current pipe exists
+ # Data checks.
pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test the spectrum id string.
- if spectrum_id not in cdp.spectrum_ids:
- raise RelaxError("The peak intensities corresponding to the spectrum
id '%s' do not exist." % spectrum_id)
+ check_mol_res_spin_data()
+ check_spectrum_id(spectrum_id)
# The scaling by NC_proc.
if hasattr(cdp, 'ncproc') and spectrum_id in cdp.ncproc:
@@ -295,6 +289,23 @@
spin.baseplane_rmsd[spectrum_id] = float(error) * scale
+def check_spectrum_id(id):
+ """Check that the give spectrum ID exists.
+
+ @param id: The spectrum ID to check for.
+ @type id: str
+ @raises: RelaxNoSpectraError if the ID does not exist.
+ """
+
+ # Check that the spectrum ID structure exists.
+ if not hasattr(cdp, 'spectrum_ids'):
+ raise RelaxNoSpectraError(id)
+
+ # Test if the spectrum ID exists.
+ if id not in cdp.spectrum_ids:
+ raise RelaxNoSpectraError(id)
+
+
def delete(spectrum_id=None):
"""Delete spectral data corresponding to the spectrum ID.
@@ -302,16 +313,10 @@
@type spectrum_id: str
"""
- # Test if the current pipe exists.
+ # Data checks.
pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if data exists.
- if not hasattr(cdp, 'spectrum_ids') or spectrum_id not in
cdp.spectrum_ids:
- raise RelaxNoSpectraError(spectrum_id)
+ check_mol_res_spin_data()
+ check_spectrum_id(spectrum_id)
# Remove the ID.
cdp.spectrum_ids.pop(cdp.spectrum_ids.index(spectrum_id))
@@ -357,12 +362,9 @@
@type subset: list of str
"""
- # Test if the current pipe exists
+ # Tests.
pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
+ check_mol_res_spin_data()
# Test if spectra have been loaded.
if not hasattr(cdp, 'spectrum_ids'):
@@ -488,12 +490,9 @@
@type verbose: bool
"""
- # Test if the current data pipe exists.
+ # Data checks.
pipes.test()
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
+ check_mol_res_spin_data()
# Check the file name.
if file == None:
@@ -612,22 +611,21 @@
@type spectrum_ids: list of str
"""
- # Test if the current pipe exists
+ # Test if the current pipe exists.
pipes.test()
-
- # Test if spectra have been loaded.
- if not hasattr(cdp, 'spectrum_ids'):
- raise RelaxError("No spectra have been loaded therefore replicates
cannot be specified.")
-
- # Test the spectrum id strings.
- for spectrum_id in spectrum_ids:
- if spectrum_id not in cdp.spectrum_ids:
- raise RelaxError("The peak intensities corresponding to the
spectrum id '%s' do not exist." % spectrum_id)
# Test for None.
if spectrum_ids == None:
warn(RelaxWarning("The spectrum ID list cannot be None."))
return
+
+ # Test if spectra have been loaded.
+ if not hasattr(cdp, 'spectrum_ids'):
+ raise RelaxError("No spectra have been loaded therefore replicates
cannot be specified.")
+
+ # Test the spectrum id strings.
+ for spectrum_id in spectrum_ids:
+ check_spectrum_id(spectrum_id)
# Test for more than one element.
if len(spectrum_ids) == 1:
@@ -726,19 +724,3 @@
# Return the list.
return repl
-
-
-def test_spectrum_id(id):
- """Test that the give spectrum ID exists.
-
- @param id: The spectrum ID to check for.
- @type id: str
- """
-
- # Check that the spectrum ID structure exists.
- if not hasattr(cdp, 'spectrum_ids'):
- raise RelaxNoSpectraError(id)
-
- # Test if the spectrum ID exists.
- if spectrum_id not in cdp.spectrum_ids:
- raise RelaxNoSpectraError(id)
r20812 - in /branches/relax_disp: ./ pipe_control/mol_res_spin.py pipe_control/spectrum.py