Author: bugman
Date: Wed May 9 09:55:11 2012
New Revision: 16131
URL: http://svn.gna.org/viewcvs/relax?rev=16131&view=rev
Log:
Merged revisions 16041,16126-16130 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r16041 | bugman | 2012-05-07 12:26:56 +0200 (Mon, 07 May 2012) | 3 lines
Missing import.
........
r16126 | bugman | 2012-05-09 09:14:08 +0200 (Wed, 09 May 2012) | 6 lines
Improved the error message system for the spin ID matching multiple spins
This is a partial response to bug #19717 (http://gna.org/bugs/?19717)
reported by Martin Ballaschk
(http://gna.org/users/mab).
........
r16127 | bugman | 2012-05-09 09:16:59 +0200 (Wed, 09 May 2012) | 6 lines
The relax_fit.py sample script deselect.read user function now has all
columns specified.
This is a partial response to bug #19717 (http://gna.org/bugs/?19717)
reported by Martin Ballaschk
(http://gna.org/users/mab).
........
r16128 | bugman | 2012-05-09 09:20:42 +0200 (Wed, 09 May 2012) | 3 lines
Updated the copyright statement.
........
r16129 | bugman | 2012-05-09 09:22:17 +0200 (Wed, 09 May 2012) | 5 lines
Updated the deselect.read user function call in the noe.py sample script to
match relax_fit.py.
All the column args are now specified.
........
r16130 | bugman | 2012-05-09 09:45:24 +0200 (Wed, 09 May 2012) | 8 lines
Improved error reporting for multiple vectors in a model-free analysis.
This was reported by Vitaly Vostrikov (vvostri att uark.edu) at
http://www.mail-archive.com/relax-users@xxxxxxx/msg00991.html (Message-ID:
<CAO2iSXE1ycB4KX1vxqk15CxbW1rpWczZAyR_bX1g6j+yA2PCTQ@xxxxxxxxxxxxxx>) and
reported at bug #18807
(https://gna.org/bugs/?18807).
........
Modified:
branches/uf_redesign/ (props changed)
branches/uf_redesign/data/exp_info.py
branches/uf_redesign/generic_fns/mol_res_spin.py
branches/uf_redesign/relax_errors.py
branches/uf_redesign/sample_scripts/noe.py
branches/uf_redesign/sample_scripts/relax_fit.py
branches/uf_redesign/specific_fns/model_free/mf_minimise.py
Propchange: branches/uf_redesign/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed May 9 09:55:11 2012
@@ -1,1 +1,1 @@
-/1.3:1-15908
+/1.3:1-16130
Modified: branches/uf_redesign/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/data/exp_info.py?rev=16131&r1=16130&r2=16131&view=diff
==============================================================================
--- branches/uf_redesign/data/exp_info.py (original)
+++ branches/uf_redesign/data/exp_info.py Wed May 9 09:55:11 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2009 Edward d'Auvergne
#
+# Copyright (C) 2009-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -25,6 +25,7 @@
# relax module imports.
from data_classes import RelaxListType, Element
+from relax_errors import RelaxError
class ExpInfo(Element):
Modified: branches/uf_redesign/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/generic_fns/mol_res_spin.py?rev=16131&r1=16130&r2=16131&view=diff
==============================================================================
--- branches/uf_redesign/generic_fns/mol_res_spin.py (original)
+++ branches/uf_redesign/generic_fns/mol_res_spin.py Wed May 9 09:55:11 2012
@@ -47,7 +47,7 @@
from data.mol_res_spin import MoleculeContainer, ResidueContainer,
SpinContainer
from generic_fns import pipes
from generic_fns import relax_re
-from relax_errors import RelaxError, RelaxNoSpinError,
RelaxResSelectDisallowError, RelaxSpinSelectDisallowError
+from relax_errors import RelaxError, RelaxNoSpinError, RelaxMultiMolIDError,
RelaxMultiResIDError, RelaxMultiSpinIDError, RelaxResSelectDisallowError,
RelaxSpinSelectDisallowError
from relax_warnings import RelaxWarning
from status import Status; status = Status()
@@ -2205,7 +2205,7 @@
# No unique identifier.
if mol_num > 1:
- raise RelaxError("The identifier " + repr(selection) + " corresponds
to more than a single molecule in the " + repr(pipe) + " data pipe.")
+ raise RelaxMultiMolIDError(selection)
# Return the molecule container.
return mol_container
@@ -2258,7 +2258,7 @@
# No unique identifier.
if res_num > 1:
- raise RelaxError("The identifier " + repr(selection) + " corresponds
to more than a single residue in the " + repr(pipe) + " data pipe.")
+ raise RelaxMultiResIDError(selection)
# Return the residue container.
return res_container
@@ -2324,7 +2324,7 @@
# No unique identifier.
if spin_num > 1:
- raise RelaxError("The identifier " + repr(selection) + " corresponds
to more than a single spin in the " + repr(pipe) + " data pipe.")
+ raise RelaxMultiSpinIDError(selection)
# Return the spin container.
if full_info:
Modified: branches/uf_redesign/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/relax_errors.py?rev=16131&r1=16130&r2=16131&view=diff
==============================================================================
--- branches/uf_redesign/relax_errors.py (original)
+++ branches/uf_redesign/relax_errors.py Wed May 9 09:55:11 2012
@@ -258,6 +258,11 @@
def __init__(self, name):
self.text = "The PDB file " + repr(name) + " could not be loaded
properly, no molecular chains could be extracted."
+# Multiple unit vectors.
+class RelaxMultiVectorError(BaseError):
+ def __init__(self):
+ self.text = "The multiple unit XH bond vectors per spin - this is
not supported by the current data pipe type."
+
# No unit vectors.
class RelaxNoVectorsError(BaseError):
def __init__(self, pipe):
@@ -578,6 +583,30 @@
def __init__(self, pipe1, pipe2):
self.text = "The number of spins do not match between pipes '%s' and
'%s'." % (pipe1, pipe2)
+# Multiple spins matching the ID.
+class RelaxMultiMolIDError(BaseError):
+ def __init__(self, id):
+ if id == '':
+ self.text = "The empty molecule ID corresponds to more than a
single molecule in the current data pipe."
+ else:
+ self.text = "The molecule ID '%s' corresponds to more than a
single molecule in the current data pipe." % id
+
+# Multiple spins matching the ID.
+class RelaxMultiResIDError(BaseError):
+ def __init__(self, id):
+ if id == '':
+ self.text = "The empty residue ID corresponds to more than a
single residue in the current data pipe."
+ else:
+ self.text = "The residue ID '%s' corresponds to more than a
single residue in the current data pipe." % id
+
+# Multiple spins matching the ID.
+class RelaxMultiSpinIDError(BaseError):
+ def __init__(self, id):
+ if id == '':
+ self.text = "The empty spin ID corresponds to more than a single
spin in the current data pipe."
+ else:
+ self.text = "The spin ID '%s' corresponds to more than a single
spin in the current data pipe." % id
+
# Cannot find the residue in the sequence.
class RelaxNoResError(BaseError):
def __init__(self, number, name=None):
Modified: branches/uf_redesign/sample_scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/sample_scripts/noe.py?rev=16131&r1=16130&r2=16131&view=diff
==============================================================================
--- branches/uf_redesign/sample_scripts/noe.py (original)
+++ branches/uf_redesign/sample_scripts/noe.py Wed May 9 09:55:11 2012
@@ -50,7 +50,7 @@
spectrum.error_analysis()
# Deselect unresolved residues.
-deselect.read(file='unresolved')
+deselect.read(file='unresolved', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
# Calculate the NOEs.
calc()
Modified: branches/uf_redesign/sample_scripts/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/sample_scripts/relax_fit.py?rev=16131&r1=16130&r2=16131&view=diff
==============================================================================
--- branches/uf_redesign/sample_scripts/relax_fit.py (original)
+++ branches/uf_redesign/sample_scripts/relax_fit.py Wed May 9 09:55:11 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2004-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -76,7 +76,7 @@
spectrum.error_analysis()
# Deselect unresolved spins.
-deselect.read(file='unresolved')
+deselect.read(file='unresolved', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
# Set the relaxation curve type.
relax_fit.select_model('exp')
Modified: branches/uf_redesign/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/model_free/mf_minimise.py?rev=16131&r1=16130&r2=16131&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/model_free/mf_minimise.py (original)
+++ branches/uf_redesign/specific_fns/model_free/mf_minimise.py Wed May 9
09:55:11 2012
@@ -31,6 +31,7 @@
from warnings import warn
# relax module imports.
+import arg_check
from float import isNaN, isInf
from generic_fns import diffusion_tensor, pipes
from generic_fns.diffusion_tensor import diff_data_exists
@@ -39,7 +40,7 @@
from multi import Processor_box
from multi_processor_commands import MF_grid_command, MF_memo,
MF_minimise_command
from physical_constants import h_bar, mu0, return_gyromagnetic_ratio
-from relax_errors import RelaxError, RelaxInfError, RelaxLenError,
RelaxNaNError, RelaxNoModelError, RelaxNoPdbError, RelaxNoResError,
RelaxNoSequenceError, RelaxNoTensorError, RelaxNoValueError,
RelaxNoVectorsError, RelaxNucleusError, RelaxProtonTypeError,
RelaxSpinTypeError
+from relax_errors import RelaxError, RelaxInfError, RelaxLenError,
RelaxMultiVectorError, RelaxNaNError, RelaxNoModelError, RelaxNoPdbError,
RelaxNoResError, RelaxNoSequenceError, RelaxNoTensorError, RelaxNoValueError,
RelaxNoVectorsError, RelaxNucleusError, RelaxProtonTypeError,
RelaxSpinTypeError
from relax_warnings import RelaxWarning
@@ -1273,6 +1274,10 @@
# Test if unit vectors exist.
if model_type != 'local_tm' and cdp.diff_tensor.type != 'sphere'
and not hasattr(spin, 'xh_vect'):
raise RelaxNoVectorsError
+
+ # Test if multiple unit vectors exist.
+ if model_type != 'local_tm' and cdp.diff_tensor.type != 'sphere'
and hasattr(spin, 'xh_vect') and arg_check.is_num_list(spin.xh_vect[0]):
+ raise RelaxMultiVectorError
# Test if the spin type has been set.
if not hasattr(spin, 'heteronuc_type'):
r16131 - in /branches/uf_redesign: ./ data/ generic_fns/ sample_scripts/ specific_fns/model_free/