Author: bugman
Date: Mon Dec 14 11:38:04 2009
New Revision: 10087
URL: http://svn.gna.org/viewcvs/relax?rev=10087&view=rev
Log:
Modified all the specific analysis overfit_deselect() methods to warn when
spins are deselected.
Modified:
1.3/specific_fns/api_common.py
1.3/specific_fns/consistency_tests.py
1.3/specific_fns/frame_order.py
1.3/specific_fns/hybrid.py
1.3/specific_fns/jw_mapping.py
1.3/specific_fns/model_free/main.py
1.3/specific_fns/n_state_model.py
1.3/specific_fns/noe.py
1.3/specific_fns/relax_fit.py
Modified: 1.3/specific_fns/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_common.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/api_common.py (original)
+++ 1.3/specific_fns/api_common.py Mon Dec 14 11:38:04 2009
@@ -177,6 +177,9 @@
def _overfit_deselect_dummy(self):
"""Dummy method, normally for deselecting spins with insufficient
data for minimisation."""
+ # Print out.
+ print("\n\nOver-fit spin deselection.\n")
+
def _return_no_conversion_factor(self, param, spin=None, spin_id=None):
"""Method for returning 1.0.
Modified: 1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/consistency_tests.py (original)
+++ 1.3/specific_fns/consistency_tests.py Mon Dec 14 11:38:04 2009
@@ -23,6 +23,7 @@
# Python module imports.
from re import search
+from warnings import warn
# relax module imports.
from api_base import API_base
@@ -32,6 +33,7 @@
from maths_fns.consistency_tests import Consistency
from physical_constants import N15_CSA, NH_BOND_LENGTH, h_bar, mu0,
return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxProtonTypeError,
RelaxSpinTypeError
+from relax_warnings import RelaxDeselectWarning
class Consistency_tests(API_base, API_common):
@@ -349,7 +351,10 @@
def overfit_deselect(self):
- """Function for deselecting spins without sufficient data to support
calculation"""
+ """Deselect spins which have insufficient data to support
calculation."""
+
+ # Print out.
+ print("\n\nOver-fit spin deselection.\n")
# Test if the sequence data is loaded.
if not exists_mol_res_spin_data():
@@ -360,13 +365,13 @@
# Check for sufficient data
if not hasattr(spin, 'relax_data'):
+ warn(RelaxDeselectWarning(spin_id, 'relaxation data is
missing'))
spin.select = False
- continue
# Require 3 or more data points
- if len(spin.relax_data) < 3:
+ elif len(spin.relax_data) < 3:
+ warn(RelaxDeselectWarning(spin_id, 'insufficient relaxation
data, 3 or more data points are required'))
spin.select = False
- continue
return_data_name_doc = """
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Mon Dec 14 11:38:04 2009
@@ -45,7 +45,7 @@
from maths_fns.rotation_matrix import two_vect_to_R
from relax_errors import RelaxError, RelaxInfError, RelaxNaNError,
RelaxNoModelError
from relax_io import open_write_file
-from relax_warnings import RelaxWarning
+from relax_warnings import RelaxWarning, RelaxDeselectWarning
class Frame_order(API_base, API_common):
Modified: 1.3/specific_fns/hybrid.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/hybrid.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/hybrid.py (original)
+++ 1.3/specific_fns/hybrid.py Mon Dec 14 11:38:04 2009
@@ -19,6 +19,9 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
#
###############################################################################
+
+# Python module imports.
+from warnings import warn
# relax module imports.
from generic_fns import pipes
@@ -26,6 +29,7 @@
from generic_fns.sequence import compare_sequence
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxPipeError,
RelaxSequenceError
import setup
+from relax_warnings import RelaxDeselectWarning
class Hybrid:
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Mon Dec 14 11:38:04 2009
@@ -22,6 +22,7 @@
# Python module imports.
from re import search
+from warnings import warn
# relax module imports.
from api_base import API_base
@@ -31,6 +32,7 @@
from maths_fns.jw_mapping import Mapping
from physical_constants import N15_CSA, NH_BOND_LENGTH, h_bar, mu0,
return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxProtonTypeError,
RelaxSpinTypeError
+from relax_warnings import RelaxDeselectWarning
class Jw_mapping(API_base, API_common):
@@ -326,6 +328,9 @@
def overfit_deselect(self):
"""Deselect spins which have insufficient data to support
calculation."""
+ # Print out.
+ print("\n\nOver-fit spin deselection.\n")
+
# Test the sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
@@ -334,13 +339,13 @@
for spin in spin_loop():
# Check if data exists.
if not hasattr(spin, 'relax_data'):
+ warn(RelaxDeselectWarning(spin_id, 'relaxation data is
missing'))
spin.select = False
- continue
# Require 3 or more data points.
- if len(spin.relax_data) < 3:
+ elif len(spin.relax_data) < 3:
+ warn(RelaxDeselectWarning(spin_id, 'insufficient relaxation
data, 3 or more data points are required'))
spin.select = False
- continue
return_data_name_doc = """
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/main.py (original)
+++ 1.3/specific_fns/model_free/main.py Mon Dec 14 11:38:04 2009
@@ -37,8 +37,9 @@
from maths_fns.mf import Mf
from minfx.generic import generic_minimise
from physical_constants import N15_CSA, NH_BOND_LENGTH
+import specific_fns
from relax_errors import RelaxError, RelaxFuncSetupError, RelaxInfError,
RelaxInvalidDataError, RelaxLenError, RelaxNaNError, RelaxNoModelError,
RelaxNoPdbError, RelaxNoResError, RelaxNoSequenceError, RelaxNoSpinSpecError,
RelaxNoTensorError, RelaxNoValueError, RelaxNoVectorsError,
RelaxNucleusError, RelaxTensorError
-import specific_fns
+from relax_warnings import RelaxDeselectWarning
@@ -2010,6 +2011,9 @@
def overfit_deselect(self):
"""Deselect spins which have insufficient data to support
minimisation."""
+ # Print out.
+ print("\n\nOver-fit spin deselection.\n")
+
# Test if sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
@@ -2020,23 +2024,28 @@
need_vect = True
# Loop over the sequence.
- for spin in spin_loop():
+ for spin, spin_id in spin_loop(return_id=True):
# Relaxation data must exist!
if not hasattr(spin, 'relax_data'):
+ warn(RelaxDeselectWarning(spin_id, 'relaxation data is
missing'))
spin.select = False
# Require 3 or more relaxation data points.
elif len(spin.relax_data) < 3:
+ warn(RelaxDeselectWarning(spin_id, 'insufficient relaxation
data, 3 or more data points are required'))
spin.select = False
# Require at least as many data points as params to prevent
over-fitting.
elif hasattr(spin, 'params') and spin.params and
len(spin.params) > len(spin.relax_data):
+ warn(RelaxDeselectWarning(spin_id, 'over-fitting - more
parameters than data points'))
spin.select = False
# Test for structural data if required.
elif need_vect and not hasattr(spin, 'xh_vect'):
+ warn(RelaxDeselectWarning(spin_id, 'structural data
missing'))
spin.select = False
elif need_vect and spin.xh_vect == None:
+ warn(RelaxDeselectWarning(spin_id, 'structural data
missing'))
spin.select = False
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Mon Dec 14 11:38:04 2009
@@ -49,7 +49,7 @@
from physical_constants import dipolar_constant, g1H, pcs_constant,
return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxInfError, RelaxModelError,
RelaxNaNError, RelaxNoModelError, RelaxNoTensorError
from relax_io import open_write_file
-from relax_warnings import RelaxWarning
+from relax_warnings import RelaxWarning, RelaxDeselectWarning
class N_state_model(API_base, API_common):
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Mon Dec 14 11:38:04 2009
@@ -154,7 +154,10 @@
def overfit_deselect(self):
- """Deselect spins which have insufficient data to support
calculation"""
+ """Deselect spins which have insufficient data to support
calculation."""
+
+ # Print out.
+ print("\n\nOver-fit spin deselection.\n")
# Test the sequence data exists.
if not exists_mol_res_spin_data():
Modified: 1.3/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=10087&r1=10086&r2=10087&view=diff
==============================================================================
--- 1.3/specific_fns/relax_fit.py (original)
+++ 1.3/specific_fns/relax_fit.py Mon Dec 14 11:38:04 2009
@@ -29,6 +29,7 @@
from numpy import array, average, dot, float64, identity, zeros
from numpy.linalg import inv
from re import match, search
+from warnings import warn
# relax module imports.
from api_base import API_base
@@ -37,6 +38,7 @@
from generic_fns import pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_loop
from relax_errors import RelaxError, RelaxFuncSetupError, RelaxLenError,
RelaxNoModelError, RelaxNoSequenceError
+from relax_warnings import RelaxDeselectWarning
# C modules.
if C_module_exp_fn:
@@ -839,6 +841,9 @@
def overfit_deselect(self):
"""Deselect spins which have insufficient data to support
minimisation."""
+ # Print out.
+ print("\n\nOver-fit spin deselection.\n")
+
# Test the sequence data exists.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
@@ -847,13 +852,13 @@
for spin in spin_loop():
# Check if data exists.
if not hasattr(spin, 'intensities'):
+ warn(RelaxDeselectWarning(spin_id, 'intensity data is
missing'))
spin.select = False
- continue
# Require 3 or more data points.
- if len(spin.intensities) < 3:
+ elif len(spin.intensities) < 3:
+ warn(RelaxDeselectWarning(spin_id, 'insufficient data, 3 or
more data points are required'))
spin.select = False
- continue
def return_data(self, spin):
r10087 - in /1.3/specific_fns: ./ model_free/