Author: bugman
Date: Mon Jul 21 09:07:47 2014
New Revision: 24577
URL: http://svn.gna.org/viewcvs/relax?rev=24577&view=rev
Log:
Updated all of the specific API calculate() methods to accept the
scaling_matrix argument.
The list of per-model scaling matrices is now created independently of the
analysis type by the
pipe_control.minimise methods for the minimise.calculate,
minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
Modified:
branches/zooming_grid_search/specific_analyses/consistency_tests/api.py
branches/zooming_grid_search/specific_analyses/frame_order/api.py
branches/zooming_grid_search/specific_analyses/jw_mapping/api.py
branches/zooming_grid_search/specific_analyses/model_free/api.py
branches/zooming_grid_search/specific_analyses/n_state_model/api.py
branches/zooming_grid_search/specific_analyses/noe/api.py
branches/zooming_grid_search/specific_analyses/relax_disp/api.py
Modified:
branches/zooming_grid_search/specific_analyses/consistency_tests/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/consistency_tests/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/consistency_tests/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/consistency_tests/api.py
Mon Jul 21 09:07:47 2014
@@ -64,15 +64,17 @@
self._PARAMS = Consistency_tests_params()
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculation of the consistency functions.
- @keyword spin_id: The spin identification string.
- @type spin_id: None or str
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The optional MC simulation index.
- @type sim_index: None or int
+ @keyword spin_id: The spin identification string.
+ @type spin_id: None or str
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: None or int
"""
# Test if the frequency has been set.
Modified: branches/zooming_grid_search/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/frame_order/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/frame_order/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/frame_order/api.py Mon
Jul 21 09:07:47 2014
@@ -105,15 +105,17 @@
yield ['pcs', spin_id, align_id]
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculate the chi-squared value for the current parameter values.
- @keyword spin_id: The spin identification string (unused).
- @type spin_id: None
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The optional MC simulation index (unused).
- @type sim_index: None or int
+ @keyword spin_id: The spin identification string (unused).
+ @type spin_id: None
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The optional MC simulation index
(unused).
+ @type sim_index: None or int
"""
# Set up the target function for direct calculation.
Modified: branches/zooming_grid_search/specific_analyses/jw_mapping/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/jw_mapping/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/jw_mapping/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/jw_mapping/api.py Mon
Jul 21 09:07:47 2014
@@ -63,15 +63,17 @@
self._PARAMS = Jw_mapping_params()
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculation of the spectral density values.
- @keyword spin_id: The spin identification string.
- @type spin_id: None or str
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The optional MC simulation index.
- @type sim_index: None or int
+ @keyword spin_id: The spin identification string.
+ @type spin_id: None or str
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: None or int
"""
# Test if the frequency has been set.
Modified: branches/zooming_grid_search/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/model_free/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/model_free/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/model_free/api.py Mon
Jul 21 09:07:47 2014
@@ -404,15 +404,17 @@
star.write()
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculation of the model-free chi-squared value.
- @keyword spin_id: The spin identification string.
- @type spin_id: str
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The optional MC simulation index.
- @type sim_index: int
+ @keyword spin_id: The spin identification string.
+ @type spin_id: str
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
"""
# Test if sequence data is loaded.
Modified: branches/zooming_grid_search/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/n_state_model/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/n_state_model/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/n_state_model/api.py Mon
Jul 21 09:07:47 2014
@@ -133,18 +133,20 @@
yield data
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculation function.
Currently this function simply calculates the NOESY flat-bottom
quadratic energy potential,
if NOE restraints are available.
- @keyword spin_id: The spin identification string (unused).
- @type spin_id: None or str
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The MC simulation index (unused).
- @type sim_index: None
+ @keyword spin_id: The spin identification string (unused).
+ @type spin_id: None or str
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The MC simulation index (unused).
+ @type sim_index: None
"""
# Set up the target function for direct calculation.
Modified: branches/zooming_grid_search/specific_analyses/noe/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/noe/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/noe/api.py (original)
+++ branches/zooming_grid_search/specific_analyses/noe/api.py Mon Jul 21
09:07:47 2014
@@ -53,7 +53,7 @@
self._PARAMS = Noe_params()
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculate the NOE and its error.
The error for each peak is calculated using the formula::
@@ -62,12 +62,14 @@
sd(NOE) = -----------------------------------------------
I(unsat)^2
- @keyword spin_id: The spin identification string.
- @type spin_id: None or str
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The MC simulation index (unused).
- @type sim_index: None
+ @keyword spin_id: The spin identification string.
+ @type spin_id: None or str
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The MC simulation index (unused).
+ @type sim_index: None
"""
# Test if the current pipe exists.
Modified: branches/zooming_grid_search/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/relax_disp/api.py?rev=24577&r1=24576&r2=24577&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/relax_disp/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/relax_disp/api.py Mon
Jul 21 09:07:47 2014
@@ -121,15 +121,17 @@
yield spin, spin_id
- def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ def calculate(self, spin_id=None, scaling_matrix=None, verbosity=1,
sim_index=None):
"""Calculate the model chi-squared value or the R2eff values for
fixed time period data.
- @keyword spin_id: The spin identification string.
- @type spin_id: None or str
- @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
- @type verbosity: int
- @keyword sim_index: The MC simulation index (unused).
- @type sim_index: None
+ @keyword spin_id: The spin identification string.
+ @type spin_id: None or str
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The MC simulation index (unused).
+ @type sim_index: None
"""
# Data checks.
r24577 - in /branches/zooming_grid_search/specific_analyses: consistency_tests/ frame_order/ jw_mapping/ model_free/ n_state...