Author: bugman
Date: Sun Jun 3 23:19:32 2012
New Revision: 16612
URL: http://svn.gna.org/viewcvs/relax?rev=16612&view=rev
Log:
All of the user_function.object.Table instances in the specific code
descriptions are now private.
This hides them from the specific API, and allows the unit tests to pass.
Modified:
branches/uf_redesign/specific_fns/jw_mapping.py
branches/uf_redesign/specific_fns/model_free/main.py
branches/uf_redesign/specific_fns/n_state_model.py
branches/uf_redesign/specific_fns/noe/main.py
branches/uf_redesign/specific_fns/relax_fit.py
Modified: branches/uf_redesign/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/jw_mapping.py?rev=16612&r1=16611&r2=16612&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/jw_mapping.py (original)
+++ branches/uf_redesign/specific_fns/jw_mapping.py Sun Jun 3 23:19:32 2012
@@ -232,17 +232,17 @@
default_value_doc = Desc_container("Reduced spectral density mapping
default values")
default_value_doc.add_paragraph("These default values are found in the
file 'physical_constants.py'.")
- table = uf_tables.add_table(label="table: J(w) default values",
caption="Reduced spectral density mapping default values.")
- table.add_headings(["Data type", "Object name", "Value"])
- table.add_row(["Bond length", "'r'", "1.02 * 1e-10"])
- table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
- table.add_row(["Heteronucleus type", "'heteronuc_type'", "'15N'"])
- table.add_row(["Proton type", "'proton_type'", "'1H'"])
- default_value_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: J(w) default values",
caption="Reduced spectral density mapping default values.")
+ _table.add_headings(["Data type", "Object name", "Value"])
+ _table.add_row(["Bond length", "'r'", "1.02 * 1e-10"])
+ _table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'", "'15N'"])
+ _table.add_row(["Proton type", "'proton_type'", "'1H'"])
+ default_value_doc.add_table(_table.label)
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")
@@ -277,16 +277,16 @@
return_data_name_doc = Desc_container("Reduced spectral density mapping
data type string matching patterns")
- table = uf_tables.add_table(label="table: J(w) data types",
caption="Reduced spectral density mapping data type string matching
patterns.")
- table.add_headings(["Data type", "Object name"])
- table.add_row(["J(0)", "'j0'"])
- table.add_row(["J(wX)", "'jwx'"])
- table.add_row(["J(wH)", "'jwh'"])
- table.add_row(["Bond length", "'r'"])
- table.add_row(["CSA", "'csa'"])
- table.add_row(["Heteronucleus type", "'heteronuc_type'"])
- table.add_row(["Proton type", "'proton_type'"])
- return_data_name_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: J(w) data types",
caption="Reduced spectral density mapping data type string matching
patterns.")
+ _table.add_headings(["Data type", "Object name"])
+ _table.add_row(["J(0)", "'j0'"])
+ _table.add_row(["J(wX)", "'jwx'"])
+ _table.add_row(["J(wH)", "'jwh'"])
+ _table.add_row(["Bond length", "'r'"])
+ _table.add_row(["CSA", "'csa'"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'"])
+ _table.add_row(["Proton type", "'proton_type'"])
+ return_data_name_doc.add_table(_table.label)
set_doc = Desc_container("Reduced spectral density mapping set details")
Modified: branches/uf_redesign/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/model_free/main.py?rev=16612&r1=16611&r2=16612&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/model_free/main.py (original)
+++ branches/uf_redesign/specific_fns/model_free/main.py Sun Jun 3 23:19:32
2012
@@ -1285,19 +1285,19 @@
default_value_doc = Desc_container("Model-free default values")
- table = uf_tables.add_table(label="table: mf default values",
caption="Model-free default values.")
- table.add_headings(["Data type", "Object name", "Value"])
- table.add_row(["Local tm", "'local_tm'", "10 * 1e-9"])
- table.add_row(["Order parameters S2, S2f, and S2s", "'s2', 's2f',
's2s'", "0.8"])
- table.add_row(["Correlation time te", "'te'", "100 * 1e-12"])
- table.add_row(["Correlation time tf", "'tf'", "10 * 1e-12"])
- table.add_row(["Correlation time ts", "'ts'", "1000 * 1e-12"])
- table.add_row(["Chemical exchange relaxation", "'rex'", "0.0"])
- table.add_row(["Bond length", "'r'", "1.02 * 1e-10"])
- table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
- table.add_row(["Heteronucleus type", "'heteronuc_type'", "'15N'"])
- table.add_row(["Proton type", "'proton_type'", "'1H'"])
- default_value_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: mf default values",
caption="Model-free default values.")
+ _table.add_headings(["Data type", "Object name", "Value"])
+ _table.add_row(["Local tm", "'local_tm'", "10 * 1e-9"])
+ _table.add_row(["Order parameters S2, S2f, and S2s", "'s2', 's2f',
's2s'", "0.8"])
+ _table.add_row(["Correlation time te", "'te'", "100 * 1e-12"])
+ _table.add_row(["Correlation time tf", "'tf'", "10 * 1e-12"])
+ _table.add_row(["Correlation time ts", "'ts'", "1000 * 1e-12"])
+ _table.add_row(["Chemical exchange relaxation", "'rex'", "0.0"])
+ _table.add_row(["Bond length", "'r'", "1.02 * 1e-10"])
+ _table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'", "'15N'"])
+ _table.add_row(["Proton type", "'proton_type'", "'1H'"])
+ default_value_doc.add_table(_table.label)
def default_value(self, param):
"""The default model-free parameter values.
@@ -1939,21 +1939,21 @@
return_data_name_doc = Desc_container("Model-free data type string
matching patterns")
- table = uf_tables.add_table(label="table: mf data type patterns",
caption="Model-free data type string matching patterns.")
- table.add_headings(["Data type", "Object name"])
- table.add_row(["Local tm", "'local_tm'"])
- table.add_row(["Order parameter S2", "'s2'"])
- table.add_row(["Order parameter S2f", "'s2f'"])
- table.add_row(["Order parameter S2s", "'s2s'"])
- table.add_row(["Correlation time te", "'te'"])
- table.add_row(["Correlation time tf", "'tf'"])
- table.add_row(["Correlation time ts", "'ts'"])
- table.add_row(["Chemical exchange", "'rex'"])
- table.add_row(["Bond length", "'r'"])
- table.add_row(["CSA", "'csa'"])
- table.add_row(["Heteronucleus type", "'heteronuc_type'"])
- table.add_row(["Proton type", "'proton_type'"])
- return_data_name_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: mf data type patterns",
caption="Model-free data type string matching patterns.")
+ _table.add_headings(["Data type", "Object name"])
+ _table.add_row(["Local tm", "'local_tm'"])
+ _table.add_row(["Order parameter S2", "'s2'"])
+ _table.add_row(["Order parameter S2f", "'s2f'"])
+ _table.add_row(["Order parameter S2s", "'s2s'"])
+ _table.add_row(["Correlation time te", "'te'"])
+ _table.add_row(["Correlation time tf", "'tf'"])
+ _table.add_row(["Correlation time ts", "'ts'"])
+ _table.add_row(["Chemical exchange", "'rex'"])
+ _table.add_row(["Bond length", "'r'"])
+ _table.add_row(["CSA", "'csa'"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'"])
+ _table.add_row(["Proton type", "'proton_type'"])
+ return_data_name_doc.add_table(_table.label)
set_doc = Desc_container("Model-free set details")
Modified: branches/uf_redesign/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/n_state_model.py?rev=16612&r1=16611&r2=16612&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/n_state_model.py (original)
+++ branches/uf_redesign/specific_fns/n_state_model.py Sun Jun 3 23:19:32
2012
@@ -1833,13 +1833,13 @@
default_value_doc = Desc_container("N-state model default values")
- table = uf_tables.add_table(label="table: N-state default values",
caption="N-state model default values.")
- table.add_headings(["Data type", "Object name", "Value"])
- table.add_row(["Probabilities", "'p0', 'p1', 'p2', ..., 'pN'", "1/N"])
- table.add_row(["Euler angle alpha", "'alpha0', 'alpha1', ...", "(c+1) *
pi / (N+1)"])
- table.add_row(["Euler angle beta", "'beta0', 'beta1', ...", "(c+1) * pi
/ (N+1)"])
- table.add_row(["Euler angle gamma", "'gamma0', 'gamma1', ...", "(c+1) *
pi / (N+1)"])
- default_value_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: N-state default values",
caption="N-state model default values.")
+ _table.add_headings(["Data type", "Object name", "Value"])
+ _table.add_row(["Probabilities", "'p0', 'p1', 'p2', ..., 'pN'", "1/N"])
+ _table.add_row(["Euler angle alpha", "'alpha0', 'alpha1', ...", "(c+1) *
pi / (N+1)"])
+ _table.add_row(["Euler angle beta", "'beta0', 'beta1', ...", "(c+1) * pi
/ (N+1)"])
+ _table.add_row(["Euler angle gamma", "'gamma0', 'gamma1', ...", "(c+1) *
pi / (N+1)"])
+ default_value_doc.add_table(_table.label)
default_value_doc.add_paragraph("In this table, N is the total number of
states and c is the index of a given state ranging from 0 to N-1. The
default probabilities are all set to be equal whereas the angles are given a
range of values so that no 2 states are equal at the start of optimisation.")
default_value_doc.add_paragraph("Note that setting the probability for
state N will do nothing as it is equal to one minus all the other
probabilities.")
@@ -2161,16 +2161,16 @@
return_data_name_doc = Desc_container("N-state model data type string
matching patterns")
- table = uf_tables.add_table(label="table: N-state data type patterns",
caption="N-state model data type string matching patterns.")
- table.add_headings(["Data type", "Object name", "Patterns"])
- table.add_row(["Probabilities", "'probs'", "'p0', 'p1', 'p2', ...,
'pN'"])
- table.add_row(["Euler angle alpha", "'alpha'", "'alpha0', 'alpha1',
..."])
- table.add_row(["Euler angle beta", "'beta'", "'beta0', 'beta1', ..."])
- table.add_row(["Euler angle gamma", "'gamma'", "'gamma0', 'gamma1',
..."])
- table.add_row(["Bond length", "'r'", "'^r$' or '[Bb]ond[ -_][Ll]ength'"])
- table.add_row(["Heteronucleus type", "'heteronuc_type'",
"'^[Hh]eteronucleus$'"])
- table.add_row(["Proton type", "'proton_type'", "'^[Pp]roton$'"])
- return_data_name_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: N-state data type patterns",
caption="N-state model data type string matching patterns.")
+ _table.add_headings(["Data type", "Object name", "Patterns"])
+ _table.add_row(["Probabilities", "'probs'", "'p0', 'p1', 'p2', ...,
'pN'"])
+ _table.add_row(["Euler angle alpha", "'alpha'", "'alpha0', 'alpha1',
..."])
+ _table.add_row(["Euler angle beta", "'beta'", "'beta0', 'beta1', ..."])
+ _table.add_row(["Euler angle gamma", "'gamma'", "'gamma0', 'gamma1',
..."])
+ _table.add_row(["Bond length", "'r'", "'^r$' or '[Bb]ond[
-_][Ll]ength'"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'",
"'^[Hh]eteronucleus$'"])
+ _table.add_row(["Proton type", "'proton_type'", "'^[Pp]roton$'"])
+ return_data_name_doc.add_table(_table.label)
return_data_name_doc.add_paragraph("The objects corresponding to the
object names are lists (or arrays) with each element corrsponding to each
state.")
def return_data_name(self, param):
Modified: branches/uf_redesign/specific_fns/noe/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/noe/main.py?rev=16612&r1=16611&r2=16612&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/noe/main.py (original)
+++ branches/uf_redesign/specific_fns/noe/main.py Sun Jun 3 23:19:32 2012
@@ -169,12 +169,12 @@
return_data_name_doc = Desc_container("NOE calculation data type string
matching patterns")
- table = uf_tables.add_table(label="table: NOE data type patterns",
caption="NOE data type string matching patterns.")
- table.add_headings(["Data type", "Object name"])
- table.add_row(["Reference intensity", "'ref'"])
- table.add_row(["Saturated intensity", "'sat'"])
- table.add_row(["NOE", "'noe'"])
- return_data_name_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: NOE data type patterns",
caption="NOE data type string matching patterns.")
+ _table.add_headings(["Data type", "Object name"])
+ _table.add_row(["Reference intensity", "'ref'"])
+ _table.add_row(["Saturated intensity", "'sat'"])
+ _table.add_row(["NOE", "'noe'"])
+ return_data_name_doc.add_table(_table.label)
def return_units(self, param):
Modified: branches/uf_redesign/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/relax_fit.py?rev=16612&r1=16611&r2=16612&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/relax_fit.py (original)
+++ branches/uf_redesign/specific_fns/relax_fit.py Sun Jun 3 23:19:32 2012
@@ -580,12 +580,12 @@
default_value_doc = Desc_container("Relaxation curve fitting default
values")
default_value_doc.add_paragraph("These values are completely arbitrary
as peak heights (or volumes) are extremely variable and the Rx value is a
compensation for both the R1 and R2 values.")
- table = uf_tables.add_table(label="table: curve-fit default values",
caption="Relaxation curve fitting default values.")
- table.add_headings(["Data type", "Object name", "Value"])
- table.add_row(["Relaxation rate", "'rx'", "8.0"])
- table.add_row(["Initial intensity", "'i0'", "10000.0"])
- table.add_row(["Intensity at infinity", "'iinf'", "0.0"])
- default_value_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: curve-fit default values",
caption="Relaxation curve fitting default values.")
+ _table.add_headings(["Data type", "Object name", "Value"])
+ _table.add_row(["Relaxation rate", "'rx'", "8.0"])
+ _table.add_row(["Initial intensity", "'i0'", "10000.0"])
+ _table.add_row(["Intensity at infinity", "'iinf'", "0.0"])
+ default_value_doc.add_table(_table.label)
def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
@@ -844,14 +844,14 @@
return_data_name_doc = Desc_container("Relaxation curve fitting data
type string matching patterns")
- table = uf_tables.add_table(label="table: curve-fit data type patterns",
caption="Relaxation curve fitting data type string matching patterns.")
- table.add_headings(["Data type", "Object name"])
- table.add_row(["Relaxation rate", "'rx'"])
- table.add_row(["Peak intensities (series)", "'intensities'"])
- table.add_row(["Initial intensity", "'i0'"])
- table.add_row(["Intensity at infinity", "'iinf'"])
- table.add_row(["Relaxation period times (series)", "'relax_times'"])
- return_data_name_doc.add_table(table.label)
+ _table = uf_tables.add_table(label="table: curve-fit data type
patterns", caption="Relaxation curve fitting data type string matching
patterns.")
+ _table.add_headings(["Data type", "Object name"])
+ _table.add_row(["Relaxation rate", "'rx'"])
+ _table.add_row(["Peak intensities (series)", "'intensities'"])
+ _table.add_row(["Initial intensity", "'i0'"])
+ _table.add_row(["Intensity at infinity", "'iinf'"])
+ _table.add_row(["Relaxation period times (series)", "'relax_times'"])
+ return_data_name_doc.add_table(_table.label)
def return_error(self, data_id):
r16612 - in /branches/uf_redesign/specific_fns: jw_mapping.py model_free/main.py n_state_model.py noe/main.py relax_fit.py