Author: semor
Date: Wed Apr 9 04:07:25 2008
New Revision: 5470
URL: http://svn.gna.org/viewcvs/relax?rev=5470&view=rev
Log:
Added missing imports and corrected calls to modules from generic_fns.
In previous revisions (5258, 5259, 5260, 5261, 5264, 5265, 5276, 5282, 5283),
as part of the
modifications to the new design, these calls to the modules were erroneously
instantiated (as is
done for the modules from specific_fns).
The reasons for these changes were specified by Edward d'Auvergne in a post
at:
https://mail.gna.org/public/relax-devel/2008-04/msg00029.html (# Message-id:
<7f080ed10804040101n5cc2c69flc3cf0a894389e8f1@xxxxxxxxxxxxxx>)
Modified:
1.3/prompt/angles.py
1.3/prompt/eliminate.py
1.3/prompt/fix.py
1.3/prompt/grace.py
1.3/prompt/molmol.py
1.3/prompt/monte_carlo.py
1.3/prompt/palmer.py
1.3/prompt/results.py
1.3/prompt/vmd.py
Modified: 1.3/prompt/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/angles.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/angles.py (original)
+++ 1.3/prompt/angles.py Wed Apr 9 04:07:25 2008
@@ -24,6 +24,7 @@
import sys
# relax module imports.
+from generic_fns import angles
from relax_errors import RelaxStrError
@@ -54,4 +55,4 @@
print text
# Execute the functional code.
- angles_obj.angles()
+ angles.angles()
Modified: 1.3/prompt/eliminate.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/eliminate.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/eliminate.py (original)
+++ 1.3/prompt/eliminate.py Wed Apr 9 04:07:25 2008
@@ -24,6 +24,7 @@
import sys
# relax module imports.
+from generic_fns import eliminate
from relax_errors import RelaxFunctionError, RelaxListStrError,
RelaxNoneStrListError, RelaxNoneTupleError
from specific_fns.model_free import Model_free
@@ -85,7 +86,7 @@
raise RelaxNoneTupleError, ('args', args)
# Execute the functional code.
- eliminate_obj.eliminate(function=function, args=args)
+ eliminate.eliminate(function=function, args=args)
# Docstring modification.
Modified: 1.3/prompt/fix.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/fix.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/fix.py (original)
+++ 1.3/prompt/fix.py Wed Apr 9 04:07:25 2008
@@ -24,6 +24,7 @@
import sys
# relax module imports.
+from generic_fns import fix
from relax_errors import RelaxBinError, RelaxIntStrError, RelaxStrError
@@ -85,4 +86,4 @@
raise RelaxBinError, ('fixed', fixed)
# Execute the functional code.
- fix_obj.fix(element=element, fixed=fixed)
+ fix.fix(element=element, fixed=fixed)
Modified: 1.3/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/grace.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/grace.py (original)
+++ 1.3/prompt/grace.py Wed Apr 9 04:07:25 2008
@@ -27,7 +27,7 @@
from relax_errors import RelaxBinError, RelaxNoneIntStrError,
RelaxNoneStrError, RelaxStrError
from doc_string import regexp_doc
import help
-from generic_fns import minimise
+from generic_fns import grace, minimise
from specific_fns.model_free import Model_free
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.noe import Noe
@@ -245,7 +245,7 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- grace_obj.write(x_data_type=x_data_type, y_data_type=y_data_type,
res_num=res_num, res_name=res_name, plot_data=plot_data, norm=norm,
file=file, dir=dir, force=force)
+ grace.write(x_data_type=x_data_type, y_data_type=y_data_type,
res_num=res_num, res_name=res_name, plot_data=plot_data, norm=norm,
file=file, dir=dir, force=force)
Modified: 1.3/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molmol.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/molmol.py (original)
+++ 1.3/prompt/molmol.py Wed Apr 9 04:07:25 2008
@@ -26,6 +26,7 @@
# relax module imports.
import colour
import help
+from generic_fns import molmol
from relax_errors import RelaxBinError, RelaxListNumError,
RelaxNoneStrError, RelaxNoneStrListError, RelaxStrError
from specific_fns.model_free.molmol import Molmol
@@ -90,7 +91,7 @@
raise RelaxStrError, ('command', command)
# Execute the functional code.
- molmol_obj.command(command=command)
+ molmol.command(command=command)
def macro_exec(self, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None):
@@ -182,7 +183,7 @@
raise RelaxListNumError, ('ending colour of the linear
gradient', colour_end)
# Execute the functional code.
- molmol_obj.macro_exec(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
+ molmol.macro_exec(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
def ribbon(self):
@@ -215,7 +216,7 @@
print text
# Execute the functional code.
- molmol_obj.ribbon()
+ molmol.ribbon()
def tensor_pdb(self, file=None):
@@ -281,7 +282,7 @@
raise RelaxStrError, ('file name', file)
# Execute the functional code.
- molmol_obj.tensor_pdb(file=file)
+ molmol.tensor_pdb(file=file)
def view(self):
@@ -300,7 +301,7 @@
print text
# Execute the functional code.
- molmol_obj.view()
+ molmol.view()
def write(self, data_type=None, style="classic", colour_start=None,
colour_end=None, colour_list=None, file=None, dir='molmol', force=0):
@@ -415,7 +416,7 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- molmol_obj.write(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list,
file=file, dir=dir, force=force)
+ molmol.write(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list,
file=file, dir=dir, force=force)
Modified: 1.3/prompt/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/monte_carlo.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/monte_carlo.py (original)
+++ 1.3/prompt/monte_carlo.py Wed Apr 9 04:07:25 2008
@@ -25,6 +25,7 @@
# relax module imports.
import help
+from generic_fns import monte_carlo
from relax_errors import RelaxIntError, RelaxNumError, RelaxStrError
@@ -83,7 +84,7 @@
raise RelaxStrError, ('method', method)
# Execute the functional code.
- monte_carlo_obj.create_data(method=method)
+ monte_carlo.create_data(method=method)
def error_analysis(self, prune=0.0):
@@ -130,7 +131,7 @@
raise RelaxNumError, ('prune', prune)
# Execute the functional code.
- monte_carlo_obj.error_analysis(prune=prune)
+ monte_carlo.error_analysis(prune=prune)
def initial_values(self):
@@ -157,7 +158,7 @@
print text
# Execute the functional code.
- monte_carlo_obj.initial_values()
+ monte_carlo.initial_values()
def off(self):
@@ -169,7 +170,7 @@
print text
# Execute the functional code.
- monte_carlo_obj.off()
+ monte_carlo.off()
def on(self):
@@ -181,7 +182,7 @@
print text
# Execute the functional code.
- monte_carlo_obj.on()
+ monte_carlo.on()
def setup(self, number=500):
@@ -211,7 +212,7 @@
raise RelaxIntError, ('number', number)
# Execute the functional code.
- monte_carlo_obj.setup(number=number)
+ monte_carlo.setup(number=number)
Modified: 1.3/prompt/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/palmer.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/palmer.py (original)
+++ 1.3/prompt/palmer.py Wed Apr 9 04:07:25 2008
@@ -25,6 +25,7 @@
# relax module imports.
import help
+from generic_fns import palmer
from relax_errors import RelaxBinError, RelaxFloatError, RelaxIntError,
RelaxNoneStrError, RelaxStrError
@@ -163,7 +164,7 @@
raise RelaxStrError, ('atom2', atom2)
# Execute the functional code.
- palmer_obj.create(dir=dir, force=force, binary=binary,
diff_search=diff_search, sims=sims, sim_type=sim_type, trim=trim,
steps=steps, constraints=constraints, nucleus=nucleus, atom1=atom1,
atom2=atom2)
+ palmer.create(dir=dir, force=force, binary=binary,
diff_search=diff_search, sims=sims, sim_type=sim_type, trim=trim,
steps=steps, constraints=constraints, nucleus=nucleus, atom1=atom1,
atom2=atom2)
def execute(self, dir=None, force=0, binary='modelfree4'):
@@ -218,7 +219,7 @@
raise RelaxStrError, ('Modelfree binary', binary)
# Execute the functional code.
- palmer_obj.execute(dir=dir, force=force, binary=binary)
+ palmer.execute(dir=dir, force=force, binary=binary)
def extract(self, dir=None):
@@ -242,4 +243,4 @@
raise RelaxNoneStrError, ('directory name', dir)
# Execute the functional code.
- palmer_obj.extract(dir=dir)
+ palmer.extract(dir=dir)
Modified: 1.3/prompt/results.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/results.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/results.py (original)
+++ 1.3/prompt/results.py Wed Apr 9 04:07:25 2008
@@ -25,6 +25,7 @@
# relax module imports.
import help
+from generic_fns import results
from relax_errors import RelaxBinError, RelaxIntError, RelaxNoneStrError,
RelaxStrError
@@ -57,7 +58,7 @@
print text
# Execute the functional code.
- results_obj.display()
+ results.display()
def read(self, file='results', dir='dir', format='columnar'):
@@ -103,7 +104,7 @@
raise RelaxStrError, ('format', format)
# Execute the functional code.
- results_obj.read(file=file, directory=dir, format=format)
+ results.read(file=file, directory=dir, format=format)
def write(self, file='results', dir='dir', force=0, format='columnar',
compress_type=1):
@@ -171,4 +172,4 @@
raise RelaxIntError, ('compression type', compress_type)
# Execute the functional code.
- results_obj.write(file=file, directory=dir, force=force,
format=format, compress_type=compress_type)
+ results.write(file=file, directory=dir, force=force, format=format,
compress_type=compress_type)
Modified: 1.3/prompt/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/vmd.py?rev=5470&r1=5469&r2=5470&view=diff
==============================================================================
--- 1.3/prompt/vmd.py (original)
+++ 1.3/prompt/vmd.py Wed Apr 9 04:07:25 2008
@@ -25,6 +25,7 @@
# relax module imports.
import help
+from generic_fns import vmd
from relax_errors import RelaxStrError
@@ -56,4 +57,4 @@
print text
# Execute the functional code.
- vmd_obj.view()
+ vmd.view()
r5470 - in /1.3/prompt: angles.py eliminate.py fix.py grace.py molmol.py monte_carlo.py palmer.py results.py vmd.py