Author: bugman
Date: Mon Aug 29 14:17:05 2011
New Revision: 14505
URL: http://svn.gna.org/viewcvs/relax?rev=14505&view=rev
Log:
All the model-free macro methods are no longer private.
The class will not be used as a base class for the model-free specific class.
Modified:
1.3/specific_fns/model_free/macro_base.py
1.3/specific_fns/model_free/molmol.py
1.3/specific_fns/model_free/pymol.py
Modified: 1.3/specific_fns/model_free/macro_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/macro_base.py?rev=14505&r1=14504&r2=14505&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/macro_base.py (original)
+++ 1.3/specific_fns/model_free/macro_base.py Mon Aug 29 14:17:05 2011
@@ -37,7 +37,7 @@
class Macro:
"""The base class for the model-free analysis Molmol and PyMOL macro
creation."""
- _classic_style_doc = ["Model-free classic style", """
+ classic_style_doc = ["Model-free classic style", """
Creator: Edward d'Auvergne
Argument string: "classic"
@@ -111,7 +111,7 @@
|________________|_____________|___________________________________________________________|
"""]
- def _classic_style(self, data_type=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
+ def classic_style(self, data_type=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
"""The classic macro style.
@keyword data_type: The parameter name or data type.
@@ -146,7 +146,7 @@
# Generate the macro header.
############################
- self._classic_header()
+ self.classic_header()
# S2.
@@ -164,7 +164,7 @@
continue
# S2 width and colour.
- self._classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
# S2f.
@@ -179,11 +179,11 @@
# Colour residues which don't have an S2f value white.
if not hasattr(spin, 's2f') or spin.s2f == None:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# S2f width and colour.
else:
- self._classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
# S2s.
@@ -198,11 +198,11 @@
# Colour residues which don't have an S2s value white.
if not hasattr(spin, 's2s') or spin.s2s == None:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# S2s width and colour.
else:
- self._classic_order_param(res_num, spin.s2s,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2s,
colour_start, colour_end, colour_list)
# Amplitude of fast motions.
@@ -223,19 +223,19 @@
# S2f width and colour (for models m5 to m8).
if hasattr(spin, 's2f') and spin.s2f != None:
- self._classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
# S2 width and colour (for models m1 and m3).
elif model == 'm1' or model == 'm3':
- self._classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
# S2 width and colour (for models m2 and m4 when te <= 200
ps).
elif (model == 'm2' or model == 'm4') and spin.te <= 200e-12:
- self._classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
# White bonds (for models m2 and m4 when te > 200 ps).
elif (model == 'm2' or model == 'm4') and spin.te > 200e-12:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Catch errors.
else:
@@ -260,15 +260,15 @@
# S2 width and colour (for models m5 to m8).
if hasattr(spin, 'ts') and spin.ts != None:
- self._classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
# S2 width and colour (for models m2 and m4 when te > 200
ps).
elif (model == 'm2' or model == 'm4') and spin.te > 200 *
1e-12:
- self._classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+ self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
# White bonds for fast motions.
else:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# te.
#####
@@ -285,7 +285,7 @@
continue
# te width and colour.
- self._classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
# tf.
@@ -303,7 +303,7 @@
continue
# tf width and colour.
- self._classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
# ts.
@@ -327,7 +327,7 @@
colour_end = 'black'
# ts width and colour.
- self._classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
# Timescale of fast motions.
@@ -348,16 +348,16 @@
# tf width and colour (for models m5 to m8).
if hasattr(spin, 'tf') and spin.tf != None:
- self._classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
# te width and colour (for models m2 and m4 when te <= 200
ps).
elif (model == 'm2' or model == 'm4') and spin.te <= 200e-12:
- self._classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
# All other residues are assumed to have a fast correlation
time of zero (statistically zero, not real zero!).
# Colour these bonds white.
else:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Timescale of slow motions.
@@ -384,15 +384,15 @@
# ts width and colour (for models m5 to m8).
if hasattr(spin, 'ts') and spin.ts != None:
- self._classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
# te width and colour (for models m2 and m4 when te > 200
ps).
elif (model == 'm2' or model == 'm4') and spin.te > 200e-12:
- self._classic_correlation_time(res_num, spin.te / 10.0,
colour_start, colour_end, colour_list)
+ self.classic_correlation_time(res_num, spin.te / 10.0,
colour_start, colour_end, colour_list)
# White bonds for the rest.
else:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Rex.
@@ -407,11 +407,11 @@
# Residues which chemical exchange.
if hasattr(spin, 'rex') and spin.rex != None:
- self._classic_rex(res_num, spin.rex, colour_start,
colour_end, colour_list)
+ self.classic_rex(res_num, spin.rex, colour_start,
colour_end, colour_list)
# White bonds for the rest.
else:
- self._classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Unknown data type.
@@ -421,7 +421,7 @@
raise RelaxUnknownDataTypeError(data_type)
- def _classic_correlation_time(self, res_num, te, colour_start,
colour_end, colour_list):
+ def classic_correlation_time(self, res_num, te, colour_start,
colour_end, colour_list):
"""Function for generating the bond width and colours for
correlation times."""
# The te value in picoseconds.
@@ -453,10 +453,10 @@
rgb_array = linear_gradient(colour_value, colour_end, colour_start,
colour_list)
# Colour the peptide bond.
- self._classic_colour(res_num, width, rgb_array)
-
-
- def _classic_order_param(self, res_num, s2, colour_start, colour_end,
colour_list):
+ self.classic_colour(res_num, width, rgb_array)
+
+
+ def classic_order_param(self, res_num, s2, colour_start, colour_end,
colour_list):
"""Function for generating the bond width and colours for order
parameters."""
# The bond width (aiming for a width range of 2 to 0 for S2 values
of 0.0 to 1.0).
@@ -488,10 +488,10 @@
rgb_array = linear_gradient(colour_value, colour_start, colour_end,
colour_list)
# Colour the peptide bond.
- self._classic_colour(res_num, width, rgb_array)
-
-
- def _classic_rex(self, res_num, rex, colour_start, colour_end,
colour_list):
+ self.classic_colour(res_num, width, rgb_array)
+
+
+ def classic_rex(self, res_num, rex, colour_start, colour_end,
colour_list):
"""Function for generating the bond width and colours for
correlation times."""
# The Rex value at the first field strength.
@@ -523,10 +523,10 @@
rgb_array = linear_gradient(colour_value, colour_end, colour_start,
colour_list)
# Colour the peptide bond.
- self._classic_colour(res_num, width, rgb_array)
-
-
- def _create_macro(self, data_type, style=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
+ self.classic_colour(res_num, width, rgb_array)
+
+
+ def create_macro(self, data_type, style=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
"""Create and return an array of macros of the model-free parameters.
@param data_type: The parameter name or data type.
@@ -548,7 +548,7 @@
# The classic style.
if style == 'classic':
- self._classic_style(data_type, colour_start, colour_end,
colour_list, spin_id)
+ self.classic_style(data_type, colour_start, colour_end,
colour_list, spin_id)
# Unknown style.
else:
Modified: 1.3/specific_fns/model_free/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/molmol.py?rev=14505&r1=14504&r2=14505&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/molmol.py (original)
+++ 1.3/specific_fns/model_free/molmol.py Mon Aug 29 14:17:05 2011
@@ -30,7 +30,7 @@
class Molmol(Macro):
"""Class containing the Molmol specific functions for model-free
analysis."""
- def _classic_colour(self, res_num=None, width=None, rgb_array=None):
+ def classic_colour(self, res_num=None, width=None, rgb_array=None):
"""Colour the given peptide bond."""
# Ca to C bond.
@@ -55,7 +55,7 @@
self.commands.append("")
- def _classic_header(self):
+ def classic_header(self):
"""Create the header for the molmol macro."""
# Hide all bonds.
@@ -71,7 +71,7 @@
def molmol_macro(self, data_type, style=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
- """Wrapper method for the _create_macro method.
+ """Wrapper method for the create_macro method.
@param data_type: The parameter name or data type.
@type data_type: str
@@ -87,4 +87,4 @@
@type spin_id: str
"""
- self._create_macro(data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list,
spin_id=spin_id)
+ self.create_macro(data_type, style=style, colour_start=colour_start,
colour_end=colour_end, colour_list=colour_list, spin_id=spin_id)
Modified: 1.3/specific_fns/model_free/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/pymol.py?rev=14505&r1=14504&r2=14505&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/pymol.py (original)
+++ 1.3/specific_fns/model_free/pymol.py Mon Aug 29 14:17:05 2011
@@ -71,7 +71,7 @@
def pymol_macro(self, data_type, style=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
- """Wrapper method for the _create_macro method.
+ """Wrapper method for the create_macro method.
@param data_type: The parameter name or data type.
@type data_type: str
@@ -87,4 +87,4 @@
@type spin_id: str
"""
- self._create_macro(data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list,
spin_id=spin_id)
+ self.create_macro(data_type, style=style, colour_start=colour_start,
colour_end=colour_end, colour_list=colour_list, spin_id=spin_id)
r14505 - in /1.3/specific_fns/model_free: macro_base.py molmol.py pymol.py