Author: bugman
Date: Fri Jan 4 11:51:04 2008
New Revision: 4308
URL: http://svn.gna.org/viewcvs/relax?rev=4308&view=rev
Log:
Prepended 'molmol_' to the start of all the Molmol functions.
Modified:
1.3/specific_fns/model_free/molmol.py
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=4308&r1=4307&r2=4308&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/molmol.py (original)
+++ 1.3/specific_fns/model_free/molmol.py Fri Jan 4 11:51:04 2008
@@ -33,7 +33,7 @@
class Molmol:
"""Class containing the Molmol specific functions for model-free
analysis."""
- def classic(self, data_type, colour_start, colour_end, colour_list):
+ def molmol_classic_style(self, data_type, colour_start, colour_end,
colour_list):
"""
Classic style
~~~~~~~~~~~~~
@@ -119,7 +119,7 @@
# Generate the macro header.
############################
- self.classic_header()
+ self.molmol_classic_header()
# S2.
@@ -137,7 +137,7 @@
continue
# S2 width and colour.
- self.classic_order_param(residue, residue.s2, colour_start,
colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.s2,
colour_start, colour_end, colour_list)
# S2f.
@@ -152,11 +152,11 @@
# Colour residues which don't have an S2f value white.
if not hasattr(residue, 's2f') or residue.s2f == None:
- self.classic_colour(res_num=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# S2f width and colour.
else:
- self.classic_order_param(residue, residue.s2f,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.s2f,
colour_start, colour_end, colour_list)
# S2s.
@@ -171,11 +171,11 @@
# Colour residues which don't have an S2s value white.
if not hasattr(residue, 's2s') or residue.s2s == None:
- self.classic_colour(res_num=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# S2s width and colour.
else:
- self.classic_order_param(residue, residue.s2s,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.s2s,
colour_start, colour_end, colour_list)
# Amplitude of fast motions.
@@ -196,19 +196,19 @@
# S2f width and colour (for models m5 to m8).
if hasattr(residue, 's2f') and residue.s2f != None:
- self.classic_order_param(residue, residue.s2f,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.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(residue, residue.s2,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.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 residue.te <=
200e-12:
- self.classic_order_param(residue, residue.s2,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.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 residue.te >
200e-12:
- self.classic_colour(res_num=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# Catch errors.
else:
@@ -233,15 +233,15 @@
# S2 width and colour (for models m5 to m8).
if hasattr(residue, 'ts') and residue.ts != None:
- self.classic_order_param(residue, residue.s2,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.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 residue.te > 200 *
1e-12:
- self.classic_order_param(residue, residue.s2,
colour_start, colour_end, colour_list)
+ self.molmol_classic_order_param(residue, residue.s2,
colour_start, colour_end, colour_list)
# White bonds for fast motions.
else:
- self.classic_colour(res_num=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# te.
#####
@@ -258,7 +258,7 @@
continue
# te width and colour.
- self.classic_correlation_time(residue, residue.te,
colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue, residue.te,
colour_start, colour_end, colour_list)
# tf.
@@ -276,7 +276,7 @@
continue
# tf width and colour.
- self.classic_correlation_time(residue, residue.tf,
colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue, residue.tf,
colour_start, colour_end, colour_list)
# ts.
@@ -300,7 +300,7 @@
colour_end = 'black'
# ts width and colour.
- self.classic_correlation_time(residue, residue.ts / 10.0,
colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue, residue.ts /
10.0, colour_start, colour_end, colour_list)
# Timescale of fast motions.
@@ -321,16 +321,16 @@
# tf width and colour (for models m5 to m8).
if hasattr(residue, 'tf') and residue.tf != None:
- self.classic_correlation_time(residue, residue.tf,
colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue,
residue.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 residue.te <=
200e-12:
- self.classic_correlation_time(residue, residue.te,
colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue,
residue.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=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# Timescale of slow motions.
@@ -357,15 +357,15 @@
# ts width and colour (for models m5 to m8).
if hasattr(residue, 'ts') and residue.ts != None:
- self.classic_correlation_time(residue, residue.ts /
10.0, colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue, residue.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 residue.te >
200e-12:
- self.classic_correlation_time(residue, residue.te /
10.0, colour_start, colour_end, colour_list)
+ self.molmol_classic_correlation_time(residue, residue.te
/ 10.0, colour_start, colour_end, colour_list)
# White bonds for the rest.
else:
- self.classic_colour(res_num=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# Rex.
@@ -380,11 +380,11 @@
# Residues which chemical exchange.
if hasattr(residue, 'rex') and residue.rex != None:
- self.classic_rex(residue, residue.rex, colour_start,
colour_end, colour_list)
+ self.molmol_classic_rex(residue, residue.rex,
colour_start, colour_end, colour_list)
# White bonds for the rest.
else:
- self.classic_colour(res_num=residue.num, width=0.3,
rgb_array=[1, 1, 1])
+ self.molmol_classic_colour(res_num=residue.num,
width=0.3, rgb_array=[1, 1, 1])
# Unknown data type.
@@ -394,7 +394,7 @@
raise RelaxUnknownDataTypeError, data_type
- def classic_colour(self, res_num=None, width=None, rgb_array=None):
+ def molmol_classic_colour(self, res_num=None, width=None,
rgb_array=None):
"""Colour the given peptide bond."""
# Ca to C bond.
@@ -419,7 +419,7 @@
self.commands.append("")
- def classic_correlation_time(self, residue, te, colour_start,
colour_end, colour_list):
+ def molmol_classic_correlation_time(self, residue, te, colour_start,
colour_end, colour_list):
"""Function for generating the bond width and colours for
correlation times."""
# The te value in picoseconds.
@@ -451,10 +451,10 @@
rgb_array = self.relax.colour.linear_gradient(colour_value,
colour_end, colour_start, colour_list)
# Colour the peptide bond.
- self.classic_colour(residue.num, width, rgb_array)
-
-
- def classic_header(self):
+ self.molmol_classic_colour(residue.num, width, rgb_array)
+
+
+ def molmol_classic_header(self):
"""Create the header for the molmol macro."""
# Hide all bonds.
@@ -469,7 +469,7 @@
self.commands.append("ColorBond 0 0 0")
- def classic_order_param(self, residue, s2, colour_start, colour_end,
colour_list):
+ def molmol_classic_order_param(self, residue, 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).
@@ -501,10 +501,10 @@
rgb_array = self.relax.colour.linear_gradient(colour_value,
colour_start, colour_end, colour_list)
# Colour the peptide bond.
- self.classic_colour(residue.num, width, rgb_array)
-
-
- def classic_rex(self, residue, rex, colour_start, colour_end,
colour_list):
+ self.molmol_classic_colour(residue.num, width, rgb_array)
+
+
+ def molmol_classic_rex(self, residue, 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.
@@ -536,10 +536,10 @@
rgb_array = self.relax.colour.linear_gradient(colour_value,
colour_end, colour_start, colour_list)
# Colour the peptide bond.
- self.classic_colour(residue.num, width, rgb_array)
-
-
- def macro(self, run, data_type, style, colour_start, colour_end,
colour_list):
+ self.molmol_classic_colour(residue.num, width, rgb_array)
+
+
+ def molmol_macro(self, run, data_type, style, colour_start, colour_end,
colour_list):
"""Create and return an array of Molmol macros of the model-free
parameters."""
# Arguments.
@@ -550,7 +550,7 @@
# The classic style.
if style == 'classic':
- self.classic(data_type, colour_start, colour_end, colour_list)
+ self.molmol_classic(data_type, colour_start, colour_end,
colour_list)
# Unknown style.
else:
r4308 - /1.3/specific_fns/model_free/molmol.py