Author: bugman
Date: Fri Mar 28 18:00:00 2014
New Revision: 22596
URL: http://svn.gna.org/viewcvs/relax?rev=22596&view=rev
Log:
Shifted the model-free classic_style_doc user function documentation to the
'uf' module.
Modified:
trunk/specific_analyses/model_free/macro_base.py
trunk/specific_analyses/model_free/uf.py
trunk/user_functions/molmol.py
trunk/user_functions/pymol_control.py
Modified: trunk/specific_analyses/model_free/macro_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/macro_base.py?rev=22596&r1=22595&r2=22596&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/macro_base.py (original)
+++ trunk/specific_analyses/model_free/macro_base.py Fri Mar 28 18:00:00
2014
@@ -30,33 +30,11 @@
from colour import linear_gradient
from lib.errors import RelaxError, RelaxStyleError, RelaxUnknownDataTypeError
from pipe_control.mol_res_spin import spin_loop
-from user_functions.data import Uf_tables; uf_tables = Uf_tables()
-from user_functions.objects import Desc_container
class Macro:
"""The base class for the model-free analysis Molmol and PyMOL macro
creation."""
-
- classic_style_doc = Desc_container("Model-free classic style")
- classic_style_doc.add_paragraph("Creator: Edward d'Auvergne")
- classic_style_doc.add_paragraph("Argument string: \"classic\"")
- classic_style_doc.add_paragraph("Description: The classic style draws
the backbone of a protein in a cylindrical bond style. Rather than colouring
the amino acids to which the NH bond belongs, the three covalent bonds of the
peptide bond from Ca to Ca in which the NH bond is located are coloured.
Deselected residues are shown as black lines.")
- classic_style_doc.add_paragraph("Supported data types:")
- table = uf_tables.add_table(label="table: model-free macro classic
style", caption="The model-free classic style for mapping model spin specific
data onto 3D molecular structures using either PyMOL or Molmol.",
caption_short="The model-free classic style for PyMOL and Molmol data
mapping.")
- table.add_headings(["Data type", "String", "Description"])
- table.add_row(["S2.", "'s2'", "The standard model-free order parameter,
equal to S2f.S2s for the two timescale models. The default colour gradient
starts at 'yellow' and ends at 'red'."])
- table.add_row(["S2f.", "'s2f'", "The order parameter of the faster of
two internal motions. Residues which are described by model-free models m1
to m4, the single timescale models, are illustrated as white neon bonds. The
default colour gradient is the same as that for the S2 data type."])
- table.add_row(["S2s.", "'s2s'", "The order parameter of the slower of
two internal motions. This functions exactly as S2f except that S2s is
plotted instead."])
- table.add_row(["Amplitude of fast motions.", "'amp_fast'", "Model
independent display of the amplite of fast motions. For residues described
by model-free models m5 to m8, the value plotted is that of S2f. However,
for residues described by models m1 to m4, what is shown is dependent on the
timescale of the motions. This is because these single timescale models can,
at times, be perfect approximations to the more complex two timescale models.
Hence if te is less than 200 ps, S2 is plotted. Otherwise the peptide bond
is coloured white. The default colour gradient is the same as that for
S2."])
- table.add_row(["Amplitude of slow motions.", "'amp_slow'", "Model
independent display of the amplite of slow motions, arbitrarily defined as
motions slower than 200 ps. For residues described by model-free models m5
to m8, the order parameter S2 is plotted if ts > 200 ps. For models m1 to
m4, S2 is plotted if te > 200 ps. The default colour gradient is the same as
that for S2."])
- table.add_row(["te.", "'te'", "The correlation time, te. The default
colour gradient starts at 'turquoise' and ends at 'blue'."])
- table.add_row(["tf.", "'tf'", "The correlation time, tf. The default
colour gradient is the same as that of te."])
- table.add_row(["ts.", "'ts'", "The correlation time, ts. The default
colour gradient starts at 'blue' and ends at 'black'."])
- table.add_row(["Timescale of fast motions", "'time_fast'", "Model
independent display of the timescale of fast motions. For models m5 to m8,
only the parameter tf is plotted. For models m2 and m4, the parameter te is
plotted only if it is less than 200 ps. All other residues are assumed to
have a correlation time of zero. The default colour gradient is the same as
that of te."])
- table.add_row(["Timescale of slow motions", "'time_slow'", "Model
independent display of the timescale of slow motions. For models m5 to m8,
only the parameter ts is plotted. For models m2 and m4, the parameter te is
plotted only if it is greater than 200 ps. All other residues are coloured
white. The default colour gradient is the same as that of ts."])
- table.add_row(["Chemical exchange", "'rex'", "The chemical exchange,
Rex. Residues which experience no chemical exchange are coloured white. The
default colour gradient starts at 'yellow' and finishes at 'red'."])
- classic_style_doc.add_table(table.label)
def classic_style(self, data_type=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
"""The classic macro style.
Modified: trunk/specific_analyses/model_free/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/uf.py?rev=22596&r1=22595&r2=22596&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/uf.py (original)
+++ trunk/specific_analyses/model_free/uf.py Fri Mar 28 18:00:00 2014
@@ -38,6 +38,27 @@
# The API object.
api_model_free = Model_free()
+
+# Classic style documentation.
+classic_style_doc = Desc_container("Model-free classic style")
+classic_style_doc.add_paragraph("Creator: Edward d'Auvergne")
+classic_style_doc.add_paragraph("Argument string: \"classic\"")
+classic_style_doc.add_paragraph("Description: The classic style draws the
backbone of a protein in a cylindrical bond style. Rather than colouring the
amino acids to which the NH bond belongs, the three covalent bonds of the
peptide bond from Ca to Ca in which the NH bond is located are coloured.
Deselected residues are shown as black lines.")
+classic_style_doc.add_paragraph("Supported data types:")
+table = uf_tables.add_table(label="table: model-free macro classic style",
caption="The model-free classic style for mapping model spin specific data
onto 3D molecular structures using either PyMOL or Molmol.",
caption_short="The model-free classic style for PyMOL and Molmol data
mapping.")
+table.add_headings(["Data type", "String", "Description"])
+table.add_row(["S2.", "'s2'", "The standard model-free order parameter,
equal to S2f.S2s for the two timescale models. The default colour gradient
starts at 'yellow' and ends at 'red'."])
+table.add_row(["S2f.", "'s2f'", "The order parameter of the faster of two
internal motions. Residues which are described by model-free models m1 to
m4, the single timescale models, are illustrated as white neon bonds. The
default colour gradient is the same as that for the S2 data type."])
+table.add_row(["S2s.", "'s2s'", "The order parameter of the slower of two
internal motions. This functions exactly as S2f except that S2s is plotted
instead."])
+table.add_row(["Amplitude of fast motions.", "'amp_fast'", "Model
independent display of the amplite of fast motions. For residues described
by model-free models m5 to m8, the value plotted is that of S2f. However,
for residues described by models m1 to m4, what is shown is dependent on the
timescale of the motions. This is because these single timescale models can,
at times, be perfect approximations to the more complex two timescale models.
Hence if te is less than 200 ps, S2 is plotted. Otherwise the peptide bond
is coloured white. The default colour gradient is the same as that for
S2."])
+table.add_row(["Amplitude of slow motions.", "'amp_slow'", "Model
independent display of the amplite of slow motions, arbitrarily defined as
motions slower than 200 ps. For residues described by model-free models m5
to m8, the order parameter S2 is plotted if ts > 200 ps. For models m1 to
m4, S2 is plotted if te > 200 ps. The default colour gradient is the same as
that for S2."])
+table.add_row(["te.", "'te'", "The correlation time, te. The default colour
gradient starts at 'turquoise' and ends at 'blue'."])
+table.add_row(["tf.", "'tf'", "The correlation time, tf. The default colour
gradient is the same as that of te."])
+table.add_row(["ts.", "'ts'", "The correlation time, ts. The default colour
gradient starts at 'blue' and ends at 'black'."])
+table.add_row(["Timescale of fast motions", "'time_fast'", "Model
independent display of the timescale of fast motions. For models m5 to m8,
only the parameter tf is plotted. For models m2 and m4, the parameter te is
plotted only if it is less than 200 ps. All other residues are assumed to
have a correlation time of zero. The default colour gradient is the same as
that of te."])
+table.add_row(["Timescale of slow motions", "'time_slow'", "Model
independent display of the timescale of slow motions. For models m5 to m8,
only the parameter ts is plotted. For models m2 and m4, the parameter te is
plotted only if it is greater than 200 ps. All other residues are coloured
white. The default colour gradient is the same as that of ts."])
+table.add_row(["Chemical exchange", "'rex'", "The chemical exchange, Rex.
Residues which experience no chemical exchange are coloured white. The
default colour gradient starts at 'yellow' and finishes at 'red'."])
+classic_style_doc.add_table(table.label)
# Default value documentation.
default_value_doc = Desc_container("Model-free default values")
Modified: trunk/user_functions/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/molmol.py?rev=22596&r1=22595&r2=22596&view=diff
==============================================================================
--- trunk/user_functions/molmol.py (original)
+++ trunk/user_functions/molmol.py Fri Mar 28 18:00:00 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
+# Copyright (C) 2003-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -35,7 +35,7 @@
import colour
from graphics import WIZARD_IMAGE_PATH
from pipe_control import molmol
-from specific_analyses.model_free.molmol import Molmol
+from specific_analyses.model_free.uf import classic_style_doc
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -150,7 +150,7 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This allows spin specific values to be mapped to
a structure through Molmol macros. Currently only the 'classic' style, which
is described below, is available.")
uf.desc.append(colour._linear_gradient_doc)
-uf.desc.append(Molmol.classic_style_doc)
+uf.desc.append(classic_style_doc)
uf.desc.append(colour.__molmol_colours_doc__)
uf.desc.append(colour.__x11_colours_doc__)
# Prompt examples.
@@ -295,7 +295,7 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This allows residues specific values to be mapped
to a structure through the creation of a Molmol '*.mac' macro which can be
executed in Molmol by clicking on 'File, Macro, Execute User...'. Currently
only the 'classic' style, which is described below, is available.")
uf.desc.append(colour._linear_gradient_doc)
-uf.desc.append(Molmol.classic_style_doc)
+uf.desc.append(classic_style_doc)
uf.desc.append(colour.__molmol_colours_doc__)
uf.desc.append(colour.__x11_colours_doc__)
# Prompt examples.
Modified: trunk/user_functions/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/pymol_control.py?rev=22596&r1=22595&r2=22596&view=diff
==============================================================================
--- trunk/user_functions/pymol_control.py (original)
+++ trunk/user_functions/pymol_control.py Fri Mar 28 18:00:00 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
+# Copyright (C) 2003-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -35,7 +35,7 @@
import colour
from graphics import WIZARD_IMAGE_PATH
from pipe_control import pymol_control
-from specific_analyses.model_free.pymol import Pymol
+from specific_analyses.model_free.uf import classic_style_doc
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -208,7 +208,7 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This allows spin specific values to be mapped to
a structure through PyMOL macros. Currently only the 'classic' style, which
is described below, is available.")
uf.desc.append(colour._linear_gradient_doc)
-uf.desc.append(Pymol.classic_style_doc)
+uf.desc.append(classic_style_doc)
uf.desc.append(colour.__molmol_colours_doc__)
uf.desc.append(colour.__x11_colours_doc__)
# Prompt examples.
@@ -353,7 +353,7 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This allows residues specific values to be mapped
to a structure through the creation of a PyMOL macro which can be executed in
PyMOL by clicking on 'File, Macro, Execute User...'. Currently only the
'classic' style, which is described below, is available.")
uf.desc.append(colour._linear_gradient_doc)
-uf.desc.append(Pymol.classic_style_doc)
+uf.desc.append(classic_style_doc)
uf.desc.append(colour.__molmol_colours_doc__)
uf.desc.append(colour.__x11_colours_doc__)
# Prompt examples.
r22596 - in /trunk: specific_analyses/model_free/ user_functions/