Author: bugman
Date: Tue Jul 3 18:20:36 2012
New Revision: 17159
URL: http://svn.gna.org/viewcvs/relax?rev=17159&view=rev
Log:
Converted the GUI model-free auto-analysis to the interatomic data design.
Modified:
branches/interatomic/gui/analyses/auto_model_free.py
Modified: branches/interatomic/gui/analyses/auto_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/gui/analyses/auto_model_free.py?rev=17159&r1=17158&r2=17159&view=diff
==============================================================================
--- branches/interatomic/gui/analyses/auto_model_free.py (original)
+++ branches/interatomic/gui/analyses/auto_model_free.py Tue Jul 3 18:20:36
2012
@@ -35,8 +35,11 @@
# relax module imports.
from auto_analyses import dauvergne_protocol
from data import Relax_data_store; ds = Relax_data_store()
+from generic_fns.interatomic import interatomic_loop
+from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
from generic_fns.pipes import has_bundle, has_pipe
-from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
+from graphics import fetch_icon
+from physical_constants import NH_BOND_LENGTH
from relax_string import LIST, PARAGRAPH, SECTION, SUBSECTION, TITLE
from specific_fns.setup import get_specific_fn
from status import Status; status = Status()
@@ -255,11 +258,9 @@
wx.CallAfter(self.field_results_dir.Enable, enable)
wx.CallAfter(self.spin_systems.Enable, enable)
wx.CallAfter(self.relax_data.Enable, enable)
+ wx.CallAfter(self.button_dipole_pair.Enable, enable)
wx.CallAfter(self.button_csa.Enable, enable)
- wx.CallAfter(self.button_r.Enable, enable)
- wx.CallAfter(self.button_h_type.Enable, enable)
- wx.CallAfter(self.button_x_type.Enable, enable)
- wx.CallAfter(self.button_vectors.Enable, enable)
+ wx.CallAfter(self.button_isotope.Enable, enable)
wx.CallAfter(self.local_tm_model_field.Enable, enable)
wx.CallAfter(self.mf_model_field.Enable, enable)
wx.CallAfter(self.grid_inc.Enable, enable)
@@ -279,50 +280,41 @@
# Sizer.
sizer = wx.BoxSizer(wx.HORIZONTAL)
+ # Dipole-dipole relaxation setup button.
+ self.button_dipole_pair =
wx.lib.buttons.ThemedGenBitmapTextButton(self, -1, None, " Dipolar
relaxation")
+
self.button_dipole_pair.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.dipole_pair",
"22x22"), wx.BITMAP_TYPE_ANY))
+ self.button_dipole_pair.SetFont(font.normal)
+ self.button_dipole_pair.SetSize((-1, 25))
+ self.button_dipole_pair.SetToolTipString("Set the Chemical Shift
Anisotropy (CSA) values via the value.set user function.")
+ self.gui.Bind(wx.EVT_BUTTON, self.setup_dipole_pair,
self.button_dipole_pair)
+ sizer.Add(self.button_dipole_pair, 1, wx.ALL|wx.EXPAND, 0)
+
# CSA button.
- self.button_csa = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1,
None, " CSA")
- self.button_csa.SetBitmapLabel(wx.Bitmap(paths.icon_16x16.add,
wx.BITMAP_TYPE_ANY))
+ self.button_csa = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1,
None, " CSA relaxation")
+
self.button_csa.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.align_tensor",
"22x22"), wx.BITMAP_TYPE_ANY))
self.button_csa.SetFont(font.normal)
- self.button_csa.SetSize((-1, 20))
+ self.button_csa.SetSize((-1, 25))
self.button_csa.SetToolTipString("Set the Chemical Shift Anisotropy
(CSA) values via the value.set user function.")
self.gui.Bind(wx.EVT_BUTTON, self.value_set_csa, self.button_csa)
sizer.Add(self.button_csa, 1, wx.ALL|wx.EXPAND, 0)
- # Bond length button.
- self.button_r = wx.lib.buttons.ThemedGenBitmapTextButton(self, -1,
None, " Bond length")
- self.button_r.SetBitmapLabel(wx.Bitmap(paths.icon_16x16.add,
wx.BITMAP_TYPE_ANY))
- self.button_r.SetFont(font.normal)
- self.button_r.SetSize((-1, 20))
- self.button_r.SetToolTipString("Set the bond length (r) values via
the value.set user function.")
- self.gui.Bind(wx.EVT_BUTTON, self.value_set_r, self.button_r)
- sizer.Add(self.button_r, 1, wx.ALL|wx.EXPAND, 0)
-
- # Proton type button.
- self.button_h_type = wx.lib.buttons.ThemedGenBitmapTextButton(self,
-1, None, " H type")
- self.button_h_type.SetBitmapLabel(wx.Bitmap(paths.icon_16x16.add,
wx.BITMAP_TYPE_ANY))
- self.button_h_type.SetFont(font.normal)
- self.button_h_type.SetSize((-1, 20))
- self.button_h_type.SetToolTipString("Set the type of proton via the
value.set user function.")
- self.gui.Bind(wx.EVT_BUTTON, self.value_set_proton_type,
self.button_h_type)
- sizer.Add(self.button_h_type, 1, wx.ALL|wx.EXPAND, 0)
-
- # Heteronucleus type button.
- self.button_x_type = wx.lib.buttons.ThemedGenBitmapTextButton(self,
-1, None, " X type")
- self.button_x_type.SetBitmapLabel(wx.Bitmap(paths.icon_16x16.add,
wx.BITMAP_TYPE_ANY))
- self.button_x_type.SetFont(font.normal)
- self.button_x_type.SetSize((-1, 20))
- self.button_x_type.SetToolTipString("Set the type of heteronucleus
via the value.set user function.")
- self.gui.Bind(wx.EVT_BUTTON, self.value_set_heteronuc_type,
self.button_x_type)
- sizer.Add(self.button_x_type, 1, wx.ALL|wx.EXPAND, 0)
-
- # Unit vectors button.
- self.button_vectors = wx.lib.buttons.ThemedGenBitmapTextButton(self,
-1, None, " Unit vectors")
-
self.button_vectors.SetBitmapLabel(wx.Bitmap(paths.icon_16x16.structure,
wx.BITMAP_TYPE_ANY))
- self.button_vectors.SetFont(font.normal)
- self.button_vectors.SetSize((-1, 20))
- self.button_vectors.SetToolTipString("Load unit vectors from PDB
files.")
- self.gui.Bind(wx.EVT_BUTTON, self.load_unit_vectors,
self.button_vectors)
- sizer.Add(self.button_vectors, 1, wx.ALL|wx.EXPAND, 0)
+ # Isotope type button (heteronucleus).
+ self.button_isotope = wx.lib.buttons.ThemedGenBitmapTextButton(self,
-1, None, " X isotope")
+
self.button_isotope.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.nuclear_symbol",
"22x22"), wx.BITMAP_TYPE_ANY))
+ self.button_isotope.SetFont(font.normal)
+ self.button_isotope.SetSize((-1, 25))
+ self.button_isotope.SetToolTipString("Set the nuclear isotope types
of the heteronuclear spins via the spin.isotope user function.")
+ self.gui.Bind(wx.EVT_BUTTON, self.spin_isotope_heteronuc,
self.button_isotope)
+ sizer.Add(self.button_isotope, 1, wx.ALL|wx.EXPAND, 0)
+
+ # Isotope type button (proton).
+ self.button_isotope = wx.lib.buttons.ThemedGenBitmapTextButton(self,
-1, None, " H isotope")
+
self.button_isotope.SetBitmapLabel(wx.Bitmap(fetch_icon("relax.nuclear_symbol",
"22x22"), wx.BITMAP_TYPE_ANY))
+ self.button_isotope.SetFont(font.normal)
+ self.button_isotope.SetSize((-1, 25))
+ self.button_isotope.SetToolTipString("Set the nuclear isotope types
of the proton spins via the spin.isotope user function.")
+ self.gui.Bind(wx.EVT_BUTTON, self.spin_isotope_proton,
self.button_isotope)
+ sizer.Add(self.button_isotope, 1, wx.ALL|wx.EXPAND, 0)
# Add the element to the box.
box.Add(sizer, 0, wx.ALL|wx.EXPAND, 0)
@@ -380,6 +372,10 @@
if hasattr(cdp, 'ri_ids') and len(cdp.ri_ids) <= 3:
missing.append("Insufficient relaxation data, 4 or more data
sets are essential for the execution of the dauvergne_protocol
auto-analysis.")
+ # Interatomic data containers.
+ if not hasattr(cdp, 'interatomic') or len(cdp.interatomic) == 0:
+ missing.append("Interatomic data (for the dipole-dipole
interaction)")
+
# Get the mode.
mode = gui_to_str(self.mode.GetValue())
@@ -397,7 +393,7 @@
if 'prolate' in data.global_models or 'oblate' in data.global_models
or 'ellipsoid' in data.global_models:
vector_check = True
- # Spin vars.
+ # Spin variables.
for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
@@ -406,25 +402,36 @@
# The message skeleton.
msg = "Spin '%s' - %s (try the %s user function)." % (spin_id,
"%s", "%s")
- # Test if the bond length has been set.
- if not hasattr(spin, 'r') or spin.r == None:
- missing.append(msg % ("bond length data", "value.set"))
-
# Test if the CSA value has been set.
if not hasattr(spin, 'csa') or spin.csa == None:
missing.append(msg % ("CSA data", "value.set"))
- # Test if the heteronucleus type has been set.
- if not hasattr(spin, 'heteronuc_type') or spin.heteronuc_type ==
None:
- missing.append(msg % ("heteronucleus type data",
"value.set"))
-
- # Test if the proton type has been set.
- if not hasattr(spin, 'proton_type') or spin.proton_type == None:
- missing.append(msg % ("proton type data", "value.set"))
+ # Test if the nuclear isotope type has been set.
+ if not hasattr(spin, 'isotope') or spin.isotope == None:
+ missing.append(msg % ("nuclear isotope data",
"spin.isotope"))
+
+ # Interatomic data container variables.
+ for interatom in interatomic_loop():
+ # Get the spin containers.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
+ # Skip deselected spins.
+ if not spin1.select:
+ continue
+ if not spin2.select:
+ continue
+
+ # The message skeleton.
+ msg = "Spin pair '%s' and '%s' - %s (try the %s user function)."
% (interatom.spin_id1, interatom.spin_id2, "%s", "%s")
+
+ # Test if the interatomic distance has been set.
+ if not hasattr(interatom, 'r') or interatom.r == None:
+ missing.append(msg % ("bond length data", "value.set"))
# Test if the unit vectors have been loaded.
- if vector_check and (not hasattr(spin, 'xh_vect') or
spin.xh_vect == None):
- missing.append(msg % ("unit vectors", "structure.vectors"))
+ if vector_check and (not hasattr(interatom, 'vector') or
interatom.vector == None):
+ missing.append(msg % ("unit vectors",
"dipole_pair.unit_vectors"))
# Return the container and list of missing data.
return data, missing
@@ -591,35 +598,6 @@
event.Skip()
- def load_unit_vectors(self, event=None):
- """Create the wizard for structure.read_pdb and structure.vectors.
-
- @keyword event: The wx event.
- @type event: wx event
- """
-
- # Change the cursor to busy.
- wx.BeginBusyCursor()
-
- # Create the wizard.
- self.vect_wizard = Wiz_window(parent=self.gui, size_x=1000,
size_y=750, title="Load unit vectors from file")
-
- # Create the PDB reading page.
- page = uf_store['structure.read_pdb'].create_page(self.vect_wizard)
- self.vect_wizard.add_page(page, skip_button=True)
-
- # Create the vector loading page.
- page = uf_store['structure.vectors'].create_page(self.vect_wizard)
- self.vect_wizard.add_page(page)
-
- # Reset the cursor.
- if wx.IsBusy():
- wx.EndBusyCursor()
-
- # Execute the wizard.
- self.vect_wizard.run()
-
-
def mode_dialog(self, event=None):
"""The calculation mode selection.
@@ -684,6 +662,76 @@
self.field_results_dir.SetValue(str_to_gui(path))
+ def setup_dipole_pair(self, event=None):
+ """Create the wizard for the dipole-dipole interaction.
+
+ @keyword event: The wx event.
+ @type event: wx event
+ """
+
+ # Change the cursor to busy.
+ wx.BeginBusyCursor()
+
+ # Create the wizard.
+ self.dipole_wizard = Wiz_window(parent=self.gui, size_x=1000,
size_y=750, title="Dipole-dipole interaction setup")
+
+ # Structural data.
+ if not hasattr(cdp, 'structure'):
+ # Create the PDB reading page.
+ page =
uf_store['structure.read_pdb'].create_page(self.dipole_wizard)
+ self.dipole_wizard.add_page(page, skip_button=True)
+
+ # Create the position reading page.
+ page =
uf_store['structure.get_pos'].create_page(self.dipole_wizard)
+ self.dipole_wizard.add_page(page, skip_button=True)
+
+ # Create the dipole_pair.define page.
+ page = uf_store['dipole_pair.define'].create_page(self.dipole_wizard)
+ page.SetValue('spin_id1', '@N')
+ page.SetValue('spin_id2', '@H')
+ self.dipole_wizard.add_page(page)
+
+ # Create the dipole_pair.set_dist page.
+ page =
uf_store['dipole_pair.set_dist'].create_page(self.dipole_wizard)
+ page.SetValue('spin_id1', '@N')
+ page.SetValue('spin_id2', '@H')
+ page.SetValue('ave_dist', NH_BOND_LENGTH)
+ self.dipole_wizard.add_page(page)
+
+ # Create the dipole_pair.unit_vectors page.
+ page =
uf_store['dipole_pair.unit_vectors'].create_page(self.dipole_wizard)
+ self.dipole_wizard.add_page(page)
+
+ # Reset the cursor.
+ if wx.IsBusy():
+ wx.EndBusyCursor()
+
+ # Execute the wizard.
+ self.dipole_wizard.run()
+
+
+ def spin_isotope_heteronuc(self, event=None):
+ """Set the nuclear isotope types of the heteronuclear spins via the
spin.isotope user function.
+
+ @keyword event: The wx event.
+ @type event: wx event
+ """
+
+ # Call the user function.
+ uf_store['spin.isotope'](isotope='15N', spin_id='@N')
+
+
+ def spin_isotope_proton(self, event=None):
+ """Set the nuclear isotope types of the proton spins via the
spin.isotope user function.
+
+ @keyword event: The wx event.
+ @type event: wx event
+ """
+
+ # Call the user function.
+ uf_store['spin.isotope'](isotope='1H', spin_id='@H')
+
+
def sync_ds(self, upload=False):
"""Synchronise the analysis frame and the relax data store, both
ways.
@@ -742,48 +790,6 @@
# Call the user function.
uf_store['value.set'](val=val, param='csa')
-
-
- def value_set_heteronuc_type(self, event=None):
- """Set the type of heteronucleus via the value.set uf.
-
- @keyword event: The wx event.
- @type event: wx event
- """
-
- # Get the default value.
- val = get_specific_fn('default_value')('heteronuc_type')
-
- # Call the user function.
- uf_store['value.set'](val=val, param='heteronuc_type')
-
-
- def value_set_proton_type(self, event=None):
- """Set the type of proton via the value.set uf.
-
- @keyword event: The wx event.
- @type event: wx event
- """
-
- # Get the default value.
- val = get_specific_fn('default_value')('proton_type')
-
- # Call the user function.
- uf_store['value.set'](val=val, param='proton_type')
-
-
- def value_set_r(self, event=None):
- """Set the bond length via the value.set uf.
-
- @keyword event: The wx event.
- @type event: wx event
- """
-
- # Get the default value.
- val = get_specific_fn('default_value')('r')
-
- # Call the user function.
- uf_store['value.set'](val=val, param='r')
r17159 - /branches/interatomic/gui/analyses/auto_model_free.py