Package mmLib :: Module Viewer :: Class GLAtomList
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Type GLAtomList

object --+        
         |        
  GLObject --+    
             |    
    GLDrawList --+
                 |
                GLAtomList

Known Subclasses:
GLChain, GLTLSAtomList

OpenGL renderer for a list of atoms. Optional arguments iare: color, U, U_color.
Method Summary
  __init__(self, **args)
  glal_calc_color(self, atom)
Sets the open-gl color for the atom.
  glal_calc_color_label(self)
Returns the label color.
  glal_calc_color_range(self, value)
Return a RGBF 3-tuple color of a color gradient for value.
  glal_calc_color_trace(self)
Returns the trace color.
  glal_calc_color_Uaxes(self, atom)
Return the color to be used for thermal axes.
  glal_calc_color_Uellipse(self, atom)
Return the color to be used for thermal ellipse.
  glal_calc_color_Urms(self, atom)
Return the color to be used for thermal peanuts.
  glal_calc_position(self, position)
Calculate a position vector with respect to the proeprty: atom_origin.
  glal_calc_U(self, atom)
Return the ADP U tensor for the atom
  glal_draw_ball_stick(self)
Draw atom with ball/stick model.
  glal_draw_cpk(self)
Draw a atom as a CPK sphere.
  glal_draw_cross(self, atm, pos)
Draws atom with a cross of lines.
  glal_draw_labels(self)
Draws atom lables.
  glal_draw_lines(self)
Draw a atom using bond lines only.
  glal_draw_trace(self)
Draws trace over all polymer backbone atoms.
  glal_draw_Uaxes(self)
Draw thermal axes at the given ADP probability level.
  glal_draw_Uellipse(self)
Draw the ADP determined probability ellipsoid.
  glal_draw_Urms(self)
Draw the ADP determined RMS displacement surface.
  glal_iter_atoms(self)
Implement in a subclass to iterate over all atoms which need to be drawn.
  glal_iter_atoms_filtered(self)
Iterate all atoms and yield the tuble (atom, visible_flag).
  glal_iter_chains(self)
Implement in a subclass to iterate one Chain object at a time, in order.
  glal_iter_fragments(self)
Implement in a subclass to iterate one Fragment object at a time, in order.
  glal_iter_models(self)
Implement in a subclass to iterate one Model object at a time, in order.
  glal_iter_visible_atoms(self)
Iterate over all visible atoms yielding the 2-tuple (atm, position).
  glal_rebuild_atom_dicts(self)
When a atom selection setting or origin changes, the atom dictionaries need to be rebuilt.
  glal_update_color_value(self, value)
Configure the color_value property from the value argument.
  glal_update_properties(self, updates, actions)
  gldl_install_draw_methods(self)
Override in children to install draw methods for a GLDrawList.
  gldl_iter_multidraw_self(self)
Specialized draw list invokation to recycle the draw list for symmetry related copies.
  glo_install_properties(self)
Called by GLObject.__init__ to install properties.
    Inherited from GLDrawList
  gldl_draw(self)
Implement in subclass to draw somthing.
  gldl_draw_method_compile(self, draw_method)
Compiles a draw method.
  gldl_draw_method_delete_compiled(self, draw_method)
Deletes the compiled draw list in the current driver.
  gldl_draw_method_delete_compiled_all_drivers(self)
  gldl_draw_method_get(self, draw_method_name)
Returns the draw metod of the given name or None if not found.
  gldl_draw_method_install(self, draw_method)
Installs a draw method to compile and render a OpenGL draw listlist.
  gldl_draw_transparent(self)
Implement in subclass to draw transparent objects.
  gldl_get_glviewer(self)
Returns the root GLViewer object.
  gldl_iter_multidraw_all(self)
When implemented as a iterator in a subclass, each time yield is invoked the GLDrawList and all its decendants will be rendered from whatever OpenGL coordinate system is set in the iterator.
  gldl_pop_matrix(self)
Pop the roatated/translated position.
  gldl_property_color_rgbf(self, prop_name)
Returns the property value as a RGBF triplet.
  gldl_push_matrix(self)
Rotate and translate to the correct position for drawing.
  gldl_redraw(self)
Triggers a redraw of the GLViewer
  gldl_render(self, driver, transparent)
Compile or force a recompile of this object's gl_draw list, and render the scene.
  gldl_render_draw_methods(self, transparent)
Render all draw methods.
  gldl_update_cb(self, updates, actions)
Properties update callback.
  glo_remove(self)
Override GLObject's remove to also delete the compiled OpenGL draw lists.
  glo_remove_child(self, child)
Override GLObject's remove to also delete the compiled OpenGL draw lists.
    Inherited from GLObject
  glo_add_child(self, child)
  glo_add_property(self, prop_desc)
Adds a new property to the GLObject.
  glo_add_update_callback(self, func)
Adds a function which is called whenever property values change.
  glo_append_child(self, child)
Adds a child GLObject to the end of the GLObject's child list.
  glo_count_descendants(self)
Counts all decendant GLObjects.
  glo_get_child(self, gl_object_id)
Returns the child GLObject matching the given gl_object_id.
  glo_get_child_path(self, glo_id_path)
Returns the object at the given path, or None if the object does not exist.
  glo_get_degree(self)
Returns the number of children (degree).
  glo_get_depth(self)
Returns the depth, the root composite is depth 0.
  glo_get_glstructure(self)
Returns the parent GLStructure object, or None if the GLObject is not a child of a GLStructure.
  glo_get_index_path(self)
Returns the tree-path to the GLObject as a list of its integer indexes.
  glo_get_lowest_common_ancestor(self, gl_object)
Returns the lowest common ancesotry of self and argument composite.
  glo_get_parent(self)
Returns the parent GLObject.
  glo_get_parent_list(self)
Returns a list of the parent GLObjects back to the root.
  glo_get_path(self)
Returns the tree-path to the composite as a list of its parent composites.
  glo_get_properties_id(self)
Returns the properties ID of this object.
  glo_get_property_desc(self, name)
Return the property description dictionary for the given property name.
  glo_get_root(self)
Returns the root GLObject.
  glo_init_properties(self, **args)
This is a special form of update which propagates all linked values, not just the changed ones.
  glo_is_descendant_of(self, gl_object)
Returns true if self composite is a decent of argument GLObject.
  glo_iter_children(self)
Iterate immediate children.
  glo_iter_preorder_traversal(self)
Preorder Traversal for GLObject composite.
  glo_iter_property_desc(self)
Iterates over all property descriptions.
  glo_link_child_property(self, name, child_gl_object_id, child_name)
Link the value of the GLObject's property to the value of a child property.
  glo_name(self)
Returns the GLObject name.
  glo_prepend_child(self, child)
Adds a child GLObject to the beginning of the GLObject's child list.
  glo_remove_update_callback(self, func)
Removes the update callback.
  glo_set_name(self, name)
Sets the GLObject name.
  glo_set_properties_id(self, gl_object_id)
Set the property name for this GLObject.
  glo_update_properties(self, **args)
Update property values and trigger update callbacks.
  glo_update_properties_path(self, glo_id_path, value)
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __hash__(x)
x.__hash__() <==> hash(x)
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __repr__(x)
x.__repr__() <==> repr(x)
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value
  __str__(x)
x.__str__() <==> str(x)

Class Variable Summary
dict glal_res_type_color_dict = {'acids': (1.0, 0.25, 0.25), ...
    Inherited from GLDrawList
list gldl_color_list = ['White', 'Black', 'Blue', 'Green', 'M...
    Inherited from GLObject
GLPropertyDefault PropertyDefault = <mmLib.Viewer.GLPropertyDefault object...

Method Details

glal_calc_color(self, atom)

Sets the open-gl color for the atom.

glal_calc_color_label(self)

Returns the label color.

glal_calc_color_range(self, value)

Return a RGBF 3-tuple color of a color gradient for value.

glal_calc_color_trace(self)

Returns the trace color.

glal_calc_color_Uaxes(self, atom)

Return the color to be used for thermal axes.

glal_calc_color_Uellipse(self, atom)

Return the color to be used for thermal ellipse.

glal_calc_color_Urms(self, atom)

Return the color to be used for thermal peanuts.

glal_calc_position(self, position)

Calculate a position vector with respect to the proeprty: atom_origin.

glal_calc_U(self, atom)

Return the ADP U tensor for the atom

glal_draw_ball_stick(self)

Draw atom with ball/stick model.

glal_draw_cpk(self)

Draw a atom as a CPK sphere.

glal_draw_cross(self, atm, pos)

Draws atom with a cross of lines.

glal_draw_labels(self)

Draws atom lables.

glal_draw_lines(self)

Draw a atom using bond lines only.

glal_draw_trace(self)

Draws trace over all polymer backbone atoms.

glal_draw_Uaxes(self)

Draw thermal axes at the given ADP probability level.

glal_draw_Uellipse(self)

Draw the ADP determined probability ellipsoid.

glal_draw_Urms(self)

Draw the ADP determined RMS displacement surface.

glal_iter_atoms(self)

Implement in a subclass to iterate over all atoms which need to be drawn.

glal_iter_atoms_filtered(self)

Iterate all atoms and yield the tuble (atom, visible_flag).

glal_iter_chains(self)

Implement in a subclass to iterate one Chain object at a time, in order. This implementation works with any implementation of glal_iter_atoms, but is very inefficent.

glal_iter_fragments(self)

Implement in a subclass to iterate one Fragment object at a time, in order. This implementation works with any implementation of glal_iter_atoms, but is very inefficent.

glal_iter_models(self)

Implement in a subclass to iterate one Model object at a time, in order. This implementation works with any implementation of glal_iter_atoms, but is very inefficent.

glal_iter_visible_atoms(self)

Iterate over all visible atoms yielding the 2-tuple (atm, position).

glal_rebuild_atom_dicts(self)

When a atom selection setting or origin changes, the atom dictionaries need to be rebuilt.

glal_update_color_value(self, value)

Configure the color_value property from the value argument.

gldl_install_draw_methods(self)

Override in children to install draw methods for a GLDrawList.
Overrides:
mmLib.Viewer.GLDrawList.gldl_install_draw_methods (inherited documentation)

gldl_iter_multidraw_self(self)

Specialized draw list invokation to recycle the draw list for symmetry related copies. Cartesian versions of the symmetry rotation and translation operators are generated by GLStructure/UnitCell classes.
Overrides:
mmLib.Viewer.GLDrawList.gldl_iter_multidraw_self

glo_install_properties(self)

Called by GLObject.__init__ to install properties.
Overrides:
mmLib.Viewer.GLDrawList.glo_install_properties (inherited documentation)

Class Variable Details

glal_res_type_color_dict

Type:
dict
Value:
{'acids': (1.0, 0.25, 0.25),
 'alchols': (1.0, 0.59999999999999998, 0.59999999999999998),
 'aliphatic': (0.5, 0.5, 0.5),
 'amides': (0.59999999999999998, 0.59999999999999998, 1.0),
 'aromatic': (0.75, 0.75, 0.75),
 'bases': (0.25, 0.25, 1.0),
 'sulfer-containing': (0.20000000000000001, 1.0, 0.20000000000000001)} 

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