mmLib.Viewer.GLAtomList

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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