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

source code

object --+        
         |        
  GLObject --+    
             |    
    GLDrawList --+
                 |
                GLAtomList
Known Subclasses:

OpenGL renderer for a list of atoms. Optional arguments iare: color, U, U_color.

Instance Methods [hide private]
 
__init__(self, **args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
glo_install_properties(self)
Called by GLObject.__init__ to install properties.
source code
 
gldl_install_draw_methods(self)
Override in children to install draw methods for a GLDrawList.
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glal_update_color_value(self, value)
Configure the color_value property from the value argument.
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glal_update_properties(self, updates, actions) source code
 
gldl_iter_multidraw_self(self)
Specialized draw list invokation to recycle the draw list for symmetry related copies.
source code
 
glal_iter_atoms(self)
Implement in a subclass to iterate over all atoms which need to be drawn.
source code
 
glal_iter_fragments(self)
Implement in a subclass to iterate one Fragment object at a time, in order.
source code
 
glal_iter_chains(self)
Implement in a subclass to iterate one Chain object at a time, in order.
source code
 
glal_iter_models(self)
Implement in a subclass to iterate one Model object at a time, in order.
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glal_iter_atoms_filtered(self)
Iterate all atoms and yield the tuble (atom, visible_flag).
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glal_rebuild_atom_dicts(self)
When a atom selection setting or origin changes, the atom dictionaries need to be rebuilt.
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glal_iter_visible_atoms(self)
Iterate over all visible atoms yielding the 2-tuple (atm, position).
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glal_calc_position(self, position)
Calculate a position vector with respect to the proeprty: atom_origin.
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glal_calc_color_range(self, value)
Return a RGBF 3-tuple color of a color gradient for value.
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glal_calc_color(self, atom)
Sets the open-gl color for the atom.
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glal_calc_color_label(self)
Returns the label color.
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glal_calc_color_trace(self)
Returns the trace color.
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glal_calc_color_Uaxes(self, atom)
Return the color to be used for thermal axes.
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glal_calc_color_Uellipse(self, atom)
Return the color to be used for thermal ellipse.
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glal_calc_color_Urms(self, atom)
Return the color to be used for thermal peanuts.
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glal_calc_U(self, atom)
Return the ADP U tensor for the atom
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glal_draw_labels(self)
Draws atom lables.
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glal_draw_cpk(self)
Draw a atom as a CPK sphere.
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glal_draw_Uaxes(self)
Draw thermal axes at the given ADP probability level.
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glal_draw_Uellipse(self)
Draw the ADP determined probability ellipsoid.
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glal_draw_Urms(self)
Draw the ADP determined RMS displacement surface.
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glal_draw_lines(self)
Draw a atom using bond lines only.
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glal_draw_ball_stick(self)
Draw atom with ball/stick model.
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glal_draw_cross(self, atm, pos)
Draws atom with a cross of lines.
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glal_draw_trace(self)
Draws trace over all polymer backbone atoms.
source code

Inherited from GLDrawList: gldl_draw, gldl_draw_method_compile, gldl_draw_method_delete_compiled, gldl_draw_method_delete_compiled_all_drivers, gldl_draw_method_get, gldl_draw_method_install, gldl_draw_transparent, gldl_get_glviewer, gldl_iter_multidraw_all, gldl_pop_matrix, gldl_property_color_rgbf, gldl_push_matrix, gldl_redraw, gldl_render, gldl_render_draw_methods, gldl_update_cb, glo_remove, glo_remove_child

Inherited from GLObject: glo_add_child, glo_add_property, glo_add_update_callback, glo_append_child, glo_count_descendants, glo_get_child, glo_get_child_path, glo_get_degree, glo_get_depth, glo_get_glstructure, glo_get_index_path, glo_get_lowest_common_ancestor, glo_get_parent, glo_get_parent_list, glo_get_path, glo_get_properties_id, glo_get_property_desc, glo_get_root, glo_init_properties, glo_is_descendant_of, glo_iter_children, glo_iter_preorder_traversal, glo_iter_property_desc, glo_link_child_property, glo_name, glo_prepend_child, glo_remove_update_callback, glo_set_name, glo_set_properties_id, glo_update_properties, glo_update_properties_path

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  glal_res_type_color_dict = {'acids': (1.0, 0.25, 0.25), 'alcho...

Inherited from GLDrawList: gldl_color_list

Inherited from GLObject: PropertyDefault

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, **args)
(Constructor)

source code 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

glo_install_properties(self)

source code 

Called by GLObject.__init__ to install properties.

Overrides: GLObject.glo_install_properties
(inherited documentation)

gldl_install_draw_methods(self)

source code 

Override in children to install draw methods for a GLDrawList.

Overrides: GLDrawList.gldl_install_draw_methods
(inherited documentation)

gldl_iter_multidraw_self(self)

source code 

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: GLDrawList.gldl_iter_multidraw_self

glal_iter_fragments(self)

source code 

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_chains(self)

source code 

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_models(self)

source code 

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.


Class Variable Details [hide private]

glal_res_type_color_dict

Value:
{'acids': (1.0, 0.25, 0.25),
 'alchols': (1.0, 0.6, 0.6),
 'aliphatic': (0.5, 0.5, 0.5),
 'amides': (0.6, 0.6, 1.0),
 'aromatic': (0.75, 0.75, 0.75),
 'bases': (0.25, 0.25, 1.0),
 'sulfer-containing': (0.2, 1.0, 0.2)}