Package schrodinger :: Package application :: Package mcpro :: Module modelsystemwizard :: Class _ChopCap

Class _ChopCap

           ui.widget.pmwwidget.schroPmwWrapper --+    
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_Pmw.Pmw_1_3.lib.PmwBase.MegaArchetype --+       |    
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       _Pmw.Pmw_1_3.lib.PmwBase.MegaWidget --+   |    
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               _Pmw.Pmw_1_3.lib.PmwGroup.Group --+    
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                         ui.widget.pmwwidget.Group --+
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                                                    _ChopCap

Class for drawing and managing the `Chop/Cap protein' panel

Instance Methods

[hide private]

__init__(self, master, model_sys, display, disp_opt_update)
`display' is the function to interact with the guide bar and to update the workspace.

toggle(self)
This is the function in response to the toggle between `chop' and `no chop'.

set_chop_rad(self, nonnative_residues=None)
Recolors the protein to give a rough idea which part of the protein will be chopped off.

chop_protein(self)
Runs mcpro_zmat to chop the protein.

check_for_nonnative_residues(self, ct)
Method checks for non-native residues that are part of a chain with at least two other native residues.

reset_protein(self)
Resets the `Chop/Cap' panel and the protein structure in the workspace.

initialize(self)
Resets/initializes the panel.

Inherited from ui.widget.pmwwidget.schroPmwWrapper: cleanup_components, grid, pack

Inherited from ui.widget.pmwwidget.schroPmwWrapper (private): _cleanup_component, _getDflts, _get_clean_dflts, _get_geometry_defaults, _repack_component, _retrievePmwDflts, _retrieveTkDflts, _update_placement

Inherited from _Pmw.Pmw_1_3.lib.PmwGroup.Group: collapse, expand, interior

Inherited from _Pmw.Pmw_1_3.lib.PmwBase.MegaWidget: after, after_cancel, after_idle, bbox, bell, bind, bind_all, bind_class, bindtags, clipboard_append, clipboard_clear, clipboard_get, colormodel, columnconfigure, config, deletecommand, event_add, event_delete, event_generate, event_info, focus, focus_displayof, focus_force, focus_get, focus_lastfor, focus_set, forget, getboolean, getvar, grab_current, grab_release, grab_set, grab_set_global, grab_status, grid_bbox, grid_columnconfigure, grid_configure, grid_forget, grid_info, grid_location, grid_propagate, grid_remove, grid_rowconfigure, grid_size, grid_slaves, image_names, image_types, info, keys, lift, lower, mainloop, nametowidget, option_add, option_clear, option_get, option_readfile, pack_configure, pack_forget, pack_info, pack_propagate, pack_slaves, place, place_configure, place_forget, place_info, place_slaves, propagate, quit, register, rowconfigure, selection_clear, selection_get, selection_handle, selection_own, selection_own_get, send, setvar, size, slaves, tk_bisque, tk_focusFollowsMouse, tk_focusNext, tk_focusPrev, tk_menuBar, tk_setPalette, tk_strictMotif, tkraise, unbind, unbind_all, unbind_class, update, update_idletasks, wait_variable, wait_visibility, wait_window, waitvar, winfo_atom, winfo_atomname, winfo_cells, winfo_children, winfo_class, winfo_colormapfull, winfo_containing, winfo_depth, winfo_exists, winfo_fpixels, winfo_geometry, winfo_height, winfo_id, winfo_interps, winfo_ismapped, winfo_manager, winfo_name, winfo_parent, winfo_pathname, winfo_pixels, winfo_pointerx, winfo_pointerxy, winfo_pointery, winfo_reqheight, winfo_reqwidth, winfo_rgb, winfo_rootx, winfo_rooty, winfo_screen, winfo_screencells, winfo_screendepth, winfo_screenheight, winfo_screenmmheight, winfo_screenmmwidth, winfo_screenvisual, winfo_screenwidth, winfo_server, winfo_toplevel, winfo_viewable, winfo_visual, winfo_visualid, winfo_visualsavailable, winfo_vrootheight, winfo_vrootwidth, winfo_vrootx, winfo_vrooty, winfo_width, winfo_x, winfo_y

Inherited from _Pmw.Pmw_1_3.lib.PmwBase.MegaArchetype: __getitem__, __setitem__, __str__, addoptions, cget, component, componentaliases, componentgroup, components, configure, createcomponent, createlabel, defineoptions, destroy, destroycomponent, hulldestroyed, initialiseoptions, isinitoption, options

Class Variables

[hide private]

DEFAULT_CHOP_RAD = "12"

Method Details

[hide private]

init(self, master, model_sys, display, disp_opt_update)
(Constructor)

`display' is the function to interact with the guide bar and to update the workspace. `disp_opt_update' is the function to reset the display-option panel and the workspace as well.

Overrides: _Pmw.Pmw_1_3.lib.PmwBase.MegaArchetype.__init__

toggle(self)

This is the function in response to the toggle between `chop' and `no chop'. This function will update the guide bar's state.

Overrides: _Pmw.Pmw_1_3.lib.PmwGroup.Group.toggle

set_chop_rad(self, nonnative_residues=None)

Recolors the protein to give a rough idea which part of the protein will be chopped off. Non-native residues are displayed in white if found

chop_protein(self)

Runs mcpro_zmat to chop the protein. This function will update the guide bar's state and the workspace.

check_for_nonnative_residues(self, ct)

Method checks for non-native residues that are part of a chain with at least two other native residues. Returns list of offending residue numbers if finds any, otherwise None

Class _ChopCap

__init__(self, master, model_sys, display, disp_opt_update) (Constructor)

toggle(self)

set_chop_rad(self, nonnative_residues=None)

chop_protein(self)

check_for_nonnative_residues(self, ct)

init(self, master, model_sys, display, disp_opt_update)
(Constructor)