Exemple #1
0
    def __init__(self, _pymol, _COb):

        # store parent
        
        self._pymol = _pymol

        # store C object for easy access
    
        self._COb = _COb
        
        # private data
    
        self.color_sc = None
        self.reaper = None
        
        # CONSTANTS (pymol/constants.py)

        self.DEFAULT_ERROR = global_cmd.DEFAULT_ERROR
        self.DEFAULT_SUCCESS = global_cmd.DEFAULT_SUCCESS
        self.QuietException = global_cmd.QuietException
        self.Shortcut = global_cmd.Shortcut
        self._load2str = global_cmd._load2str
        self.boolean_dict = global_cmd.boolean_dict
        self.boolean_sc = global_cmd.boolean_sc
        self.fb_action = global_cmd.fb_action
        self.fb_mask = global_cmd.fb_mask
        self.fb_module = global_cmd.fb_module
        self.fb_debug = global_cmd.fb_debug # this cannot be right...
        self.file_ext_re = global_cmd.file_ext_re
        self.gz_ext_re = global_cmd.gz_ext_re
        self.loadable = global_cmd.loadable
        self.nt_hidden_path_re = global_cmd.nt_hidden_path_re
        self.palette_dict = global_cmd.palette_dict
        self.palette_sc = global_cmd.palette_sc
        self.parsing = global_cmd.parsing
        self.quote_alpha_list_re = global_cmd.quote_alpha_list_re
        self.repres = global_cmd.repres
        self.repres_sc = global_cmd.repres_sc
        self.safe_alpha_list_eval = global_cmd.safe_alpha_list_eval
        self.safe_list_eval = global_cmd.safe_list_eval
        self.safe_oname_re = global_cmd.safe_oname_re
        self.sanitize_alpha_list_re = global_cmd.sanitize_alpha_list_re
        self.sanitize_list_re = global_cmd.sanitize_list_re
        self.space_sc = global_cmd.space_sc
        self.stereo_dict = global_cmd.stereo_dict
        self.stereo_sc = global_cmd.stereo_sc
        self.toggle_dict = global_cmd.toggle_dict
        self.toggle_sc = global_cmd.toggle_sc
        self.window_dict = global_cmd.window_dict
        self.window_sc = global_cmd.window_sc

        
        # GLOBAL FUNCTIONS

        self.exp_path = global_cmd.exp_path

        # deferred initiailization
        
        global_cmd._deferred_init_pymol_internals(_pymol)
        
        # PRIVATE FUNCTIONS (requiring '_self' as a keyword argument)
        
        # locking.py

        self.reaper = None

        if 1:
            # use own locks (for performance)
            self.lock_api = _pymol.lock_api
            self.lock_api_c = _pymol.lock_api_c
            self.lock_api_data = _pymol.lock_api_data            
            self.lock_api_glut = _pymol.lock_api_glut
            self.lock_api_status = _pymol.lock_api_status
        else:
            # use global locks (for debugging)
            self.lock_api = global_cmd._pymol.lock_api
            self.lock_api_c = global_cmd._pymol.lock_api_c
            self.lock_api_data = global_cmd._pymol.lock_api_data            
            self.lock_api_glut = global_cmd._pymol.lock_api_glut
            self.lock_api_status = global_cmd._pymol.lock_api_status

        self.lock_api_allow_flush = 1

        self.lock_c = global_cmd.lock_c
        self.unlock_c = global_cmd.unlock_c
        self.lock_data = global_cmd.lock_data
        self.unlock_data = global_cmd.unlock_data
        self.lock_status_attempt = global_cmd.lock_status_attempt
        self.lock_status = global_cmd.lock_status
        self.unlock_status = global_cmd.unlock_status
        self.lock_glut = global_cmd.lock_glut
        self.unlock_glut = global_cmd.unlock_glut
        self.lock_without_glut = global_cmd.lock_without_glut
        self.lock = global_cmd.lock
        self.lock_attempt = global_cmd.lock_attempt
        self.unlock = global_cmd.unlock
        self.is_glut_thread = global_cmd.is_glut_thread
        self.setup_global_locks = global_cmd.setup_global_locks
        self.interrupt = global_cmd.interrupt
        self.block_flush = global_cmd.block_flush
        self.unblock_flush = global_cmd.unblock_flush        
        
        # pymol/checking.py

        self._raising = global_cmd._raising
        self.is_dict = global_cmd.is_dict
        self.is_error = global_cmd.is_error
        self.is_list = global_cmd.is_list
        self.is_ok = global_cmd.is_ok
        self.is_sequence = global_cmd.is_sequence
        self.is_string = global_cmd.is_string
        self.is_tuple = global_cmd.is_tuple

        # from pymol/feedingback.py

        self._feedback = global_cmd._feedback
        
        # from pymol/internal.py
        
        self._adjust_coord = global_cmd._adjust_coord
        self._coordset_update_spawn = global_cmd._coordset_update_spawn
        self._coordset_update_thread = global_cmd._coordset_update_thread
        self._copy_image = global_cmd._copy_image
        self._do = global_cmd._do
        self._dump_floats = global_cmd._dump_floats
        self._dump_ufloats = global_cmd._dump_ufloats
        self._fake_drag = global_cmd._fake_drag
        self._get_color_sc = global_cmd._get_color_sc
        self._get_feedback = global_cmd._get_feedback
        self._interpret_color = global_cmd._interpret_color
        self._interpret_color = global_cmd._interpret_color
        self._invalidate_color_sc = global_cmd._invalidate_color_sc
        self._invalidate_color_sc = global_cmd._invalidate_color_sc
        self._load = global_cmd._load
        self._mpng = global_cmd._mpng
        self._object_update_spawn = global_cmd._object_update_spawn
        self._object_update_thread = global_cmd._object_update_thread
        self._png = global_cmd._png
        self._quit = global_cmd._quit
        self._ray_anti_spawn = global_cmd._ray_anti_spawn
        self._ray_hash_spawn = global_cmd._ray_hash_spawn
        self._ray_spawn = global_cmd._ray_spawn
        self._refresh = global_cmd._refresh
        self._sgi_stereo = global_cmd._sgi_stereo
        self._validate_color_sc = global_cmd._validate_color_sc
        self._cache_set = global_cmd._cache_set
        self._cache_get = global_cmd._cache_get
        self._cache_clear = global_cmd._cache_clear
        self._cache_mark = global_cmd._cache_mark
        self._cache_purge = global_cmd._cache_purge

        # now we create the command langauge

        from pymol import keywords

        self.keyword = keywords.get_command_keywords()
        self.kw_list = self.keyword.keys()

        keywords.fix_list(self.kw_list)
        self.kwhash = self.Shortcut(self.kw_list)
        keywords.fix_dict(self.keyword)

        self.controlling = pymol.controlling
        self.completing = pymol.completing
        self.controlling = pymol.controlling
        self.editing = pymol.editing
        self.exporting = pymol.exporting
        self.moving = pymol.moving
        self.creating = pymol.creating
        self.viewing = pymol.viewing
        self.setting = pymol.setting
        self.commanding = pymol.commanding

        self.help_only = keywords.get_help_only_keywords()
        self.help_sc = self.Shortcut(self.keyword.keys()+self.help_only.keys())

        
        self.selection_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('public')+['all'])
        self.object_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('objects'))
        self.map_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(gnot('object:map'))
        self.contour_sc =  lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(
            gnot('object:mesh')+gnot('object:surface'))
        
        self.fb_action_sc = pymol.feedingback.fb_action_sc
        self.fb_module_sc = pymol.feedingback.fb_module_sc
        self.fb_mask_sc = pymol.feedingback.fb_mask_sc
        
        self.auto_arg = pymol.completing.get_auto_arg_list(self)
        self.color_sc = None

        # keyboard configuration
                
        from pymol import keyboard
        
        self.special = keyboard.get_special(self)

        self.shft_special = keyboard.get_shft_special(self)        
        self.alt_special = keyboard.get_alt_special(self)        
        self.ctrl_special = keyboard.get_ctrl_special(self)
        self.ctsh_special = keyboard.get_ctsh_special(self)

        self.ctrl = keyboard.get_ctrl(self)        
        self.alt = keyboard.get_alt(self)
Exemple #2
0
    def __init__(self, _pymol, _COb):
        global cmd
        cmd = self
        # store parent

        self._pymol = _pymol

        # store C object for easy access

        self._COb = _COb

        # private data

        self.color_sc = None
        self.reaper = None

        # CONSTANTS (pymol/constants.py)

        self.fb_debug = global_cmd.fb_debug  # this cannot be right...

        # deferred initiailization

        global_cmd._deferred_init_pymol_internals(_pymol)

        # PRIVATE FUNCTIONS (requiring '_self' as a keyword argument)

        # locking.py

        self.reaper = None

        if 1:
            # use own locks (for performance)
            self.lock_api = _pymol.lock_api
            self.lock_api_c = _pymol.lock_api_c
            self.lock_api_data = _pymol.lock_api_data
            self.lock_api_glut = _pymol.lock_api_glut
            self.lock_api_status = _pymol.lock_api_status
        else:
            # use global locks (for debugging)
            self.lock_api = global_cmd._pymol.lock_api
            self.lock_api_c = global_cmd._pymol.lock_api_c
            self.lock_api_data = global_cmd._pymol.lock_api_data
            self.lock_api_glut = global_cmd._pymol.lock_api_glut
            self.lock_api_status = global_cmd._pymol.lock_api_status

        self.lock_api_allow_flush = 1

        # now we create the command langauge

        from pymol import keywords

        self.keyword = keywords.get_command_keywords()
        self.kw_list = self.keyword.keys()

        keywords.fix_list(self.kw_list)
        self.kwhash = self.Shortcut(self.kw_list)
        keywords.fix_dict(self.keyword)

        self.help_only = keywords.get_help_only_keywords()
        self.help_sc = self.Shortcut(self.keyword.keys() +
                                     self.help_only.keys())

        self.selection_sc = lambda sc=self.Shortcut, gn=self.get_names: sc(
            gn('public') + ['all'])
        self.object_sc = lambda sc=self.Shortcut, gn=self.get_names: sc(
            gn('objects'))
        self.map_sc = lambda sc=self.Shortcut, gnot=self.get_names_of_type: sc(
            gnot('object:map'))
        self.contour_sc = lambda sc=self.Shortcut, gnot=self.get_names_of_type: sc(
            gnot('object:mesh') + gnot('object:surface'))
        self.group_sc = lambda sc=self.Shortcut, gnot=self.get_names_of_type: sc(
            gnot('object:group'))

        self.fb_action_sc = pymol.feedingback.fb_action_sc
        self.fb_module_sc = pymol.feedingback.fb_module_sc
        self.fb_mask_sc = pymol.feedingback.fb_mask_sc

        self.auto_arg = pymol.completing.get_auto_arg_list(self)
        self.color_sc = None

        # keyboard configuration

        from pymol import keyboard

        self.special = keyboard.get_special(self)

        self.shft_special = keyboard.get_shft_special(self)
        self.alt_special = keyboard.get_alt_special(self)
        self.ctrl_special = keyboard.get_ctrl_special(self)
        self.ctsh_special = keyboard.get_ctsh_special(self)

        self.ctrl = keyboard.get_ctrl(self)
        self.alt = keyboard.get_alt(self)
Exemple #3
0
    def __init__(self, _pymol, _COb):
        global cmd
        cmd = self
        # store parent
        
        self._pymol = _pymol

        # store C object for easy access
    
        self._COb = _COb
        
        # private data
    
        self.color_sc = None
        self.reaper = None
        
        # CONSTANTS (pymol/constants.py)

        self.fb_debug = global_cmd.fb_debug # this cannot be right...
        
        # deferred initiailization
        
        global_cmd._deferred_init_pymol_internals(_pymol)
        
        # PRIVATE FUNCTIONS (requiring '_self' as a keyword argument)
        
        # locking.py

        self.reaper = None

        if 1:
            # use own locks (for performance)
            self.lock_api = _pymol.lock_api
            self.lock_api_c = _pymol.lock_api_c
            self.lock_api_data = _pymol.lock_api_data            
            self.lock_api_glut = _pymol.lock_api_glut
            self.lock_api_status = _pymol.lock_api_status
        else:
            # use global locks (for debugging)
            self.lock_api = global_cmd._pymol.lock_api
            self.lock_api_c = global_cmd._pymol.lock_api_c
            self.lock_api_data = global_cmd._pymol.lock_api_data            
            self.lock_api_glut = global_cmd._pymol.lock_api_glut
            self.lock_api_status = global_cmd._pymol.lock_api_status

        self.lock_api_allow_flush = 1

        # now we create the command langauge

        from pymol import keywords

        self.keyword = keywords.get_command_keywords()
        self.kw_list = self.keyword.keys()

        keywords.fix_list(self.kw_list)
        self.kwhash = self.Shortcut(self.kw_list)
        keywords.fix_dict(self.keyword)

        self.help_only = keywords.get_help_only_keywords()
        self.help_sc = self.Shortcut(self.keyword.keys()+self.help_only.keys())

        
        self.selection_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('public')+['all'])
        self.object_sc = lambda sc=self.Shortcut,gn=self.get_names:sc(gn('objects'))
        self.map_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(gnot('object:map'))
        self.contour_sc =  lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(gnot('object:mesh')+gnot('object:surface'))
        self.group_sc = lambda sc=self.Shortcut,gnot=self.get_names_of_type:sc(gnot('object:group'))

        self.fb_action_sc = pymol.feedingback.fb_action_sc
        self.fb_module_sc = pymol.feedingback.fb_module_sc
        self.fb_mask_sc = pymol.feedingback.fb_mask_sc
        
        self.auto_arg = pymol.completing.get_auto_arg_list(self)
        self.color_sc = None

        # keyboard configuration
                
        from pymol import keyboard
        
        self.special = keyboard.get_special(self)

        self.shft_special = keyboard.get_shft_special(self)        
        self.alt_special = keyboard.get_alt_special(self)        
        self.ctrl_special = keyboard.get_ctrl_special(self)
        self.ctsh_special = keyboard.get_ctsh_special(self)

        self.ctrl = keyboard.get_ctrl(self)        
        self.alt = keyboard.get_alt(self)
Exemple #4
0
    def __init__(self, _pymol, _COb):

        # store parent

        self._pymol = _pymol

        # store C object for easy access

        self._COb = _COb

        # private data

        self.color_sc = None
        self.reaper = None

        # CONSTANTS (pymol/constants.py)

        self.DEFAULT_ERROR = global_cmd.DEFAULT_ERROR
        self.DEFAULT_SUCCESS = global_cmd.DEFAULT_SUCCESS
        self.QuietException = global_cmd.QuietException
        self.Shortcut = global_cmd.Shortcut
        self._load2str = global_cmd._load2str
        self.boolean_dict = global_cmd.boolean_dict
        self.boolean_sc = global_cmd.boolean_sc
        self.fb_action = global_cmd.fb_action
        self.fb_mask = global_cmd.fb_mask
        self.fb_module = global_cmd.fb_module
        self.fb_debug = global_cmd.fb_debug  # this cannot be right...
        self.file_ext_re = global_cmd.file_ext_re
        self.gz_ext_re = global_cmd.gz_ext_re
        self.loadable = global_cmd.loadable
        self.nt_hidden_path_re = global_cmd.nt_hidden_path_re
        self.palette_dict = global_cmd.palette_dict
        self.palette_sc = global_cmd.palette_sc
        self.parsing = global_cmd.parsing
        self.quote_alpha_list_re = global_cmd.quote_alpha_list_re
        self.repres = global_cmd.repres
        self.repres_sc = global_cmd.repres_sc
        self.safe_alpha_list_eval = global_cmd.safe_alpha_list_eval
        self.safe_list_eval = global_cmd.safe_list_eval
        self.safe_oname_re = global_cmd.safe_oname_re
        self.sanitize_alpha_list_re = global_cmd.sanitize_alpha_list_re
        self.sanitize_list_re = global_cmd.sanitize_list_re
        self.space_sc = global_cmd.space_sc
        self.stereo_dict = global_cmd.stereo_dict
        self.stereo_sc = global_cmd.stereo_sc
        self.toggle_dict = global_cmd.toggle_dict
        self.toggle_sc = global_cmd.toggle_sc
        self.window_dict = global_cmd.window_dict
        self.window_sc = global_cmd.window_sc

        # GLOBAL FUNCTIONS

        self.exp_path = global_cmd.exp_path

        # deferred initiailization

        global_cmd._deferred_init_pymol_internals(_pymol)

        # PRIVATE FUNCTIONS (requiring '_self' as a keyword argument)

        # locking.py

        self.reaper = None

        if 1:
            # use own locks (for performance)
            self.lock_api = _pymol.lock_api
            self.lock_api_c = _pymol.lock_api_c
            self.lock_api_data = _pymol.lock_api_data
            self.lock_api_glut = _pymol.lock_api_glut
            self.lock_api_status = _pymol.lock_api_status
        else:
            # use global locks (for debugging)
            self.lock_api = global_cmd._pymol.lock_api
            self.lock_api_c = global_cmd._pymol.lock_api_c
            self.lock_api_data = global_cmd._pymol.lock_api_data
            self.lock_api_glut = global_cmd._pymol.lock_api_glut
            self.lock_api_status = global_cmd._pymol.lock_api_status

        self.lock_api_allow_flush = 1

        self.lock_c = global_cmd.lock_c
        self.unlock_c = global_cmd.unlock_c
        self.lock_data = global_cmd.lock_data
        self.unlock_data = global_cmd.unlock_data
        self.lock_status_attempt = global_cmd.lock_status_attempt
        self.lock_status = global_cmd.lock_status
        self.unlock_status = global_cmd.unlock_status
        self.lock_glut = global_cmd.lock_glut
        self.unlock_glut = global_cmd.unlock_glut
        self.lock_without_glut = global_cmd.lock_without_glut
        self.lock = global_cmd.lock
        self.lock_attempt = global_cmd.lock_attempt
        self.unlock = global_cmd.unlock
        self.is_glut_thread = global_cmd.is_glut_thread
        self.setup_global_locks = global_cmd.setup_global_locks
        self.interrupt = global_cmd.interrupt
        self.block_flush = global_cmd.block_flush
        self.unblock_flush = global_cmd.unblock_flush

        # pymol/checking.py

        self._raising = global_cmd._raising
        self.is_dict = global_cmd.is_dict
        self.is_error = global_cmd.is_error
        self.is_list = global_cmd.is_list
        self.is_ok = global_cmd.is_ok
        self.is_sequence = global_cmd.is_sequence
        self.is_string = global_cmd.is_string
        self.is_tuple = global_cmd.is_tuple

        # from pymol/feedingback.py

        self._feedback = global_cmd._feedback

        # from pymol/internal.py

        self._adjust_coord = global_cmd._adjust_coord
        self._coordset_update_spawn = global_cmd._coordset_update_spawn
        self._coordset_update_thread = global_cmd._coordset_update_thread
        self._copy_image = global_cmd._copy_image
        self._do = global_cmd._do
        self._dump_floats = global_cmd._dump_floats
        self._dump_ufloats = global_cmd._dump_ufloats
        self._fake_drag = global_cmd._fake_drag
        self._get_color_sc = global_cmd._get_color_sc
        self._get_feedback = global_cmd._get_feedback
        self._interpret_color = global_cmd._interpret_color
        self._interpret_color = global_cmd._interpret_color
        self._invalidate_color_sc = global_cmd._invalidate_color_sc
        self._invalidate_color_sc = global_cmd._invalidate_color_sc
        self._load = global_cmd._load
        self._mpng = global_cmd._mpng
        self._object_update_spawn = global_cmd._object_update_spawn
        self._object_update_thread = global_cmd._object_update_thread
        self._png = global_cmd._png
        self._quit = global_cmd._quit
        self._ray_anti_spawn = global_cmd._ray_anti_spawn
        self._ray_hash_spawn = global_cmd._ray_hash_spawn
        self._ray_spawn = global_cmd._ray_spawn
        self._refresh = global_cmd._refresh
        self._sgi_stereo = global_cmd._sgi_stereo
        self._validate_color_sc = global_cmd._validate_color_sc
        self._cache_set = global_cmd._cache_set
        self._cache_get = global_cmd._cache_get
        self._cache_clear = global_cmd._cache_clear
        self._cache_mark = global_cmd._cache_mark
        self._cache_purge = global_cmd._cache_purge

        # now we create the command langauge

        from pymol import keywords

        self.keyword = keywords.get_command_keywords()
        self.kw_list = self.keyword.keys()

        keywords.fix_list(self.kw_list)
        self.kwhash = self.Shortcut(self.kw_list)
        keywords.fix_dict(self.keyword)

        self.controlling = pymol.controlling
        self.completing = pymol.completing
        self.controlling = pymol.controlling
        self.editing = pymol.editing
        self.exporting = pymol.exporting
        self.moving = pymol.moving
        self.creating = pymol.creating
        self.viewing = pymol.viewing
        self.setting = pymol.setting
        self.commanding = pymol.commanding

        self.help_only = keywords.get_help_only_keywords()
        self.help_sc = self.Shortcut(self.keyword.keys() +
                                     self.help_only.keys())

        self.selection_sc = lambda sc=self.Shortcut, gn=self.get_names: sc(
            gn('public') + ['all'])
        self.object_sc = lambda sc=self.Shortcut, gn=self.get_names: sc(
            gn('objects'))
        self.map_sc = lambda sc=self.Shortcut, gnot=self.get_names_of_type: sc(
            gnot('object:map'))
        self.contour_sc = lambda sc=self.Shortcut, gnot=self.get_names_of_type: sc(
            gnot('object:mesh') + gnot('object:surface'))

        self.fb_action_sc = pymol.feedingback.fb_action_sc
        self.fb_module_sc = pymol.feedingback.fb_module_sc
        self.fb_mask_sc = pymol.feedingback.fb_mask_sc

        self.auto_arg = pymol.completing.get_auto_arg_list(self)
        self.color_sc = None

        # keyboard configuration

        from pymol import keyboard

        self.special = keyboard.get_special(self)

        self.shft_special = keyboard.get_shft_special(self)
        self.alt_special = keyboard.get_alt_special(self)
        self.ctrl_special = keyboard.get_ctrl_special(self)
        self.ctsh_special = keyboard.get_ctsh_special(self)

        self.ctrl = keyboard.get_ctrl(self)
        self.alt = keyboard.get_alt(self)