is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| cmd.py (pymol-open-source-2.2.0) | : | cmd.py (pymol-open-source-2.3.0) |
|---|
| | |
| skipping to change at line 93 | | skipping to change at line 93 |
|---|
| | |
| if wizarding.session_save_wizard not in _pymol._session_save_tasks: | | if wizarding.session_save_wizard not in _pymol._session_save_tasks: |
| _pymol._session_save_tasks.append(wizarding.session_save_wizard) | | _pymol._session_save_tasks.append(wizarding.session_save_wizard) |
| | |
| # take care of some deferred initialization | | # take care of some deferred initialization |
| | |
| _pymol._view_dict_sc = Shortcut({}) | | _pymol._view_dict_sc = Shortcut({}) |
| _pymol._scene_dict_sc = Shortcut({}) | | _pymol._scene_dict_sc = Shortcut({}) |
| | |
| # | | # |
|
| if __name__=='pymol.cmd': | | if True: |
| | |
|
| import traceback | | |
| import sys | | import sys |
| | |
| # pymol2.cmd2 exposes a weak reference, this is not possible (and not | | # pymol2.cmd2 exposes a weak reference, this is not possible (and not |
| # necessary) on the module level, so we simply make a self reference. | | # necessary) on the module level, so we simply make a self reference. |
| _weakrefproxy = sys.modules[__name__] | | _weakrefproxy = sys.modules[__name__] |
| | |
|
| try: | | if True: |
| | |
| import re | | import re |
| from pymol import _cmd | | from pymol import _cmd |
| import string | | import string |
| import threading | | import threading |
| import pymol | | import pymol |
| import os | | import os |
| from . import parsing | | from . import parsing |
| import time | | import time |
| | |
| | |
| skipping to change at line 153 | | skipping to change at line 152 |
|---|
| else: | | else: |
| _expandvars = os.path.expandvars | | _expandvars = os.path.expandvars |
| | |
| def exp_path(path): | | def exp_path(path): |
| path = as_pathstr(path) | | path = as_pathstr(path) |
| return _expandvars(os.path.expanduser(path)) | | return _expandvars(os.path.expanduser(path)) |
| | |
| def as_pathstr(path): | | def as_pathstr(path): |
| # On Windows, always work with unicode file names. On Unix, | | # On Windows, always work with unicode file names. On Unix, |
| # UTF-8 byte strings seem to be fine, so keep them for now. | | # UTF-8 byte strings seem to be fine, so keep them for now. |
|
| if isinstance(path, bytes) and sys.platform == 'win32': | | if isinstance(path, bytes) and pymol.IS_WINDOWS: |
| for encoding in ('utf-8', 'mbcs'): | | for encoding in ('utf-8', 'mbcs'): |
| try: | | try: |
| return path.decode(encoding) | | return path.decode(encoding) |
| except UnicodeError: | | except UnicodeError: |
| pass | | pass |
| return path | | return path |
| | |
| #-------------------------------------------------------------------- | | #-------------------------------------------------------------------- |
| # locks and threading | | # locks and threading |
| | |
| | |
| skipping to change at line 219 | | skipping to change at line 218 |
|---|
| _load = internal._load | | _load = internal._load |
| _mpng = internal._mpng | | _mpng = internal._mpng |
| _object_update_spawn = internal._object_update_spawn | | _object_update_spawn = internal._object_update_spawn |
| _object_update_thread = internal._object_update_thread | | _object_update_thread = internal._object_update_thread |
| _png = internal._png | | _png = internal._png |
| _quit = internal._quit | | _quit = internal._quit |
| _ray_anti_spawn = internal._ray_anti_spawn | | _ray_anti_spawn = internal._ray_anti_spawn |
| _ray_hash_spawn = internal._ray_hash_spawn | | _ray_hash_spawn = internal._ray_hash_spawn |
| _ray_spawn = internal._ray_spawn | | _ray_spawn = internal._ray_spawn |
| _refresh = internal._refresh | | _refresh = internal._refresh |
|
| _sgi_stereo = internal._sgi_stereo | | |
| _special = internal._special | | _special = internal._special |
| _validate_color_sc = internal._validate_color_sc | | _validate_color_sc = internal._validate_color_sc |
| _cache_get = internal._cache_get | | _cache_get = internal._cache_get |
| _cache_set = internal._cache_set | | _cache_set = internal._cache_set |
| _cache_clear = internal._cache_clear | | _cache_clear = internal._cache_clear |
| _cache_purge = internal._cache_purge | | _cache_purge = internal._cache_purge |
| _cache_mark = internal._cache_mark | | _cache_mark = internal._cache_mark |
| _sdof = internal._sdof | | _sdof = internal._sdof |
| | |
| # when adding, remember to also edit cmd2.py | | # when adding, remember to also edit cmd2.py |
| | |
| skipping to change at line 424 | | skipping to change at line 422 |
|---|
| | |
| # Table for argument autocompletion | | # Table for argument autocompletion |
| | |
| from . import completing | | from . import completing |
| | |
| auto_arg = completing.get_auto_arg_list() | | auto_arg = completing.get_auto_arg_list() |
| | |
| color_sc = None | | color_sc = None |
| | |
| raw_image_callback = None | | raw_image_callback = None |
|
| | | |
| except: | | |
| print("Error: unable to initalize the pymol.cmd module") | | |
| traceback.print_exc() | | |
| sys.exit(0) | | |
| | |
| else: | | |
| from pymol.cmd import * | | |
| | | |
| End of changes. 6 change blocks. |
|---|
| 5 lines changed or deleted | | 3 lines changed or added |
|---|
"Fossies" - the Fresh Open Source Software Archive 