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.
| externing.py (pymol-v1.8.6.0.tar.bz2) | : | externing.py (pymol-v2.1.0.tar.bz2) |
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| | |
| skipping to change at line 32 | | skipping to change at line 32 |
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| from . import parsing | | from . import parsing |
| import threading | | import threading |
| cmd = __import__("sys").modules["pymol.cmd"] | | cmd = __import__("sys").modules["pymol.cmd"] |
| import traceback | | import traceback |
| | |
| from glob import glob | | from glob import glob |
| from .cmd import _cmd,lock,unlock,Shortcut,QuietException, \ | | from .cmd import _cmd,lock,unlock,Shortcut,QuietException, \ |
| _feedback,fb_module,fb_mask, exp_path, \ | | _feedback,fb_module,fb_mask, exp_path, \ |
| DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error | | DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error |
| | |
|
| | try: |
| | from os import getcwdu |
| | except ImportError: |
| | from os import getcwd as getcwdu |
| | |
| def cd(dir="~",complain=1,quiet=1): | | def cd(dir="~",complain=1,quiet=1): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| "cd" changes the current working directory. | | "cd" changes the current working directory. |
| | |
| USAGE | | USAGE |
| | |
| cd <path> | | cd <path> |
| | |
| SEE ALSO | | SEE ALSO |
| | |
| pwd, ls, system | | pwd, ls, system |
| ''' | | ''' |
| dir = exp_path(dir) | | dir = exp_path(dir) |
| try: | | try: |
| os.chdir(dir) # raises on error | | os.chdir(dir) # raises on error |
| if not quiet: | | if not quiet: |
|
| print(" cd: now in %s"%os.getcwd()) | | print(" cd: now in %s" % getcwdu()) |
| except: | | except: |
| if complain: | | if complain: |
| traceback.print_exc() | | traceback.print_exc() |
| return DEFAULT_SUCCESS | | return DEFAULT_SUCCESS |
| | |
| def pwd(): | | def pwd(): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| Print current working directory. | | Print current working directory. |
| | |
| USAGE | | USAGE |
| | |
| pwd | | pwd |
| | |
| SEE ALSO | | SEE ALSO |
| | |
| cd, ls, system | | cd, ls, system |
| ''' | | ''' |
|
| print(os.getcwd()) | | print(getcwdu()) |
| return DEFAULT_SUCCESS | | return DEFAULT_SUCCESS |
| | |
| def ls(pattern=None): | | def ls(pattern=None): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| List contents of the current working directory. | | List contents of the current working directory. |
| | |
| USAGE | | USAGE |
| | |
| | |
| skipping to change at line 94 | | skipping to change at line 99 |
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| EXAMPLES | | EXAMPLES |
| | |
| ls | | ls |
| ls *.pml | | ls *.pml |
| | |
| SEE ALSO | | SEE ALSO |
| | |
| cd, pwd, system | | cd, pwd, system |
| ''' | | ''' |
| if pattern==None: | | if pattern==None: |
|
| pattern = "*" | | pattern = u"*" |
| else: | | else: |
| pattern = exp_path(pattern) | | pattern = exp_path(pattern) |
| if '*' not in pattern: | | if '*' not in pattern: |
| lst = glob(os.path.join(pattern, '*')) | | lst = glob(os.path.join(pattern, '*')) |
| else: | | else: |
| lst = [] | | lst = [] |
| if not len(lst): | | if not len(lst): |
| lst = glob(pattern) | | lst = glob(pattern) |
| if len(lst): | | if len(lst): |
| lst.sort() | | lst.sort() |
| lst = parsing.list_to_str_list(lst) | | lst = parsing.list_to_str_list(lst) |
| for a in lst: | | for a in lst: |
| print(a) | | print(a) |
| else: | | else: |
| print(" ls: Nothing found. Is that a valid path?") | | print(" ls: Nothing found. Is that a valid path?") |
| return DEFAULT_SUCCESS | | return DEFAULT_SUCCESS |
| | |
|
| def system(command,async=0,_self=cmd): | | def system(command, async_=0, _self=cmd, **kwargs): |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| "system" executes a command in a subshell under Unix or Windows. | | "system" executes a command in a subshell under Unix or Windows. |
| | |
| USAGE | | USAGE |
| | |
| system command | | system command |
| | |
| PYMOL API | | PYMOL API |
| | |
| skipping to change at line 139 | | skipping to change at line 144 |
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| | |
| if async is 0 (default), then the result code from "system" is returned in r | | if async is 0 (default), then the result code from "system" is returned in r |
| | |
| if async is 1, then the command is run in a separate thread whose object is | | if async is 1, then the command is run in a separate thread whose object is |
| returned | | returned |
| | |
| SEE ALSO | | SEE ALSO |
| | |
| ls, cd, pwd | | ls, cd, pwd |
| ''' | | ''' |
|
| | async_ = int(kwargs.pop('async', async_)) |
| | |
| | if kwargs: |
| | raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs)) |
| | |
| r = None | | r = None |
|
| if async: | | if async_: |
| r = threading.Thread(target=_cmd.system,args=(str(command),1)) | | r = threading.Thread(target=_cmd.system,args=(str(command),1)) |
| r.start() | | r.start() |
| else: | | else: |
| r = _cmd.system(_self._COb,str(command),0) | | r = _cmd.system(_self._COb,str(command),0) |
| return r # special meaning | | return r # special meaning |
| | |
| def paste(_self=cmd): # INTERNAL | | def paste(_self=cmd): # INTERNAL |
| r=DEFAULT_SUCCESS | | r=DEFAULT_SUCCESS |
| lst = [] | | lst = [] |
| if hasattr(pymol,"machine_get_clipboard"): | | if hasattr(pymol,"machine_get_clipboard"): |
| | | |
| End of changes. 7 change blocks. |
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| 5 lines changed or deleted | | 15 lines changed or added |
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