385 lines
13 KiB
Python
385 lines
13 KiB
Python
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#A* -------------------------------------------------------------------
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#B* This file contains source code for the PyMOL computer program
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#C* Copyright (c) Schrodinger, LLC.
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#D* -------------------------------------------------------------------
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#E* It is unlawful to modify or remove this copyright notice.
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#F* -------------------------------------------------------------------
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#G* Please see the accompanying LICENSE file for further information.
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#H* -------------------------------------------------------------------
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#I* Additional authors of this source file include:
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#-*
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#-*
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#-*
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#Z* -------------------------------------------------------------------
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# cmd.py
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# Python interface module for PyMol
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#
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# **This is the only module which should be/need be imported by
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# ** PyMol API Based Programs
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# NOTE: Output tweaking via the "quiet" parameter of API functions.
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#
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# Many PyMOL API functions have a "quiet" parameter which is used to
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# customize output depending on when and where the routine was called.
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#
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# As defined, quiet should be 1. Called from an external module, output
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# to the console should be minimal.
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#
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# However, when a command is run through the parser (often manually) the
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# user expects a little more feedback. The parser will automatically
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# set "quiet" to zero
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#
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# In rare cases, certain nonserious error or warning output should
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# also be suppressed. Set "quiet" to 2 for this behavior.
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def _deferred_init_pymol_internals(_pymol):
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# set up some global session tasks
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if viewing.session_restore_views not in _pymol._session_restore_tasks:
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_pymol._session_restore_tasks.append(viewing.session_restore_views)
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if viewing.session_save_views not in _pymol._session_save_tasks:
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_pymol._session_save_tasks.append(viewing.session_save_views)
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if viewing.session_restore_scenes not in _pymol._session_restore_tasks:
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_pymol._session_restore_tasks.append(viewing.session_restore_scenes)
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if wizarding.session_restore_wizard not in _pymol._session_restore_tasks:
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_pymol._session_restore_tasks.append(wizarding.session_restore_wizard)
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if wizarding.session_save_wizard not in _pymol._session_save_tasks:
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_pymol._session_save_tasks.append(wizarding.session_save_wizard)
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# take care of some deferred initialization
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_pymol._view_dict_sc = Shortcut({})
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#
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if True:
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import sys
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# pymol2.cmd2 exposes a weak reference, this is not possible (and not
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# necessary) on the module level, so we simply make a self reference.
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_weakrefproxy = sys.modules[__name__]
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if True:
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import re
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from pymol import _cmd
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import string
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import threading
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import pymol
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import os
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from . import parsing
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import time
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_pymol = pymol
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from .shortcut import Shortcut
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from chempy import io
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#######################################################################
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# symbols for early export
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#######################################################################
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from .constants import *
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from .constants import _load2str
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fb_debug = sys.stderr # can redirect python debugging output elsewhere if desred...
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#--------------------------------------------------------------------
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# convenient type and result checking
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from .checking import *
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from .checking import _raising
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#-------------------------------------------------------------------
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# path expansion, including our fixes for Win32
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def _nt_expandvars(path): # allow for //share/folder$/file
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path = nt_hidden_path_re.sub(r"$$\\",path)
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return os.path.expandvars(path)
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if "nt" in sys.builtin_module_names:
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_expandvars = _nt_expandvars
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else:
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_expandvars = os.path.expandvars
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def exp_path(path):
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path = as_pathstr(path)
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return _expandvars(os.path.expanduser(path))
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def as_pathstr(path):
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# On Windows, always work with unicode file names. On Unix,
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# UTF-8 byte strings seem to be fine, so keep them for now.
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if isinstance(path, bytes) and pymol.IS_WINDOWS:
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for encoding in ('utf-8', 'mbcs'):
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try:
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return path.decode(encoding)
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except UnicodeError:
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pass
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return path
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#--------------------------------------------------------------------
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# locks and threading
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reaper = None
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# the following locks are used by both C and Python to insure that no more than
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# one active thread enters PyMOL at a given time.
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lock_api = pymol.lock_api
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lock_api_status = pymol.lock_api_status
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lock_api_glut = pymol.lock_api_glut
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lock_api_data = pymol.lock_api_data
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lock_api_allow_flush = 1
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from .locking import *
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lockcm = LockCM()
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#--------------------------------------------------------------------
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# status monitoring
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from .monitoring import *
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#--------------------------------------------------------------------
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# Feedback
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from .feedingback import *
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from .feedingback import _feedback
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#--------------------------------------------------------------------
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# internal API routines
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from . import internal
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_alt = internal._alt
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_coordset_update_spawn = internal._coordset_update_spawn
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_coordset_update_thread = internal._coordset_update_thread
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_copy_image = internal._copy_image
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_call_in_gui_thread = lambda func: func()
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_call_with_opengl_context = _call_in_gui_thread
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_ctrl = internal._ctrl
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_ctsh = internal._ctsh
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_do = internal._do
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_dump_floats = internal._dump_floats
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_dump_ufloats = internal._dump_ufloats
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_fake_drag = internal._fake_drag
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_get_color_sc = internal._get_color_sc
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_get_feedback = internal._get_feedback
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_interpret_color = internal._interpret_color
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_invalidate_color_sc = internal._invalidate_color_sc
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_mpng = internal._mpng
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_object_update_spawn = internal._object_update_spawn
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_object_update_thread = internal._object_update_thread
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_quit = internal._quit
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_ray_anti_spawn = internal._ray_anti_spawn
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_ray_hash_spawn = internal._ray_hash_spawn
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_ray_spawn = internal._ray_spawn
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_refresh = internal._refresh
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_special = internal._special
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_validate_color_sc = internal._validate_color_sc
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_cache_get = internal._cache_get
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_cache_set = internal._cache_set
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_cache_clear = internal._cache_clear
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_cache_purge = internal._cache_purge
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_cache_mark = internal._cache_mark
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_sdof = internal._sdof
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#######################################################################
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# now import modules which depend on the above
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#######################################################################
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from . import editor
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#######################################################################
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# cmd module functions...
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#######################################################################
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# for extending the language
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from .commanding import declare_command, extend, extendaa, alias
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# for documentation etc
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from .helping import python_help
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def write_html_ref(file):
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'''Write the PyMOL Command Reference to an HTML file'''
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f=open(file,'w')
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kees = [a for a in keywords.get_command_keywords()
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if not a.startswith('_') and keyword[a][0] != python_help]
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kees.sort()
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title = 'PyMOL Command Reference'
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f.write('''<html>
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<head>
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<title>%s</title>
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<style type='text/css'>
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body, p, h1, h2 {
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font-family: sans-serif;
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}
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p.api {
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font:small monospace;
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color:#999;
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}
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pre.example {
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background-color: #ccc;
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padding: 5px;
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}
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li {
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display: block;
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width: 10em;
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float: left;
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}
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</style>
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</head>
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<body>
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<h1>%s</h1>
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<p>This is the list of all PyMOL commands which can be used in the PyMOL
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command line and in PML scripts. The command descriptions found in this
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file can also be printed to the PyMOL text buffer with the
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<a href="#help">help</a> command. Example:</p>
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<pre class="example">PyMOL>help color
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...</pre>
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<p>The list of arguments for a command (the "usage") can be queried on
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the command line with a questionmark. Example:</p>
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<pre class="example">PyMOL>color ?
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Usage: color color [, selection [, quiet [, flags ]]]</pre>
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<p>The square brackets ("[" and "]") indicate optional arguments and are
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not part of the syntax.</p>
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<p>If the PyMOL command interpreter doesn't understand some input, it passes
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it to the Python interpreter. This means that single-line Python expressions
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can be put into PML scripts or typed into the command line. Prefixing a line
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with a slash (/) forces the interpreter to pass it to Python. See also the
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<a href="#python">python</a> command to input multi-line Python scripts.</p>
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<p>This file can be generated on the PyMOL command line:</p>
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<pre class="example">PyMOL>cmd.write_html_ref('pymol-command-ref.html')</pre>
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<hr size=1>
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<ul>
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''' % (title, title))
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for a in kees:
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f.write("<li><a href='#%s'>%s</a></li>" % (a, a))
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f.write('</ul><br style="clear: both">')
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def make_see_also_link(m):
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w = m.group()
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if w in kees:
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return "<a href='#%s'>%s</a>" % (w, w)
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return w
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for a in kees:
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func = keyword[a][0]
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doc = (getattr(func, '__doc__') or 'UNDOCUMENTED').strip(). \
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replace("<", "<"). \
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replace(">", ">").splitlines()
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# attemt to do some HTML formatting
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isseealso = False
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for i, line in enumerate(doc):
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if not line.strip():
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continue
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isindented = line[:1].isspace()
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if isindented:
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if isseealso:
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doc[i] = re.sub(r'\w+', make_see_also_link, line)
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elif line.isupper():
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isseealso = line.startswith('SEE ALSO')
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doc[i] = '<b>' + line + '</b>'
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f.write("<hr size=1><h2 id='%s'>%s</h2>" % (a, a))
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f.write("<pre>%s</pre>" % ('\n'.join(doc)))
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f.write("<p class='api'>api: %s.%s</p>" % (func.__module__, func.__name__))
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f.write("</BODY></HTML>")
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f.close()
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print("PyMOL Command Reference written to %s" % (os.path.abspath(file)))
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#####################################################################
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# Here is where the PyMOL Command Language and API are built.
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#####################################################################
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# first we need to import a set of symbols into the local namespace
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from .api import *
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# deferred initialization
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_deferred_init_pymol_internals(pymol)
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# now we create the command langauge
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from . import keywords
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keyword = keywords.get_command_keywords()
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kw_list = list(keyword.keys())
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keywords.fix_list(kw_list)
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kwhash = Shortcut(kw_list)
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keywords.fix_dict(keyword)
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# informational or API-only functions which don't exist in the
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# PyMOL command language namespace
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help_only = keywords.get_help_only_keywords()
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help_sc = Shortcut(list(keyword.keys())+list(help_only.keys()))
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# keyboard configuration
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from . import keyboard
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key_mappings = keyboard.get_default_keys()
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selection_sc = lambda sc=Shortcut,gn=get_names:sc(gn('public')+[
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'not ', 'and ', 'or ', 'first ', 'last ', 'in ', 'like ',
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'byobject ', 'bysegi ', 'bychain ', 'byres ', 'bycalpha ',
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'bymolecule ',
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'bound_to ', 'neighbor ', 'extend ', 'within ', 'around ',
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'expand ', 'gap ', 'near_to ', 'beyond ',
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'model ', 'chain ', 'segi ', 'resn ', 'resi ', 'name ', 'alt ', 'index ',
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'id ', 'rank ',
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'partial_charge ', 'formal_charge ', 'b ', 'q ', 'ss ', 'elem ',
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'rep ', 'color ', 'pepseq ',
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'all', 'enabled', 'visible', 'bonded', 'protected', 'masked',
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'organic', 'inorganic', 'solvent', 'polymer', 'guide', 'hetatm',
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'hydrogens', 'backbone', 'sidechain', 'metals', 'donors',
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'acceptors',
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'polymer.protein', 'polymer.nucleic',
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'center', 'origin',
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])
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object_sc = lambda sc=Shortcut,gn=get_names:sc(gn('objects'))
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map_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:map'))
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contour_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:mesh')+gnot('object:surface'))
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group_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:group'))
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# Table for argument autocompletion
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from . import completing
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auto_arg = completing.get_auto_arg_list()
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color_sc = None
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|
|
||
|
|
raw_image_callback = None
|