1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626
|
'''
PyMOL Molecular Graphics System
Copyright (c) Schrodinger, Inc.
Supported ways to launch PyMOL:
If $PYMOL_PATH is a non-default location, it must be set and exported
before launching PyMOL.
From a terminal:
shell> python /path/to/pymol/__init__.py [args]
From a python main thread:
>>> # with GUI
>>> import pymol
>>> pymol.finish_launching()
>>> # without GUI
>>> import pymol
>>> pymol.finish_launching(['pymol', '-cq'])
'''
from __future__ import absolute_import
from __future__ import print_function
import os
import sys
import __main__
if __name__ == '__main__':
# PyMOL launched as "python pymol/__init__.py"
# or via execfile(".../pymol/__init__.py",...) from main
# or as "python -m pymol.__init__"
if 'pymol' not in sys.modules:
# "python /abc/pymol/__init__.py" will add /abc/pymol to PYTHONPATH
# (we don't want that), but not /abc and not the current directory (we
# want those)
pymol_base = os.path.dirname(os.path.realpath(__file__))
site_packages = os.path.dirname(pymol_base)
# remove /abc/pymol
if pymol_base in sys.path:
sys.path.remove(pymol_base)
# add /abc
if site_packages not in sys.path:
sys.path.insert(0, site_packages)
# add current directory
if '' not in sys.path:
sys.path.insert(0, '')
# arguments default to sys.argv... but also support execfile(...)
# from a terminal where the user could set pymol_argv
args = getattr(__main__, "pymol_argv", None)
# standard launch (consume main thread)
import pymol
pymol.launch(args)
# this should never be reached because PyMOL will exit the process
raise SystemExit
IS_PY2 = sys.version_info[0] == 2
IS_PY3 = sys.version_info[0] == 3
IS_WINDOWS = sys.platform.startswith('win')
IS_MACOS = sys.platform.startswith('darwin')
IS_LINUX = sys.platform.startswith('linux')
if IS_PY3:
# legacy string API, still used by Pmw for example
import string
for attr in ['capitalize', 'count', 'find', 'index', 'lower',
'replace', 'rstrip', 'split', 'strip', 'upper', 'zfill']:
setattr(string, attr, getattr(str, attr))
string.letters = string.ascii_letters
string.lowercase = string.ascii_lowercase
string.join = lambda words, sep=' ': sep.join(words)
string.atoi = int
import _thread as thread
else:
import thread
from imp import find_module
import copy
import threading
import re
import time
import traceback
import math
from . import invocation
def _init_internals(_pymol):
# Create a temporary object "stored" in the PyMOL global namespace
# for usage with evaluate based-commands such as alter
_pymol.stored = Scratch_Storage()
# Create a permanent object in the PyMOL global namespace
# that will be picked and unpickled along with the session
_pymol.session = Session_Storage()
# This global will be non-None if logging is active
# (global variable used for efficiency)
_pymol._log_file = None
# This global will be non-None if an external gui
# exists. It mainly exists so that events which occur
# in the Python thread can be handed off to the
# external GUI thread through one or more FIFO Queues
# (global variable used for efficiency)
_pymol._ext_gui = None
# lists of functions to call when saving and restoring pymol session objects
# The entry 'None' represents the PyMOL C-API function call
_pymol._session_save_tasks = [ None ]
_pymol._session_restore_tasks = [ None ]
# cached results (as a list):
# [ [size, (hash1, hash2, ... ), (inp1, inp2, ...), output],
# [size, (hash1, hash2, ... ), (inp1, inp2, ...), output],
# ... ]
_pymol._cache = []
# standard input reading thread
_pymol._stdin_reader_thread = None
# stored views
_pymol._view_dict = {}
_pymol._view_dict_sc = None
# stored scenes
_pymol._scene_dict_sc = None
_pymol._scene_counter = 1
_pymol._scene_quit_on_action = ''
# get us a private invocation pseudo-module
_pymol._invocation = Scratch_Storage()
_pymol._invocation.options = copy.deepcopy(invocation.options)
_pymol._invocation.get_user_config = invocation.get_user_config
_pymol._invocation.parse_args = invocation.parse_args
# these locks are to be shared by all PyMOL instances within a
# single Python interpeter
_pymol.lock_api = threading.RLock() # mutex for API calls from the outside
_pymol.lock_api_c = threading.RLock() # mutex for C management of python threads
_pymol.lock_api_status = threading.RLock() # mutex for PyMOL status info
_pymol.lock_api_glut = threading.RLock() # mutex for GLUT avoidance
_pymol.lock_api_data = threading.RLock() # mutex for internal data structures
def get_version_message(v=None):
'''
Get an informative product + version string
'''
if not v:
v = _cmd.get_version()
p = "PyMOL %s " % v[0]
p += "Incentive Product" if invocation.options.incentive_product else \
"Open-Source"
if v[5]:
p += ", svn rev %s" % v[5]
return p
def guess_pymol_path():
'''
Guess PYMOL_PATH from typical locations and return it as string.
'''
init_file = os.path.abspath(__file__)
pymol_path_candidates = [
# $PYMOL_PATH == <site-packages>/pymol/pymol_path
os.path.join(os.path.dirname(init_file), 'pymol_path'),
# $PYMOL_PATH/modules/pymol/__init__.py
re.sub(r"[\/\\]modules[\/\\]pymol[\/\\]__init__\.py[c]*$", "", init_file),
# /usr/share/pymol
os.path.join(sys.prefix, 'share', 'pymol'),
find_module('pymol')[1]
]
for pymol_path in pymol_path_candidates:
if os.path.isdir(pymol_path):
return pymol_path
return '.'
def setup_environ():
# guess PYMOL_PATH if unset
if 'PYMOL_PATH' not in os.environ:
os.environ['PYMOL_PATH'] = guess_pymol_path()
# other PyMOL variables
if 'PYMOL_DATA' not in os.environ:
os.environ['PYMOL_DATA'] = os.path.join(os.environ['PYMOL_PATH'], 'data')
if 'PYMOL_SCRIPTS' not in os.environ:
os.environ['PYMOL_SCRIPTS'] = os.path.join(os.environ['PYMOL_PATH'], 'scripts')
os.environ['TUT'] = os.path.join(os.environ['PYMOL_DATA'], 'tut')
# auto-detect bundled FREEMOL (if present)
if 'FREEMOL' not in os.environ:
for test_path in ['ext', 'freemol']:
test_path = os.path.join(os.environ['PYMOL_PATH'], test_path)
if os.path.isdir(test_path):
os.environ['FREEMOL'] = test_path
break
# include FREEMOL's libpy in sys.path (if present)
if 'FREEMOL' in os.environ:
freemol_libpy = os.path.join(os.environ['FREEMOL'], "libpy")
if os.path.isdir(freemol_libpy) and freemol_libpy not in sys.path:
sys.path.append(freemol_libpy)
# set Tcl/Tk environment if we ship it in ext/lib
pymol_path = os.environ['PYMOL_PATH']
for varname, dirname in [
('TCL_LIBRARY', 'tcl8.5'),
('TK_LIBRARY', 'tk8.5')]:
dirname = os.path.join(pymol_path, "ext", "lib", dirname)
if os.path.isdir(dirname):
os.environ[varname] = dirname
def exec_str(self, string):
'''
Execute string in "self" namespace (used from C)
'''
try:
exec(string, self.__dict__, self.__dict__)
except Exception:
traceback.print_exc()
return None
def exec_deferred(self):
'''
Execute the stuff from invocations.options.deferred
'''
try:
from socket import error as socket_error
except ImportError:
socket_error = None
print('import socket failed')
cmd = self.cmd
_pymol = cmd._pymol
# read from stdin (-p)
if self.invocation.options.read_stdin and not _pymol._stdin_reader_thread:
try:
t = _pymol._stdin_reader_thread = \
threading.Thread(target=cmd._parser.stdin_reader)
t.setDaemon(1)
t.start()
except:
traceback.print_exc()
# do the deferred stuff
try:
if cmd.ready():
cmd.config_mouse(quiet=1)
for a in self.invocation.options.deferred:
if a[0:4] == "_do_":
cmd.do(a[4:])
else:
cmd.load(a, quiet=0)
except CmdException as e:
print(e)
print(" Error: Argument processing aborted due to exception (above).")
except socket_error:
# this (should) only happen if we're opening a PWG file on startup
# and the port is busy. For now, simply bail...
cmd.wizard("message",["Socket.error: ","",
"\\999Assigned socket in use.","",
"\\779Is PyMOL already launched?","",
"\\966Shutting down..."])
cmd.refresh()
cmd.do("time.sleep(2);cmd.quit()")
def adapt_to_hardware(self):
'''
optimize for (or workaround) specific hardware
'''
cmd = self.cmd
vendor, renderer, version = cmd.get_renderer()
# Quadro cards don't support GL_BACK in stereo contexts
if vendor.startswith('NVIDIA'):
if 'Quadro' in renderer:
if invocation.options.show_splash:
print(" Adapting to Quadro hardware.")
cmd.set('stereo_double_pump_mono', 1)
elif vendor.startswith('Mesa'):
if renderer[0:18]=='Mesa GLX Indirect':
pass
elif vendor.startswith('ATI'):
if renderer[0:17] == 'FireGL2 / FireGL3': # obsolete ?
if invocation.options.show_splash:
print(" Adapting to FireGL hardware.")
cmd.set('line_width', 2, quiet=1)
if IS_WINDOWS:
if sys.getwindowsversion()[0] > 5:
# prevent color corruption by calling glFlush etc.
cmd.set('ati_bugs', 1)
if 'Radeon HD' in renderer:
if invocation.options.show_splash:
print(" Adjusting settings to improve performance for ATI cards.")
if cmd.get_setting_int("use_shaders")==0:
# limit frame rate to 30 fps to avoid ATI "jello"
# where screen updates fall way behind the user.
cmd.set("max_ups", 30)
elif vendor.startswith('Microsoft'):
if renderer[0:17] == 'GDI Generic':
cmd.set('light_count', 1)
cmd.set('spec_direct', 0.7)
elif vendor.startswith("Intel"):
if "Express" in renderer:
if invocation.options.show_splash:
print(" Disabling shaders for Intel Express graphics")
cmd.set("use_shaders", 0)
elif (vendor == 'nouveau'
or ' R300 ' in vendor # V: X.Org R300 Project, R: Gallium 0.4 on ATI RV370
):
if invocation.options.show_splash:
print(" Detected blacklisted graphics driver. Disabling shaders.")
cmd.set("use_shaders", 0)
# find out how many processors we have, and adjust hash
# table size to reflect available RAM
try:
import multiprocessing
ncpu = multiprocessing.cpu_count()
if ncpu > 1:
cmd.set("max_threads", ncpu)
if invocation.options.show_splash:
print(" Detected %d CPU cores."%ncpu, end=' ')
print(" Enabled multithreaded rendering.")
except:
pass
# store our adapted state as default
cmd.reinitialize("store")
def launch_gui(self):
'''
Launch if requested:
- external GUI
'''
pymol_path = os.getenv('PYMOL_PATH', '')
try:
poll = IS_MACOS
if self.invocation.options.external_gui == 3:
if 'DISPLAY' not in os.environ:
os.environ['DISPLAY'] = ':0.0'
if self.invocation.options.external_gui in (1, 3):
__import__(self.invocation.options.gui)
sys.modules[self.invocation.options.gui].__init__(self, poll,
skin = self.invocation.options.skin)
# import plugin system
import pymol.plugins
except:
traceback.print_exc()
def prime_pymol():
'''
Set the current thread as the glutThread
'''
global glutThread
if not glutThread:
glutThread = thread.get_ident()
def _launch_no_gui():
import pymol2
p = pymol2.SingletonPyMOL()
p.start()
# TODO sufficient?
while (p.idle() or p.getRedisplay() or
invocation.options.keep_thread_alive or
cmd.get_modal_draw() or
cmd.get_setting_int('keep_alive') or
cmd._pymol._stdin_reader_thread is not None):
p.draw()
# TODO needed?
cmd.sync()
p.stop()
def launch(args=None, block_input_hook=0):
'''
Run PyMOL with args
Only returns if we are running pretend GLUT.
'''
if args is None:
args = sys.argv
invocation.parse_args(args)
if invocation.options.gui == 'pmg_qt':
if invocation.options.no_gui:
return _launch_no_gui()
try:
from pmg_qt import pymol_qt_gui
sys.exit(pymol_qt_gui.execapp())
except ImportError:
print('Qt not available, using GLUT/Tk interface')
invocation.options.gui = 'pmg_tk'
prime_pymol()
_cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
def finish_launching(args=None):
'''
Start the PyMOL process in a thread
'''
global glutThreadObject
if cmd._COb is not None:
return
import pymol
# legacy
if args is None:
args = getattr(pymol, 'pymol_argv', None)
if args is None:
args = getattr(__main__, 'pymol_argv', sys.argv)
if True:
# run PyMOL in thread
invocation.options.keep_thread_alive = 1
cmd.reaper = threading.currentThread()
glutThreadObject = threading.Thread(target=launch,
args=(list(args), 1))
glutThreadObject.start()
e = threading.Event()
# wait for the C library to initialize
while cmd._COb is None:
e.wait(0.01)
# make sure symmetry module has time to start...
while not hasattr(pymol, 'xray'):
e.wait(0.01)
class CmdException(Exception):
'''
Exception type for PyMOL commands
'''
label = "Error"
def __init__(self, message='', label=None):
self.message = message
if message:
self.args = (message,)
if label:
self.label = label
def __str__(self):
return " %s: %s" % (self.label, self.message)
class IncentiveOnlyException(CmdException):
'''
Exception type for features that are not available in Open-Source PyMOL
'''
label = "Incentive-Only-Error"
def __init__(self, message=''):
if not message:
try:
funcname = sys._getframe(1).f_code.co_name
message = '"%s" is not available in Open-Source PyMOL' % (funcname,)
except:
message = 'Not available in Open-Source PyMOL'
message += '\n\n' \
' Please visit http://pymol.org if you are interested in the\n' \
' full featured "Incentive PyMOL" version.\n'
super(IncentiveOnlyException, self).__init__(message)
class Scratch_Storage:
'''
Generic namespace
'''
def __reduce__(self):
# for loading Python 3 (new-style class) pickle with Python 2
return (self.__class__, (), self.__dict__)
def get_unused_name(self, prefix='tmp'):
'''
Get an unused name from this namespace
'''
i = 1
while True:
name = prefix + str(i)
if not hasattr(self, name):
setattr(self, name, None)
return name
i += 1
class Session_Storage:
'''
Generic namespace
'''
def __reduce__(self):
# for loading Python 3 (new-style class) pickle with Python 2
return (self.__class__, (), self.__dict__)
def _colortype(cmd):
# backwards compatible color index type for iterate, which used
# to expose colors as RGB tuples
get_color_tuple = cmd.get_color_tuple
class Color(int):
def __getitem__(self, i):
return get_color_tuple(self)[i]
def __len__(self):
return 3
return Color
######### VARIABLES ############################
glutThread = 0
######### ENVIRONMENT ##########################
setup_environ()
# initialize instance-specific module/object internals
_init_internals(sys.modules[__name__])
# maximize responsiveness
sys.setcheckinterval(1)
# get X-window support (machine_get_clipboard)
if 'DISPLAY' in os.environ:
from .xwin import *
########## C MODULE ############################
import pymol._cmd
_cmd = sys.modules['pymol._cmd']
from . import cmd
cmd._COb = None
try:
import epymol
except ImportError:
pass
########## WORKAROUND TO PREVENT "import cmd" ##############################
# Previous versions of PyMOL did relative imports and thus allowd
# "import cmd" in pymol scripts to import the pymol.cmd module. To be more
# strict and for compatibility with python3 we use absolute imports now,
# which unfortunately will import an unrelated "cmd" module from the default
# python library, and even worse will corrupt the pymol namespace with it.
# The following causes an import error for "import cmd":
class _NoCmdFinder:
def find_spec(self, fullname, path=None, target=None):
if path is None and fullname == 'cmd':
msg = 'use "from pymol import cmd" instead of "import cmd"'
raise CmdException(msg)
return None
find_module = find_spec
sys.meta_path.insert(0, _NoCmdFinder())
########## LEGACY PRINT STATEMENT FOR PYMOL COMMAND LINE ###################
if IS_PY3:
def _print_statement(*args, **_):
'''Legacy Python-2-like print statement for the PyMOL command line'''
kw = {}
if args and args[0].startswith('>>'):
kw['file'] = eval(args[0][2:])
args = args[1:]
if args and not args[-1]:
kw['end'] = ' '
args = args[:-1]
args = [eval(a) for a in args]
print(*args, **kw)
cmd.extend('print', _print_statement)
|