class GlobalPyMOL:
"""
SingletonPyMOL that works like the parallel but that waits for the other thread to release it.
Use with a context manager!
"""
pymol = pymol2.SingletonPyMOL()
pymol.start()
pymol.cmd.set('fetch_path', tempfolder)
pylock = Lock()
def __init__(self):
pass
def __enter__(self):
if not self.pylock.acquire(timeout=60):
# something hung up.
self.pymol.cmd.remove('*')
self.pymol.cmd.delete('*')
self.pylock.release() #pointless roundtrip to be safe.
self.pylock.acquire()
return self.pymol
else:
self.pymol.cmd.delete('*')
return self.pymol
def __exit__(self, exc_type, exc_val, exc_tb):
self.pymol.cmd.delete('*')
self.pylock.release()
def kill(self):
## the assumption is that it died.
self.pymol.cmd.reinitialize() #dangerous for other threads.
if self.pylock.locked():
self.pylock.release()
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()
if self.fuser.debug:
print(f'Final position for model {self.name}.....')
self.describe()
return self
def roll(self, φ):
"""
Whereas they are aligned on the x-axis with the y,z coordinates of C and N termini near 0,0.
They can rotate around the X. roll. This is good to remove clashes.
"""
self.pymol.cmd.rotate([1, 0, 0], φ, selection=self.name, camera=0)
self.angle_fix()
return self
if __name__ == '__main__':
import pymol2, argparse
parser = argparse.ArgumentParser(
description='Combine structures for a Uniprot')
parser.add_argument('uniprot',
type=str,
help='Uniprot to generate a combined model')
args = parser.parse_args()
with pymol2.SingletonPyMOL() as pymol:
Fuser.pymol = pymol
w = Fuser.from_uniprot(args.uniprot, debug=False)
w.order()
w.save()
#w.add_xyz()