pele.gui.double_ended_connect_runner

Module source

tools to run the double ended connect in a separte process and make sure the the minima and transition states found are incorporated back into the master database

class pele.gui.double_ended_connect_runner.OutLog

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class OutLog:

for redirecting stdout or stderr

everytime something is written to this object, it is sent through the pipe conn.

from http://www.riverbankcomputing.com/pipermail/pyqt/2009-February/022025.html

class pele.gui.double_ended_connect_runner.DECProcess

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class DECProcess(mp.Process):

This object will run in a separate process and will actually do the connect run

when the run is finished the minima and transition states found will be sent back through the pipe as UnboundMinimum and UnboundTransitionState objects

Parameters:

commpipe

child end of a mp.Pipe()

system

min1, min2

the minima to try to connect

pipe_stdoutbool

if true log messages will be sent back through the pipe

return_smoothed_pathbool

if the run ends successfully the smoothed path will be sent back through the pipe

DECProcess.clean_up()

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def clean_up(self):

send the lists of transition states and minima back to the parent process

class pele.gui.double_ended_connect_runner.DECRunner

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class DECRunner(QtCore.QObject):

Spawn a double ended connect run in a child process

This will spawn a new process and deal with the communication

Parameters:

system

databaseDatabase

The minima and transition states found will be added to the database after the connect run is finished

min1, min2Munimum objects

the minima to try to connect

outstreaman object with attribute outstream.write(mystring)

the log messages from the connect run will be redirected here

return_smoothed_pathbool

if True the final smoothed path will be calculated

Attributes:

on_finishedSignal

this signal will be called when the connect job is finished

DECRunner.poll()

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def poll(self):

this does the checking in the background to see if any messages have been passed

DECRunner.start()

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def start(self):

start the connect job

DECRunner.add_minima_transition_states()

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def add_minima_transition_states(self, new_minima, new_ts):

Add the minima and transition states found to the database

convert the UnboundMinimum and UnboundTransitionStates to ones bound to self.database

DECRunner.finished()

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def finished(self):

the job is finished, do some clean up