charmm-gui interface

[jamesmkrieger]

If something fails with running then now the object is still instantiated and can be run again. This is based on the DaliRecord class.

[jamesmkrieger]

This still doesn't work actually:

@>     Next step: Setup Periodic Boundary Condition
@> Waiting for error check, sleep for 2 s
---------------------------------------------------------------------------
JavascriptException                       Traceback (most recent call last)
<ipython-input-2-fb44476534e1> in <module>
----> 1 cgb = CharmmGUIBrowser('UK_B117_D614G_on7KDJ_1up.pdb', saveas='UK_7kdj_charmm-gui.tgz')

c:\users\james\code\prody\prody\database\charmmgui.py in __init__(self, fname, **kwargs)
    116             raise TypeError('saveas should be a string')
    117
--> 118         self.isSuccess = self.run(**kwargs)
    119
    120     def download(self, browser=None, link=None, saveas=None):

c:\users\james\code\prody\prody\database\charmmgui.py in run(self, cwd, ndir, fname, segids, job_type, saveas, timeout, browser_type, **kwargs)     
    391                 return False
    392
--> 393         status = self.next_step(browser, "Generate Equilibration and Dynamics", **kwargs)
    394         if status == False:
    395             return False

c:\users\james\code\prody\prody\database\charmmgui.py in next_step(self, browser, text, timeout, **kwargs)
    251             text = self.text
    252
--> 253         browser.execute_script("proceed()")
    254         status = True
    255

~\.conda\envs\prody\lib\site-packages\splinter\driver\webdriver\__init__.py in execute_script(self, script, *args)
    297
    298     def execute_script(self, script, *args):
--> 299         return self.driver.execute_script(script, *args)
    300
    301     def evaluate_script(self, script, *args):

~\.conda\envs\prody\lib\site-packages\selenium\webdriver\remote\webdriver.py in execute_script(self, script, *args)
    634         return self.execute(command, {
    635             'script': script,
--> 636             'args': converted_args})['value']
    637
    638     def execute_async_script(self, script, *args):

~\.conda\envs\prody\lib\site-packages\selenium\webdriver\remote\webdriver.py in execute(self, driver_command, params)
    319         response = self.command_executor.execute(driver_command, params)
    320         if response:
--> 321             self.error_handler.check_response(response)
    322             response['value'] = self._unwrap_value(
    323                 response.get('value', None))

~\.conda\envs\prody\lib\site-packages\selenium\webdriver\remote\errorhandler.py in check_response(self, response)
    240                 alert_text = value['alert'].get('text')
    241             raise exception_class(message, screen, stacktrace, alert_text)
--> 242         raise exception_class(message, screen, stacktrace)
    243
    244     def _value_or_default(self, obj, key, default):

JavascriptException: Message: javascript error: proceed is not defined
  (Session info: chrome=87.0.4280.88)