MAWS.py is a 4 years old program that uses Amber/AmberTools as calculation platform. Although I follow program user guide instructions, I do not know how to debug and find the solution to raise self._value IndexError: list index out of range
I replaced the force field(ff) specified in MAWS.py with a newer Amber ff.
As I am not familiar with python code and where the error could be generated I recommend to download the MAWS.py code from GitHub Repository: https://github.com/igemsoftware/Heidelberg_15
python3 MAWS_rev1.py -b 0.01 -i 200 -s 200 -l 15 -t 0.01 -f pdb -y HYBRID Prot1a.frcmod /home/bcramer/workdir-amber/Prot_1/
['DGN', 'DAN', 'DTN', 'DCN']
Choosing from candidates ...
Constructing Ligand/Aptamer complex ...
Constructing Ligand/Aptamer complex ...
etc..................
Loading Aptamer/Ligand complex ...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "MAWS_rev1.py", line 1090, in initial
ligand_range = get_ligand_range(aptamer_top.topology)
File "MAWS_rev1.py", line 197, in get_ligand_range
return [get_ligand(topology)[0], len(get_ligand(topology))]
IndexError: list index out of range
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "MAWS_rev1.py", line 1357, in <module>
positions_and_Ntides = loop()
File "MAWS_rev1.py", line 1237, in loop
pos_Nt_S_task = pool.map(initial, alphabet)
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/bcramer/miniconda3/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
IndexError: list index out of range
Related
Ignoring exception in on_message
Traceback (most recent call last):
File "/opt/virtualenvs/python3/lib/python3.8/site-packages/discord/client.py", line 343, in _run_event
await coro(*args, **kwargs)
File "main.py", line 162, in on_message
checo_fifa()
File "main.py", line 99, in checo_fifa
Debts['checo'] = Debts['checo']+1
TypeError: string indices must be integers
line 162 is:
if msg.startswith('$checo fifa'):
checo_fifa()
await message.channel.send('+1')
line 99 is:
def checo_fifa():
Debts['checo'] = Debts['checo']+1
Debts is a dictionary containing the key 'Checo' as well as a value of 0. There are some more usernames in the dictionary as well as functions pointing to all of them. Weirdly enough, the program worked for a while but now it only returns this when writing the command in discord.
Any help with this would be greatly appreciated.
You cannot add +1 to a string or a list, only to an integer. So you would have to convert this to a integer (if possible) e.g. with
def checo_fifa():
Debts['checo'] = int(Debts['checo']) + 1
#bot.command()
async def test(ctx):
with open("C:\\bot\\cn.txt", 'r') as file:
lines = file.readlines()
for line in lines:
values = line.split("|")
for value in values:
dbdc = [dbdc for dbdc in values[2:3] if dbdc == 'DOOMBIRD DOOMCAVE' and list.count[0] < 6]
print(dbdc[0])
Right now, it's displaying the users who don't exceed the value 6, so that works, but it's not filtering it out to match the text.
What I am trying to make it do, is read the txt file, match values**[3]** to the text, ie 'DOOMBIRD DOOMCAVE'. Then, I want it to check [1] to see if it shows up more than 6 times. Finally, once those conditions are met, I want it to print the results. Unfortunately, it pops up with Index out of range.
[error message][1]
text file:
Declaring ID|Declaring Ruler|Declaring Nation|Declaring Alliance|Declaring Alliance ID|Declaring Team|Receiving ID|Receiving Ruler|Receiving Nation|Receiving Alliance|Receiving Alliance ID|Receiving Team|Status|Money|Technology|Soldiers|Date|Reason|Aid ID|
Ignoring exception in command test:
Traceback (most recent call last):
File "C:\Users\justi\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\discord\ext\commands\core.py", line 85, in wrapped
ret = await coro(*args, **kwargs)
File "c:\bot\eraserhead.py", line 343, in test
print(dbdc[0])
IndexError: list index out of range
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Users\justi\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\discord\ext\commands\bot.py", line 902, in invoke
await ctx.command.invoke(ctx)
File "C:\Users\justi\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\discord\ext\commands\core.py", line 864, in invoke
await injected(*ctx.args, **ctx.kwargs)
File "C:\Users\justi\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\discord\ext\commands\core.py", line 94, in wrapped
raise CommandInvokeError(exc) from exc
discord.ext.commands.errors.CommandInvokeError: Command raised an exception: IndexError: list index out of range```
So I was digging around some datasets, and trying to use pandas to analyze then and i stumbled across the following error.. and my brain froze :(
here is the snippet where the exception is being raised
import pandas as pd
from sklearn.datasets import load_breast_cancer
X, y = load_breast_cancer(return_X_y=True)
data = pd.DataFrame(X)
data['class'] = y
data.head()
data.tail()
data.columns
print('length of data is', len(data))
data.shape
data.info()
here's the error trackback
C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\Scripts\python.exe C:/Users/97150/PycharmProjects/EmbeddedLinux/AI/project.py
length of data is 569
Traceback (most recent call last):
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\core\indexes\base.py", line 2889, in get_loc
return self._engine.get_loc(casted_key)
File "pandas\_libs\index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
File "pandas\_libs\index.pyx", line 97, in pandas._libs.index.IndexEngine.get_loc
File "pandas\_libs\hashtable_class_helper.pxi", line 1675, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas\_libs\hashtable_class_helper.pxi", line 1683, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 30
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:/Users/97150/PycharmProjects/EmbeddedLinux/AI/project.py", line 42, in <module>
data.info()
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\core\frame.py", line 2587, in info
self, verbose, buf, max_cols, memory_usage, null_counts
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\io\formats\info.py", line 250, in info
self._verbose_repr(lines, ids, dtypes, show_counts)
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\io\formats\info.py", line 335, in _verbose_repr
dtype = dtypes[i]
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\core\series.py", line 882, in __getitem__
return self._get_value(key)
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\core\series.py", line 991, in _get_value
loc = self.index.get_loc(label)
File "C:\Users\97150\PycharmProjects\EmbeddedLinux\venv\lib\site-packages\pandas\core\indexes\base.py", line 2891, in get_loc
raise KeyError(key) from err
KeyError: 30
Process finished with exit code 1
note: I'm using PyCharm community 2020.2, and checked for updates and such, and nothing changed
So, turned out, pandas is straight up acting weird.
removing the () from the data.info() fixed the issue :)
You can alternatively try passing verbose=True and null_counts=True arguments to the .info() method to display the result(you can just use verbose argument if you don't want to consider null values).
data.info(verbose=True, null_counts=True)
Let me know if things work out for you.
I'm trying to make dictionary attack on zip file using Pool to increase speed.
But I face next error in Python 3.6, while it works in Python 2.7:
Traceback (most recent call last):
File "zip_crack.py", line 42, in <module>
main()
File "zip_crack.py", line 28, in main
for result in results:
File "/usr/lib/python3.6/multiprocessing/pool.py", line 761, in next
raise value
File "/usr/lib/python3.6/multiprocessing/pool.py", line 450, in _ handle_tasks
put(task)
File "/usr/lib/python3.6/multiprocessing/connection.py", line 206, in send
self._send_bytes(_ForkingPickler.dumps(obj))
File "/usr/lib/python3.6/multiprocessing/reduction.py", line 51, in dumps
cls(buf, protocol).dump(obj)
TypeError: cannot serialize '_io.BufferedReader' object
I tried to search for same errors but couldn't find answer that can help here.
Code looks like this
def crack(pwd, f):
try:
key = pwd.strip()
f.extractall(pwd=key)
return True
except:
pass
z_file = zipfile.ZipFile("../folder.zip")
with open('words.dic', 'r') as passes:
start = time.time()
lines = passes.readlines()
pool = Pool(50)
results = pool.imap_unordered(partial(crack, f=z_file), lines)
pool.close()
for result in results:
if result:
pool.terminate()
break
pool.join()
I also tried another approach using map
with contextlib.closing(Pool(50)) as pool:
pool.map(partial(crack, f=z_file), lines)
which worked great and found passwords quickly in Python 2.7 but it throws same exception in python 3.6
I am trying to make a code that will ask for a user input and if that input is not given in a set amount of time will assume a default value and continue through the rest of the code without requiring the user to hit enter. I am running in Python 3.5.1 on Windows 10.
I have looked through: Keyboard input with timeout in Python, How to set time limit on raw_input, Timeout on a function call, and Python 3 Timed Input black boxing the answers but none of the answers are suitable as they are not usable on Windows (principally use of signal.SIGALRM which is only available on linux), or require a user to hit enter in order to exit the input.
Based upon the above answers however i have attempted to scrap together a solution using multiprocessing which (as i think it should work) creates one process to ask for the input and creates another process to terminate the first process after the timeout period.
import multiprocessing
from time import time,sleep
def wait(secs):
if secs == 0:
return
end = time()+secs
current = time()
while end>current:
current = time()
sleep(.1)
return
def delay_terminate_process(process,delay):
wait(delay)
process.terminate()
process.join()
def ask_input(prompt,term_queue,out_queue):
command = input(prompt)
process = term_queue.get()
process.terminate()
process.join()
out_queue.put(command)
##### this doesn't even remotly work.....
def input_with_timeout(prompt,timeout=15.0):
print(prompt)
astring = 'no input'
out_queue = multiprocessing.Queue()
term_queue = multiprocessing.Queue()
worker1 = multiprocessing.Process(target=ask_input,args=(prompt,term_queue,out_queue))
worker2 = multiprocessing.Process(target=delay_terminate_process,args=(worker1,timeout))
worker1.daemon = True
worker2.daemon = True
term_queue.put(worker2)
print('Through overhead')
if __name__ == '__main__':
print('I am in if statement')
worker2.start()
worker1.start()
astring = out_queue.get()
else:
print('I have no clue what happened that would cause this to print....')
return
print('returning')
return astring
please = input_with_timeout('Does this work?',timeout=10)
But this fails miserably and yields:
Does this work?
Through overhead
I am in if statement
Traceback (most recent call last):
File "C:\Anaconda3\lib\multiprocessing\queues.py", line 241, in _feed
obj = ForkingPickler.dumps(obj)
File "C:\Anaconda3\lib\multiprocessing\reduction.py", line 50, in dumps
cls(buf, protocol).dump(obj)
File "C:\Anaconda3\lib\multiprocessing\queues.py", line 58, in __getstate__
context.assert_spawning(self)
File "C:\Anaconda3\lib\multiprocessing\context.py", line 347, in assert_spawning
' through inheritance' % type(obj).__name__
RuntimeError: Queue objects should only be shared between processes through inheritance
Does this work?
Through overhead
I have no clue what happened that would cause this to print....
Does this work?Process Process-1:
Traceback (most recent call last):
File "C:\Anaconda3\lib\multiprocessing\queues.py", line 241, in _feed
obj = ForkingPickler.dumps(obj)
File "C:\Anaconda3\lib\multiprocessing\reduction.py", line 50, in dumps
cls(buf, protocol).dump(obj)
File "C:\Anaconda3\lib\multiprocessing\process.py", line 287, in __reduce__
'Pickling an AuthenticationString object is '
TypeError: Pickling an AuthenticationString object is disallowed for security reasons
Traceback (most recent call last):
File "C:\Anaconda3\lib\multiprocessing\process.py", line 254, in _bootstrap
self.run()
File "C:\Anaconda3\lib\multiprocessing\process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "C:\Anaconda3\saved_programs\a_open_file4.py", line 20, in ask_input
command = input(prompt)
EOFError: EOF when reading a line
Does this work?
Through overhead
I have no clue what happened that would cause this to print....
Traceback (most recent call last):
File "C:\Anaconda3\lib\multiprocessing\queues.py", line 241, in _feed
obj = ForkingPickler.dumps(obj)
File "C:\Anaconda3\lib\multiprocessing\reduction.py", line 50, in dumps
cls(buf, protocol).dump(obj)
File "C:\Anaconda3\lib\multiprocessing\queues.py", line 58, in __getstate__
context.assert_spawning(self)
File "C:\Anaconda3\lib\multiprocessing\context.py", line 347, in assert_spawning
' through inheritance' % type(obj).__name__
RuntimeError: Queue objects should only be shared between processes through inheritance
Process Process-2:
Traceback (most recent call last):
File "C:\Anaconda3\lib\multiprocessing\process.py", line 254, in _bootstrap
self.run()
File "C:\Anaconda3\lib\multiprocessing\process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "C:\Anaconda3\saved_programs\a_open_file4.py", line 16, in delay_terminate_process
process.terminate()
File "C:\Anaconda3\lib\multiprocessing\process.py", line 113, in terminate
self._popen.terminate()
AttributeError: 'NoneType' object has no attribute 'terminate'
I really don't understand the multiprocessing module well and although I have read the official docs am unsure why this error occurred or why it appears to have ran through the function call 3 times in the process. Any help on how to either resolve the error or achieve an optional user input in a cleaner manner will be much appreciated by a noob programmer. Thanks!