I get msms.exe has stopped working with this simple script, please help me debug it. I tried it with a different pdb, same result. You might want to take a look at ResidueDepth.py.
AssertionError: Failed to generate surface file using command:
msms -probe_radius 1.5 -if C:\Users\Ahmad\AppData\Local\Temp\tmp2pa74le2 -of C:\Users\Ahmad\AppData\Local\Temp\tmpf7zqwkg6 > C:\Users\Ahmad\AppData\Local\Temp\tmpncvn65g4
from Bio.PDB import PDBParser, ResidueDepth
p = PDBParser()
s = p.get_structure("X", '1crn.pdb')
model = s[0]
rd = ResidueDepth(model, '1crn.pdb')
print(rd[(chain_id, res_id)])
The ResidueDepth code depends on pdb_to_xyzr, which is a BASH script that cannot run on windows. An issue was created regarding this problem here.
Related
I'm working on https://github.com/JsBergbau/MiTemperature2 with raspberry pi 3 model b. It's working properly on its own infinite loop but I am not able to catch the output from the terminal. How can I reach to output by using python?
Here is the part of printing:
measurement_time = datetime.datetime.fromtimestamp(measurement.timestamp)
print(measurement_time)
humidity=int.from_bytes(data[2:3],byteorder='little')
print("Temperature: " + str(temp))
print("Humidity: " + str(humidity))
voltage=int.from_bytes(data[3:5],byteorder='little') / 1000.
print("Battery voltage:",voltage,"V")
measurement.temperature = temp
measurement.humidity = humidity
measurement.voltage = voltage
measurement.sensorname = args.name
batteryLevel = min(int(round((voltage - 2.1),2) * 100), 100) #3.1 or above --> 100% 2.1 --> 0 %
measurement.battery = batteryLevel
print("Battery level:",batteryLevel)
measurement_time = datetime.datetime.fromtimestamp(measurement.timestamp)
Here is the script I run on terminal:
python3 LYWSD03MMC.py -d AA:BB:CC:DD:EE:FF
And here is the output:
2021-08-05 11:21:24
Temperature: 24.79
Humidity: 47
Battery voltage: 3.092 V
Battery level: 99
here is the run command and sample output, thanks for helps, best regards.
Change your code so it returns the information instead of just printing it. If you have code which looks like
something = some_function_call(123)
print(something)
other_one = different_function("some data here?").strip()
print(other_one)
probably refactor to
def get_something(number):
return some_function_call(number)
def get_other_one():
return different_function("some data here?").strip()
if __name__ == '__main__':
print(get_something(123))
print(get_other_one())
Now, you can create additional code which retrieves these values without printing them, and does whatever it wants with them. Put them on a web site? Upload them to a database? Rot13 encrypt them and send an email to Bill Gates? Your imagination is the limit.
How exactly you design your code is a broad topic where many books have been written, and more will be. A common arrangement is to make sure the useful parts are in modular functions which do one thing only (ideally without any side effects) so you can import this code and use it from other programs. (That's why the if __name__ part is useful. It makes sure code inside the block doesn't run when you import this file.)
Have you had a closer look at the code? There is a callback option. This is the easiest way to get values from this script. Or is this question more academically on how to capture python output?
If not, that should help you:
Documentation where callback is described:
https://github.com/JsBergbau/MiTemperature2#callback-for-processing-the-data
Accessing the single values:
In sendToInflux.sh https://github.com/JsBergbau/MiTemperature2/blob/master/sendToInflux.sh is an example in which argument are the values like temperature and so on.
Or when using sendToFile.sh it gives line by line
sensorname,temperature,humidity,voltage,humidityCalibrated,timestamp MySensor 20.61 54 2.944 49 1582120122
That data should be easy to process by python or awk.
add commandline
2>&1 | tee result.txt
it can save command line output
If you are running a command from python you can use subprocess.check_output to get the returning output from the terminal. Don't work if the called script runs forever.
Like this:
output = subprocess.check_output([sys.executable, 'LYWSD03MMC.py', '-d', 'AA:BB:CC:DD:EE:FF']).decode()
I was working on something an I this is actually my first time so things are not that clear for me yet, I ran this code :
pip install nipype
from nipype import Node, Workflow
from nipype.interfaces.fsl import SliceTimer, MCFLIRT, Smooth
slicetimer = Node(SliceTimer(index_dir=False,
interleaved=True,
time_repetition=2.5),
name="slicetimer")
mcflirt = Node(MCFLIRT(mean_vol=True,
save_plots=True),
name="mcflirt")
smooth = Node(Smooth(fwhm=4), name="smooth")
preproc01 = Workflow(name='preproc01', base_dir="dir_path")
preproc01.connect([(slicetimer, mcflirt, [('slice_time_corrected_file', 'in_file')]),
(mcflirt, smooth, [('out_file', 'in_file')])])
slicetimer.inputs.in_file = "file_path"
preproc01.run('MultiProc')
This is the error shown when I run the last line of code :
"Could not import plugin module: nipype.pipeline.plugins"
There is one more problem :
When I try to run this code :
preproc01.write_graph(graph2use='orig')
This is the error message shown :
'No command "dot" found on host. Please check that the corresponding package is installed.'
please if anyone knows the solution help me out.
BTW I an doing this from a video series, here is the link :https://www.youtube.com/watch?v=4FVGn8vodkc&t=4414s
Nipype showcase section.
I'm currently working on a script that creates a tray icon that allows the user to adjust screen brightness through menu options. The source code, written in python 3.6.8, can be found as a paste HERE. There seems to be an error message coming up when trying to select one of the brightness options, seen HERE. I did some reading and found that the error I'm getting (0x8004100c) refers to a feature or operation not being supported. Are there any workarounds available for this?
Thank you in advance.
code: https://pastebin.com/sLbyE9yb
error: https://pastebin.com/Xs7wHk73
WMI error reference: https://learn.microsoft.com/en-us/windows/win32/wmisdk/wmi-error-constants
gist: https://gist.github.com/imri0t/12e768e3d7e08734b85ae532d56090e1
(also if anyone can let me know if there's a way to keep the script from dying after an action is made it would be appreciated)
modules needed: pip install infi.systray / pip install wmi
code snip that I believe produces the error:
from infi.systray import SysTrayIcon
import wmi
def brightness_50(systray):
'''brightness: 50%'''
b = 50
c = wmi.WMI(namespace='root\\wmi')
br = c.WmiMonitorBrightnessMethods()[0]
br.WmiSetBrightness(3, b) #b will be a precentage / 100
menu = (("brightness: 100%", None, brightness_50))
systray = SysTrayIcon("icon.ico", "brightness", menu)
systray.start()
I have written a PyQGIS script that uses gdals warp. The piece of code doing this for me is as follows:
warp = 'gdalwarp -ot Byte -q -of GTiff -tr 2.81932541777e-05 -2.81932541777e-05 -tap -cutline %s -crop_to_cutline -co COMPRESS=DEFLATE -co PREDICTOR=1 -co ZLEVEL=6 -wo OPTIMIZE_SIZE=TRUE %s %s' % (instrv, ('"' + pathsplitedit + '"'), outputpath2)
call (warp)
So I have this in a loop and all is good. However each time it executes a new command window is opened, which isn't ideal as it loops through up 100 features in a shapefile. Is there a way I can not have the command window open at all? Any help is really appreciated!!
Since GDAL 2.1 (which recent versions of QGIS use) you can access the command line utilities from the bindings itself, which has a lot of benefits.
Your call becomes something like this, notice that i didn't copy all your creation options, its just to give you an idea on how to use it.
warpopts = gdal.WarpOptions(outputType=gdal.GDT_Byte,
format='GTiff',
xRes=2.81932541777e-05,
yRes=-2.81932541777e-05,
cutlineDSName='cutline_vec.shp',
cropToCutline=True,
targetAlignedPixels=True,
options=['COMPRESS=DEFLATE'])
ds = gdal.Warp('raster_out.tif', 'raster_in.tif', options=warpopts)
ds = None
One of the benefits is that the input files don't have to be on-disk but can also be opened gdal/ogr Datasets. The gdal.Warp cmd also returns the output file as an opened Dataset, which you can then pass on to other commands.
I want to try to add all the step details - Expected, Actual, Status,
etc. to a QC Run for a testcase of a TestSet from a Python Script
living outside the Quality Center.
I have come till here (code given below) and I don't know how to add
Step Expected and Step Actual Result. If anyone knows how do it,
please help me out!! Please, I don't want any QTP solutions.
Thanks,
Code-
# Script name - add_tsrun.py
# C:\Python27\python.exe
# This script lives locally on a Windows machine that has - Python 2.7, Win32 installed, IE8
# Dependencies on Windows Machine - Python 2.7, PythonWin32 installed, IE8, a QC Account, connectivity to QCServer
import win32com.client, os
tdc = win32com.client.Dispatch("TDApiOle80.TDConnection")
tdc.InitConnection('http://QCSERVER:8080/qcbin')
tdc.Login('USERNAME', 'PASSWORD')
tdc.Connect('DOMAIN_NAME', 'PROJECT')
tsFolder = tdc.TestSetTreeManager.NodeByPath('Root\\test_me\\sub_folder')
tsList = tsFolder.FindTestSets('testset1')
ts_object = tsList.Item(1)
ts_dir = os.path.dirname('testset1')
ts_name = os.path.basename('testset1')
tsFolder = tdc.TestSetTreeManager.NodeByPath(ts_dir)
tsList = tsFolder.FindTestSets(ts_name)
ts_object = tsList.Item(1)
TSTestFact = ts_object.TSTestFactory
TestSetTestsList = TSTestFact.NewList("")
ts_instance = TestSetTestsList.Item(1)
newItem = ts_instance.RunFactory.AddItem(None) # newItem == Run Object
newItem.Status = 'No Run'
newItem.Name = 'Run 03'
newItem.Post()
newItem.CopyDesignSteps() # Copy Design Steps
newItem.Post()
steps = newItem.StepFactory.NewList("")
step1 = steps[0]
step1.Status = "Not Completed"
step1.post()
## How do I change the Actual Result??
## I can access the Actual, Expected Result by doing this, but not change it
step1.Field('ST_ACTUAL') = 'My actual result' # This works in VB, not python as its a Syntax error!!
Traceback ( File "<interactive input>", line 1
SyntaxError: can't assign to function call
Hope this helps you guys out there. If you know the answer to set the
Actual Result, please help me out and let me know. Thanks,
Amit
As Ethan Furman answered in your previous question:
In Python () represent calls to functions, while [] represent indexing and mapping.
So in other words, you probably want to do step1.Field['ST_ACTUAL'] = 'My actual result'
Found the answer after a lot of Google Search :)
Simple -> Just do this:
step1.SetField("ST_ACTUAL", "my actual result") # Wohhooooo!!!!
If the above code fails to work, try to do the following:-
(OPTIONAL) Set your win32 com as follows- (Making ''Late Binding'')
# http://oreilly.com/catalog/pythonwin32/chapter/ch12.html
a. Start PythonWin, and from the Tools menu, select the item COM Makepy utility.
b. Using Windows Explorer, locate the client subdirectory (OTA COM Type Library)
under the main win32com directory and double-click the file makepy.py.
Thank you all...