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Bug report insane.py
- buuhuu
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8 years 4 months ago #5310
by buuhuu
Bug report insane.py was created by buuhuu
There is a small mistake in the provided insane.py script in the download section.
When is comes to asymmetry in membranes in line 108 and 109 it is written:
lo_lipd = math.sqrt(options["-a"].value)
up_lipd = options["-au"].value or lo_lipd
i suppose it should be:
lo_lipd = math.sqrt(options["-a"].value)
up_lipd = math.sqrt(options["-au"].value) or lo_lipd
Maybe someone else was wondering why his asymmetrical membrane did look crappy.
Best
Eric
When is comes to asymmetry in membranes in line 108 and 109 it is written:
lo_lipd = math.sqrt(options["-a"].value)
up_lipd = options["-au"].value or lo_lipd
i suppose it should be:
lo_lipd = math.sqrt(options["-a"].value)
up_lipd = math.sqrt(options["-au"].value) or lo_lipd
Maybe someone else was wondering why his asymmetrical membrane did look crappy.
Best
Eric
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- tsjerk
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8 years 4 months ago #5311
by tsjerk
Replied by tsjerk on topic Bug report insane.py
Hi Eric,
Thanks for reporting this. Silly mistake.
Cheers,
Tsjerk
Thanks for reporting this. Silly mistake.
Cheers,
Tsjerk
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- cneale
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8 years 3 weeks ago #5463
by cneale
Replied by cneale on topic Bug report insane.py
The version of insane.py that I just downloaded yesterday from
www.cgmartini.nl/index.php/tools2/proteins-and-bilayers
does not have this fix included. You might consider including a note on the download page that known bug-fixes are not necessarily included in the distribution and the user should search this list (with a link to
www.cgmartini.nl/index.php/forum
). You might also consider defining a keyword that you could direct the user to search and then when a bug is found the developer could reply to the thread including that keyword to make searching easier?
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- cneale
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8 years 3 weeks ago #5464
by cneale
Replied by cneale on topic Bug report insane.py
Actually, with that code change I get an error in insane.py , so I am presuming that the code is good to go as it is...
$ ./insane.py -o cg.gro -p cg.top -l POPC:1 -x 10 -y 10 -z 10
Traceback (most recent call last):
File "./insane.py", line 831, in <module>
up_lipd = math.sqrt(options["-au"].value) or lo_lipd
TypeError: a float is required
Note, the code seems to work fine when I don't make the change noted in this thread (at least for symmetric bilayers, I didn't try asymmetric).
$ ./insane.py -o cg.gro -p cg.top -l POPC:1 -x 10 -y 10 -z 10
Traceback (most recent call last):
File "./insane.py", line 831, in <module>
up_lipd = math.sqrt(options["-au"].value) or lo_lipd
TypeError: a float is required
Note, the code seems to work fine when I don't make the change noted in this thread (at least for symmetric bilayers, I didn't try asymmetric).
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- flaviyan
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8 years 3 weeks ago #5467
by flaviyan
Replied by flaviyan on topic Bug report insane.py
cneale,
The expression is
up_lipd = math.sqrt(options["-au"].value or lo_lipd)
where the 'or' statement evaluates options["-au"].value and if its not True takes the argument lo_lipid.
The expression is
up_lipd = math.sqrt(options["-au"].value or lo_lipd)
where the 'or' statement evaluates options["-au"].value and if its not True takes the argument lo_lipid.
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- cneale
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8 years 3 weeks ago #5474
by cneale
Replied by cneale on topic Bug report insane.py
confirmed this new code does not throw an error. Thank you.
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