Actually it does work, I tested it (on ubuntu 14.04).
#make a ton of empty files
for i in {1..1000000} ; do touch tmpfilename_${i}.txt ; done
ls *.txt
>Argument list too long.
#this works
for f in *.txt ; do echo $f ; done
On 6/27/2015 6:01 AM, Dmitri Maziuk wrote:
> On 6/26/2015 11:26 AM, Matthew Baumgartner wrote:
>> That is a limitation of linux there is a maximum length of the command
>> line. You should be able to use a for loop in bash like:
>>
>> for f in *.pdb ; do babel ${f} -omol2 ${f%.*}.mol2 ; done
>>
>> The ${s%.*} bit is some bash string manipulation for stripping the file
>> extension.
> Not gonna work because the error is from the shell expanding '*.pdb' to
> a "too long" list. Shell expansion is still there in the above.
>
> If you move all your pdb files in one directory, just "for f in `ls` ;
> do obabel ..." will do. Otherwise there's a million ways to check the
> extension, but they all require jumping through extra hoops.
>
> Dima
>
>
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