Re: [Open Babel] Limits on number of input files

[mfisher <mf...@Ta...>]

Thanks for the reply, but there are significant differences in what you did
relative to what I'm trying to do.  You took a single .smi file, split it
then recombined it without conversion.  I'm trying to convert individual
.mol files into SMILES strings in a single .smi file.  

As to errors in file 701, that doesn't seem to be the case.  I've started
with 701, gone to 1400 and converted with no trouble.  If 701 had errors, it
shouldn't convert at all, right?  The limit seems strictly on how many .mol
files I start with.  I can literally select 1000 .mol files, start the
conversion and write down which file failed, then start there with another
1000 .mol files and see failure at the next 700 mark.  In fact, that's
exactly how I got through the smaller directory -- select a lot, see where
it crashes, select only to that point, convert, save to a unique file name,
start at the previous crash point, select a lot, see where it crashes, etc.
until I reached the end.  

When I get back to that project, I intend to try Noel's idea, but I admit to
being lazy enough to prefer to use the GUI.


Chris Morley wrote:
> 
> Michael Fisher wrote:
>> I’ve started using the OpenBabel GUI.  I have two directories with .mol 
>> files I want to get SMILES strings for.  One has about 3500 files, the 
>> other >13000.  There appears to be an input file limit of about 700 
>> files.  Obviously, I could do 700 at a time, but I then have to 
>> concatenate all the files (at least twenty for the big directory).  Am I 
>> right that there’s a limit?  Is there a way to get around it?  
> 
> It seems to work for me.
> 
> I used the recently released v2.2.1 GUI on Windows XP, although I 
> don't think there was any change which should make it different from 
> v2.2.0. Not having several thousand SMILES files to hand, I took a 
> file with 3603 molecules in SMILES format and did a smi to smi 
> conversion to output file A*.smi. This splitting operation produced 
> 3603 files, A1.smi ... A3603.smi
> 
> I then did another smi to smi conversion from A*.smi to recombined.smi 
> and got file containing all 3603 molecules. I think this is the sort 
> of agglomeration operation you wanted to do, and it worked ok.
> 
> I also tried doing another smi to smi conversion from A*.smi to 
> B*.smi and got another 3603 files BA1.smi ...BA3603.smi. So a batch 
> conversion also worked ok.
> 
> There seems to be a bug in displaying the input files when there is a 
> wildcard character, but this occurs only when the mousewheel is 
> operated, and isn't size related.
> 
> I don't see any reason why the Windows command line shouldn't do these 
> operations ok, and putting the input file name in quotes, as Noel 
> mentioned, should get over the embedded spaces.
> 
> I think your problem may be an erroneous SMILES in the 701st file. Try 
>   checking "Continue with next object after error, if possible" or -e 
> on the command line.
> 
> Chris
> 
>> 
>> FYI, the filenames contain numerous spaces, periods and commas, so the 
>> command line version of babel (which I’ve tried) crashes.  Also, I’m 
>> presently stuck doing this in Windows XP.  If I switch to Fedora, will 
>> the command line version ignore punctuations?  Will there still be a 
>> limit on input files in the GUI?
> 
> 
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