[Open Babel] RE: OpenBabel-discuss digest, Vol 1 #610 - 3 msgs

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[Open Babel] RE: OpenBabel-discuss digest, Vol 1 #610 - 3 msgs

drc-2
Hi,

I tried this with the latest snapshot

 /usr/local/bin/babel   '/Users/user/Desktop/acetophenones.sdf' all-osdf '/Users/user/Desktop/myfile.sdf'    -h


and I get

Cannot read input format ""

Works fine with version 1

Similar error with -d, -p etc.

Chris





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Re: [Open Babel] RE: OpenBabel-discuss digest, Vol 1 #610 - 3 msgs

Chris Morley-3
[hidden email] wrote:

> Hi,
>
> I tried this with the latest snapshot
>
>  /usr/local/bin/babel   '/Users/user/Desktop/acetophenones.sdf' all-osdf '/Users/user/Desktop/myfile.sdf'    -h
>
>
> and I get
>
> Cannot read input format ""
>
> Works fine with version 1
>
> Similar error with -d, -p etc.
>
The problem is the "all". I guess this option is used by
some other program. By default OB converts all the
molecules in the input file(s) anyway. If it is a natural
thing to type we could arrange for OB to ignore it.
(Computers should adapt to people, not vice versa.) I
assume that the re will be no space within "all-osdf"?

Chris


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Re: [Open Babel] RE: OpenBabel-discuss digest, Vol 1 #610 - 3 msgs

Geoffrey Hutchison

>>  /usr/local/bin/babel   '/Users/user/Desktop/acetophenones.sdf'  
>> all-osdf '/Users/user/Desktop/myfile.sdf'    -h

Huh. I had no idea what that would do with v.1.x, so I looked at the  
code. The "all-osdf" bit is completely ignored. Well, it's initially  
set as the output file name, but then OB-1.x comes across another  
file name and makes *that* the output file name.

I'm not sure if you wanted "all-osdf" to mean anything. If you did,  
it was completely ignored before.

IMHO, that's a bug in 1.x -- it shouldn't just ignore something the  
user supplied.

In the case of the 2.0 snapshot response:
> Cannot read input format ""

Well, that's not too helpful either. Basically, it tried to figure  
out what format "all-osdf" was (before it even checks if there's a  
file by that name) and of course without an extension, it gave up.  
Probably a more meaningful error message would be something like:

Cannot read input format "" for file "all-osdf"

But what exactly did you want "all-osdf" to mean?

Cheers,
-Geoff


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Re: [Open Babel] RE: OpenBabel-discuss digest, Vol 1 #610 - 3 msgs

drc-2
In reply to this post by drc-2
Hi,

I was looking at my (very old notes from the original version of babel?), and using a syntax that worked before. It sounds like I need reprogramming!

No problem,

Thanks

Chris


> Message Received: Nov 04 2005, 11:51 PM
> From: "Geoffrey Hutchison" <[hidden email]>
> To: "drc" <[hidden email]>
> Cc: [hidden email]
> Subject: Re: [Open Babel] RE: OpenBabel-discuss digest, Vol 1 #610 - 3 msgs
>
>
> >>  /usr/local/bin/babel   '/Users/user/Desktop/acetophenones.sdf'  
> >> all-osdf '/Users/user/Desktop/myfile.sdf'    -h
>
> Huh. I had no idea what that would do with v.1.x, so I looked at the  
> code. The "all-osdf" bit is completely ignored. Well, it's initially  
> set as the output file name, but then OB-1.x comes across another  
> file name and makes *that* the output file name.
>
> I'm not sure if you wanted "all-osdf" to mean anything. If you did,  
> it was completely ignored before.
>
> IMHO, that's a bug in 1.x -- it shouldn't just ignore something the  
> user supplied.
>
> In the case of the 2.0 snapshot response:
> > Cannot read input format ""
>
> Well, that's not too helpful either. Basically, it tried to figure  
> out what format "all-osdf" was (before it even checks if there's a  
> file by that name) and of course without an extension, it gave up.  
> Probably a more meaningful error message would be something like:
>
> Cannot read input format "" for file "all-osdf"
>
> But what exactly did you want "all-osdf" to mean?
>
> Cheers,
> -Geoff
>
>



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