I can't answer the specifics, but I think this brings us back to the
utility of being able to compile an all-in-one .so (or .dll) for
OpenBabel that functions. This would be great to have for scripting
languages, bundling with other applications, etc, etc.
- Noel
On 9 June 2010 07:00, Jérôme Pansanel <j.pansa...@pansanel.net> wrote:
> Hi,
>
> This is an old thread, but the problem remains. I'm porting Mychem for MySQL
> 5.1, and it is not a piece of cake. MySQL has a new security 'feature' that
> requires to put the mychem library in the plugin directory
> (/usr/lib/mysql/plugin on Linux). When using this code, the SetInAndOutFormat
> function fails :
> #################################################################
> ...
>
> OBConversion conv(&inStream,&outStream);
> OBFormat* inFormat = conv.FindFormat("smi");
> OBFormat* outFormat = conv.FindFormat("mol");
>
> if (conv.SetInAndOutFormats(inFormat, outFormat)) {
> // Set options
> ...
> #################################################################
>
>
> Fredrik Wallner has found the following fix:
> #################################################################
> ...
>
> OBConversion conv(&inStream,&outStream);
> OBFormat* inFormat = conv.FormatFromMIME("chemical/x-daylight-smiles");
> OBFormat* outFormat = conv.FormatFromMIME("chemical/x-mdl-molfile");
>
> if (conv.SetInAndOutFormats(inFormat, outFormat)) {
> // Set options
> ...
> #################################################################
>
>
> But it can not work for every case (i.e. inchi has no mime type). Did you find
> a fix for loading all the symbols associated with the format plugins ? May be
> a
> linker option could help ?
>
> Cheers,
>
> Jerome Pansanel
>
>
> Le mardi 18 novembre 2008 16:55:18, Geoffrey Hutchison a écrit :
>> > Mychem has been updated in order to work with Open Babel 3.
>>
>> I think you mean Open Babel 2.2. The library "so" version is 3, but
>> the "external" version is 2.2.
>>
>> > - By default, the file formats are not recognized. For example,
>> > conv.SetInFormat("SMI") returns false. The library libopenbabel.so.3
>> > must be
>> > loaded with dlopen to work correctly.
>>
>> ...
>>
>> > - The descriptors (TPSA, MR and logP) are not loaded. The fix is to
>> > initialize
>>
>> > each descriptor with:
>> For reasons I don't completely understand, the loader on Linux is a
>> bit strange (compared, say to Mac OS X or Windows). We've noticed
>> similar problems with scripting languages.
>>
>> If you write code which links to libopenbabel.so in C++, the library
>> itself runs dlopen. However, in other environments on Linux, the
>> *symbols* associated with these "plugins" are not actually available
>> to anything. In Python, the fix is:
>>
>> sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
>>
>> Strangely, the library does this internally, but it doesn't seem to
>> help:
>> return dlopen(lib_name.c_str(), RTLD_LAZY | RTLD_GLOBAL) != 0;
>>
>> Hope that helps,
>> -Geoff
>>
>> P.S. If there's someone reading who has a better knowledge of Linux
>> "ld" behavior, I'd be thrilled to know if there's a good solution for
>> the library. It seems like the Linux loader expects application
>> binaries to load libraries and plugins and NOT for libraries to load
>> plugins themselves.
>
> --
> Jerome Pansanel
> IPHC
> 23, rue du Loess BP 28
> F-67037 STRASBOURG CEDEX 2
> Tel: +33 (0)3 88 10 66 24
> Fax: +33 (0)3 88 10 62 34
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit. See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
