On 6/8/10 11:00 PM, Jérôme Pansanel 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
Postgres has the same requirement. I found that all I needed was to put
libopenbabel.so
libinchi.so
into its /usr/local/pgsql/lib, and everything else worked. It was able to find
all of the other dynamically-loaded libraries with no problem. The key was
libinchi.so, which unexpectedly had to be included along with libopenbabel.so.
On the other hand, I was not able to use BABEL_LIBDIR. The openbabel plugins
must be located in the "prefix" directory (configure) or CMAKE_INSTALL_PREFIX
(cmake) when you compiled it. BABEL_LIBDIR just didn't work with Postgres.
Craig
> (/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.
>
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