Re: [OpenBabel-scripting] Using GetSupportedInputFormat from Python

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On 17/05/07, Jens Thomas <j.m...@dl...> wrote:
> Hi Noel,
>
> I've just worked out that the problem arose because I hadn't installed
> anything and was running it directly from the build directory. I assume
> it looks in a set directory for the files to dynamically configure the
> supported formats. Can this be changed with an environment variable?
The answer is yes.You need to set LD_LIBRARY_PATH to point to the
directory containing libopenbabel.so, etc. You still need to run "make
install" beforehand, though, to install all the formats to the correct
location. I describe both "local" and "global" intalls on the wiki
page.

> Anyway, it's not important as once I'd installed everything into a
> directory structure it then worked fine.

> I should probably mention that I hit problems with the default version
> of SWIG on Ubuntu wasn't able to handle the "-naturalvar" flag, so I had
> to install swig 1.3.31 to get the build to work.
I will add this to the install notes.

> Many thanks for your help.
>
> Jens
>
> Noel O'Boyle wrote:
> > The good news is that all the Python stuff seems to be working fine
> > (no initialisation necessary). The bad news is that the C++ stuff
> > isn't working properly.
> >
> > I'm betting that if you try "babel -H" and look under "The following
> > file formats are recognized", you will see nothing there. Which is
> > what you're also seeing in python. To verify, try to convert a file
> > using babel. This is because the file formats are loaded dynamically
> > as plugins, so there can be problems if you compile with particular
> > settings.
> >
> > How exactly are you compiling the software? Did you follow the
> > instructions on the web exactly (see
> > http://openbabel.sourceforge.net/wiki/Install_%28source_code%29), or
> > are you doing something different? I'm using an old version of Ubuntu
> > myself, so there's no reason we can't get it to work.
> >
> > Regards
> >   Noel
> >
> > On 15/05/07, Jens Thomas <j.m...@dl...> wrote:
> >> Hello!
> >>
> >> It's taken me a little while to grind through all the usual little
> >> hiccups that come when building an unfamiliar code straight out of the
> >> repository, but I've now got what (I think) is the correct version.
> >>
> >> I checked out the code at r1954 and patched with r1958 as suggested
> >> by Noel.
> >>
> >> However, I'm not getting anything from pybel.informats or
> >> OBConversion.GetSupportedInputFormats as shown below:
> >>
> >>
> >> Python 2.4.3 (#2, Oct  6 2006, 07:52:30)
> >> [GCC 4.0.3 (Ubuntu 4.0.3-1ubuntu5)] on linux2
> >> Type "help", "copyright", "credits" or "license" for more information.
> >>  >>> import pybel
> >>  >>> pybel.informats
> >> {}
> >>  >>> pybel.outformats
> >> {}
> >>  >>> import openbabel
> >>  >>> obc = openbabel.OBConversion()
> >>  >>> i= obc.GetSupportedInputFormat()
> >>  >>> print i
> >> ()
> >>  >>> dir(i)
> >> ['__add__', '__class__', '__contains__', '__delattr__', '__doc__',
> >> '__eq__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__',
> >> '__getslice__', '__gt__', '__hash__', '__init__', '__iter__', '__le__',
> >> '__len__', '__lt__', '__mul__', '__ne__', '__new__', '__reduce__',
> >> '__reduce_ex__', '__repr__', '__rmul__', '__setattr__', '__str__']
> >>
> >>
> >> Is there some sort of initialisation I need to do to get the dictionary
> >> populated?
> >>
> >> Many thanks,
> >>
> >> Jens
> >>
> >> Noel O'Boyle wrote:
> >> > I've already noticed that the latest SVN is not compatible with SWIG
> >> > due to changes introducted at r1954. You'll need to check out r1953,
> >> > and use "svn merge -r 1957:1958" to patch with r1958.
> >> >
> >> > Noel
> >> >
> >> > On 14/05/07, Jens Thomas <j.m...@dl...> wrote:
> >> >> Hi Noel, Jerome and Chris,
> >> >>
> >> >> Firstly, many thanks for the quick response and warm welcome to the
> >> >> list! Please accept my apologies for not replying sooner, but I've
> >> been
> >> >> away without access to email.
> >> >>
> >> >> I've tried checking out the latest version of openbabel from SVN
> >> onto my
> >> >> Ubuntu box (Dapper on a Pentium 4) so that I can try some of the
> >> changes
> >> >> you've committed. I ran a normal configure (./configure), but the
> >> make
> >> >> currently fails with:
> >> >>
> >> >> make[2]: Leaving directory `/home/jmht/openbabel/test/cmltest'
> >> >> make[2]: Entering directory `/home/jmht/openbabel/test'
> >> >> g++ -DHAVE_CONFIG_H -I. -I../src  -I../include
> >> >> -DTESTDATADIR="\"../test/files/\""   -g -O2 -MT roundtrip.o -MD
> >> -MP -MF
> >> >> .deps/roundtrip.Tpo -c -o roundtrip.o roundtrip.cpp
> >> >> mv -f .deps/roundtrip.Tpo .deps/roundtrip.Po
> >> >> /bin/sh ../libtool --tag=CXX   --mode=link g++  -g -O2   -o roundtrip
> >> >> roundtrip.o ../src/libopenbabel.la -ldl -lm
> >> >> mkdir .libs
> >> >> g++ -g -O2 -o .libs/roundtrip roundtrip.o
> >> ../src/.libs/libopenbabel.so
> >> >> -ldl -lm -Wl,--rpath -Wl,/usr/local/lib
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBFormat::FormatFromMIME(char const*)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBPlugin::Display(std::basic_string<char,
> >> >> std::char_traits<char>, std::allocator<char> >&, char const*, char
> >> >> const*)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for
> >> >> OpenBabel::OBDescriptor'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBDescriptor::Compare(OpenBabel::OBBase*,
> >> >> std::basic_istream<char, std::char_traits<char> >&, bool)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to `vtable for
> >> >> OpenBabel::OBPlugin'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBPlugin::ListAsVector(char const*, char const*,
> >> >> std::vector<std::basic_string<char, std::char_traits<char>,
> >> >> std::allocator<char> >, std::allocator<std::basic_string<char,
> >> >> std::char_traits<char>, std::allocator<char> > > >&)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for
> >> >> OpenBabel::OBPlugin'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBDescriptor::AddProperties(OpenBabel::OBBase*,
> >> >> std::basic_string<char, std::char_traits<char>,
> >> std::allocator<char> >
> >> >> const&)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBDescriptor::GetStringValue(OpenBabel::OBBase*,
> >> >> std::basic_string<char, std::char_traits<char>, std::allocator<char>
> >> >> >&)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBDescriptor::FilterCompare(OpenBabel::OBBase*,
> >> >> std::basic_istream<char, std::char_traits<char> >&, bool)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBFormat::RegisterFormat(char const*, char const*)'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to `typeinfo for
> >> >> OpenBabel::OBDescriptor'
> >> >> ../src/.libs/libopenbabel.so: undefined reference to
> >> >> `OpenBabel::OBDescriptor::DeleteProperties(OpenBabel::OBBase*,
> >> >> std::basic_string<char, std::char_traits<char>,
> >> std::allocator<char> >
> >> >> const&)'
> >> >> collect2: ld returned 1 exit status
> >> >> make[2]: *** [roundtrip] Error 1
> >> >>
> >> >> I'm not that familiar with C++ and so am bit stuck as to how to sort
> >> >> this one out.
> >> >>
> >> >> Do you have any suggestions?
> >> >>
> >> >> Best wishes,
> >> >>
> >> >> Jens
> >> >>
> >> >>
> >> >> Noel O'Boyle wrote:
> >> >> > On 12/05/07, Chris Morley <c.m...@ds...> wrote:
> >> >> >
> >> >> >> In the revamped code for formats (and other plugins) recently
> >> >> committed
> >> >> >> to SVN HEAD (for the next OB version) I tried to maintain backward
> >> >> >> compatibility as far as possible. So
> >> >> OBConversion::SupportedInputFormat()
> >> >> >> works as before but, you'll be pleased to hear, without the
> >> >> '[Read-only]'.
> >> >> >>
> >> >> > Sounds good but SWIG doesn't like the new code. When I try to
> >> compile
> >> >> > openbabel_python.cpp, I get:
> >> >> >
> >> >> > ../../include/openbabel/fingerprint.h:48: error: 'static
> >> >> > std::map<const char*, OpenBabel::OBPlugin*,
> >> >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const
> >> char*
> >> >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
> >> >> > cannot be overloaded
> >> >> > ../../include/openbabel/fingerprint.h:43: error: with 'static
> >> >> > std::map<const char*, OpenBabel::OBPlugin*,
> >> >> > OpenBabel::OBPlugin::CharPtrLess, std::allocator<std::pair<const
> >> char*
> >> >> > const, OpenBabel::OBPlugin*> > >& OpenBabel::OBFingerprint::Map()'
> >> >> > ../../include/openbabel/fingerprint.h:53: error: 'static
> >> >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()'
> >> cannot
> >> >> > be overloaded
> >> >> > ../../include/openbabel/fingerprint.h:43: error: with 'static
> >> >> > OpenBabel::OBFingerprint*& OpenBabel::OBFingerprint::Default()'
> >> >> > ../../include/openbabel/fingerprint.h: In constructor
> >> >> > 'OpenBabel::OBFingerprint::OBFingerprint(std::string, bool)':
> >> >> > ../../include/openbabel/fingerprint.h:63: error: no match for
> >> >> > 'operator[]' in 'OpenBabel::OBFingerprint::Map()[ID]'
> >> >> > /usr/include/c++/4.0.2/bits/stl_map.h:331: note: candidates are:
> >> _Tp&
> >> >> > std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const _Key&)
> >> [with
> >> >> > _Key = const char*, _Tp = OpenBabel::OBPlugin*, _Compare =
> >> >> > OpenBabel::OBPlugin::CharPtrLess, _Alloc =
> >> >> > std::allocator<std::pair<const char* const,
> >> OpenBabel::OBPlugin*> >]
> >> >> >
> >> >> >
> >> >> >> But in an effort to provide more choice on the form of the output,
> >> >> there
> >> >> >> are three functions which provide a list of formats(or other
> >> plugin
> >> >> >> classes): OBPlugin::ListAsVector, ListAsString and List. The first
> >> >> two
> >> >> >> were intended to be compatible with scripting, although I need
> >> some
> >> >> >> advice here. ListAsString returns a (big) std::string, but
> >> >> ListAsVector
> >> >> >> has a parameter which is a reference to a std::vector. If this is
> >> >> >> incompatible with scripting languages I should change it.
> >> >> >>
> >> >> > There's no problem with vectors in general; these are simply
> >> >> > translated to lists by SWIG.
> >> >> >
> >> >> >
> >> >> >> All three have a parameter which can control what is in the
> >> >> output. For
> >> >> >> example if it contains "verbose" it output the whole
> >> description, not
> >> >> >> just the first line. So it would be easy to add code (4 extra
> >> >> lines) to
> >> >> >> output only the IDs if that would be useful:
> >> >> >> ListAsVector("formats","in/ids", stringvector)
> >> >> >>
> >> >> >> Post-processing in pybel I'm sure is useful, but if the C++
> >> code was
> >> >> >> adequate it could serve other scripting languages as well.
> >> >> >>
> >> >> > I think so too. In the meanwhile, I would like to push out a
> >> Windows
> >> >> > Python release based on 2.1.0 with the current pybel
> >> enhancements. I'm
> >> >> > going to try to get this together this weekend and do some testing.
> >> >> >
> >> >> > Noel
> >> >> >
> >> >> >
> >> >> >> Chris
> >> >> >>
> >> >> >> Noel O'Boyle wrote:
> >> >> >>
> >> >> >>> After looking at the C++ code, I realise that maybe returning
> >> a list
> >> >> >>> of strings is the only choice for SupportedInputFormat. Anyway,
> >> >> in the
> >> >> >>> meanwhile I've added some code to pybel, so that if you access
> >> >> >>> pybel.informats or outformats, you will get a dictionary of
> >> >> supported
> >> >> >>> formats.
> >> >> >>>
> >> >> >>> On 12/05/07, Noel O'Boyle <bao...@gm...> wrote:
> >> >> >>>
> >> >> >>>> Actually, a vector of std::strings had not yet been
> >> swigified, so I
> >> >> >>>> needed to added to a line to openbabel-python.i to set it up
> >> >> (not yet
> >> >> >>>> checked in). However, there's an additional problem, which
> >> >> Jerome may
> >> >> >>>> like to address.
> >> >> >>>>
> >> >> >>>> The data that's returned is similar to:
> >> >> >>>> ('acr -- ACR format [Read-only]', 'alc -- Alchemy format', ... )
> >> >> >>>>
> >> >> >>>> whereas it would make more sense to me either to return:
> >> >> >>>> ('acr', 'alc', ...)
> >> >> >>>> or
> >> >> >>>> a std::map (i.e. a Python dict) of ['acr' : 'ACR format', 'alc':
> >> >> >>>> 'Alchemy format']
> >> >> >>>>
> >> >> >>>> Note that the text [Read-only] is not really necessary in a
> >> list of
> >> >> >>>> supported input formats.
> >> >> >>>>
> >> >> >>>> Since this function was added for the benefit of scripting
> >> >> interfaces,
> >> >> >>>> it makes sense to make it as easy as possible to access the
> >> list of
> >> >> >>>> formats.
> >> >> >>>>
> >> >> >>>> Noel
> >> >> >>>>
> >> >> >>>> On 11/05/07, Noel O'Boyle <bao...@gm...> wrote:
> >> >> >>>>
> >> >> >>>>> Hello again Jens,
> >> >> >>>>>
> >> >> >>>>> Good to hear from you on this list... :-)
> >> >> >>>>>
> >> >> >>>>> On 10/05/07, Jens Thomas <j.m...@dl...> wrote:
> >> >> >>>>>
> >> >> >>>>>> Hi,
> >> >> >>>>>>
> >> >> >>>>>> I'm trying to enable our ccp1gui code
> >> >> >>>>>> (http://sourceforge.net/projects/ccp1gui/) to use openbabel so
> >> >> that we
> >> >> >>>>>> no longer have to support so many formats.
> >> >> >>>>>>
> >> >> >>>>>> I've got most of the machinery in place, but am a bit stuck on
> >> >> how to
> >> >> >>>>>> dynamically determine what input formats are supported by
> >> >> openbabel.
> >> >> >>>>>>
> >> >> >>>>>> I originally tried to use OBConversion.GetNextFormat, but ran
> >> >> into the
> >> >> >>>>>> ground fairly quickly. I then discovered the post at:
> >> >> >>>>>>
> >> >> >>>>>>
> >> >>
> >> http://sourceforge.net/mailarchive/forum.php?thread_name=200702191105.25888.j.pansanel%40pansanel.net&forum_name=openbabel-scripting
> >>
> >> >>
> >> >> >>>>>>
> >> >> >>>>>> which suggest that I should be able to get what I want using
> >> >> >>>>>> GetSupportedInputFormat(), however, I'm currently pretty
> >> >> clueless as to
> >> >> >>>>>> how I extract the information from the object. I get something
> >> >> back as
> >> >> >>>>>> shown below, but I'd appreciated any advice on what I then
> >> >> need to do
> >> >> >>>>>> with it.
> >> >> >>>>>>
> >> >> >>
> >> >>
> >> -------------------------------------------------------------------------
> >>
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> >> >> >> _______________________________________________
> >> >> >> OpenBabel-scripting mailing list
> >> >> >> Ope...@li...
> >> >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >> >> >>
> >> >> >>
> >> >> >
> >> >> >
> >> >>
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> >>
> >> >>
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> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >
> >>
> >>
> >
>
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