Re: [OpenBabel-scripting] Using GetSupportedInputFormat from Python

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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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