Re: [Open Babel] Open Babel in the browser

[Igor Filippov [Contr]]

I've never heard about ChemJSON before, but...

> 
> Where does it say which one's "C1" and which one's "H7"? All I can tell
> from this is all atoms are linked with the same type of bond ("1" stands
> for "aromatic" perhaps?) What do you draw if the "-0.932892" is missing
> from the json the client sent you?
> 
Wouldn't the same criticism apply to most other formats such as SDF?

> If you want it machine-usable, you need at least the table of elements,
> the table of bond "numbers" (might as well use names), and atoms encoded
> as (element, index) pairs. Connections as (atom1, atom2, bond) tuples
> and 3d coordinates as (x, y, z) tuples.
> 

It seems to contain this information, though in a slightly different
format instead of a list of tuples. It does not have a table of elements
but it would be a little surprising if for any molecule you would have
to carry the whole periodic table within the same file.

I think the actual criticism here is that there is no documented schema
for this file format, but it seems the format is so trivial it's
basically self-documenting...

I think a more valid question would be whether there is a need for 101
different chemical formats...

Igor

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Re: [Open Babel] Intro to using Open Babel

[Igor Filippov [Contr]]

It's great, Noel, but... no MCS in OpenBabel? :(
I completely agree that my implementation is not perfect but it does 
work within some reasonable limits...

Igor

On 12/4/2012 12:48 PM, Craig James wrote:
> Very nice ... thanks for doing this.  Things like this should be
> available in the OB documentation as a resource for those starting new
> projects or trying to make a presentation to their management.
>
> Craig
>
> On Tue, Dec 4, 2012 at 3:31 AM, Noel O'Boyle  > wrote:
>
> Hi all,
>
> Here are some introductory slides to features and usage of Open Babel:
> http://baoilleach.blogspot.co.uk/2012/12/intro-to-open-babel.html
>
> Regards,
> Noel
>
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Re: [Open Babel] FP2 reference and description for fingerprints

[Igor Filippov [Contr]]

Wow - I never realized there are API documentation for 2.3.x branch -
thank you Chris! I just always went through the front page -
openbabel.org and didn't know there is backdoor to the more recent docs.

Igor


On Wed, 2012-08-29 at 09:50 -0400, Chris Morley wrote:
> On 28/08/2012 16:58, Jaehong Shin wrote:
> > hello All,
> >
> > I am using openbael and have a quick question about the reference of
> > fingerprint implemented in openbabel.
> > I am just wondering if I can get the reference for the fingerprints FP2
> > and FP3. Actually, I would like to have the description for each
> > fingerprint e.g. atom type or path or fragment for SAR analysis.
> 
> There is OpenBabel documentation at http://openbabel.org/docs/2.3.1 
> which might help.
> 
> FP4 uses the set of SMARTS in data/SMARTS_InteLigand.txt. Similarly FP3 
> uses the SMARTS patterns in data/patterns.txt, but I would not recommend 
> using it because it is too incomplete.
> 
> The structural feature producing each bit can be seen using fingerprint 
> format (obtain the documentation by  obabel -L ftp ).
> There is a blog post showing how to visualize the FP2 fragments at
> http://baoilleach.blogspot.co.uk/2012/01/visualising-fragments-in-path-based.html.
> 
> Chris
> >
> > Thank you in advance
> > --
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> >
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[Open Babel] wavy bonds

[Igor Filippov [Contr]]

Dear colleagues,

Is it possible to set a bond as "wavy" or to check if it has "wavy"
attribute in OB similar to SetWedge() and IsWedge()?


Best regards,
Igor



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Re: [Open Babel] Problems building OB 2.3.1 with static libs

[Igor Filippov [Contr]]

Thank you, Tim!
The static lib works now on both OSX and MinGW (with eigen3).

There seem to be a problem with InChI generation though - it looks like
inchi format got lost in the static library generation.

Another tiny additional feature request - it seems that libopenbabel.a
lands in /usr/local/bin instead of /usr/local/lib on MinGW
(CMAKE_INSTALL_PREFIX=/usr/local) - this is not a showstopper, but would
be nice to get rid of. I think it might be a leftover from the days when
libopenbabel.dll had to be in the same folder with the executables
obabel.exe etc.

Igor

On Tue, 2012-07-31 at 17:56 -0400, Tim Vandermeersch wrote:
> Hi,
> 
> On Tue, Jul 31, 2012 at 11:50 PM, Igor Filippov [Contr]
>  wrote:
> > Answering my own email - it seems if I surround lines 303 and 304 in
> > tools/obabel.cpp with:
> >
> > #if  defined(USING_DYNAMIC_LIBS)
> > ...
> > #endif
> >
> > I will get everything compiling nicely in MinGW.
> > Would it be possible to commit it to svn?
> 
> Yes, I'm working on the problem right now and this is the correct fix
> I also have here. It has to be similar to the code in babel.cpp and
> since it is a static build the DLHandler class is not build and
> therefore the symbol was undefined. Regarding the
> ChemDrawBinaryFromat: it seems that this was renamed to
> ChemDrawBinaryXFromat. I'll commit the change in a few minutes.
> 
> Tim
> 
> > Igor
> >
> >
> >
> > On Tue, 2012-07-31 at 17:16 -0400, Filippov, Igor (NIH/NCI) [C] wrote:
> >> This is very helpful - thank you!
> >> I was able to make a static libopenbabel on OS X 10.5 with eigen3 and
> >> edited plugin.cpp.
> >>
> >> Unfortunately there seem to be more problems with MinGW build - I'm
> >> getting the following error - perhaps someone knows what to do:
> >>
> >> [ 79%] Built target openbabel
> >> [ 79%] Built target babel
> >> Linking CXX executable ../bin/obabel.exe
> >> CMakeFiles/obabel.dir/obabel.obj: In function `main':
> >> c:/msys/1.0/home/igor/openbabel-svn/tools/obabel.cpp:304: undefined
> >> reference to
> >>  `DLHandler::findFiles(std::vector >> std::allocator >&,
> >> std::string const&)'
> >> collect2: ld returned 1 exit status
> >> make[2]: *** [bin/obabel.exe] Error 1
> >> make[1]: *** [tools/CMakeFiles/obabel.dir/all] Error 2
> >> make: *** [all] Error 2
> >>
> >> Igor
> >>
> >>
> >>
> >>
> >> On Tue, 2012-07-31 at 01:02 -0400, Björn Grüning wrote:
> >> > Am Montag, den 30.07.2012, 22:43 -0400 schrieb Geoff Hutchison:
> >> > > > I am having some problems to compile OpenBabel on Ubuntu with static
> >> > > > libs.  The compiler is GNU (GCC/G++), Eigen3, Zlib, Cairo and XML2
> >> > > > libraries were installed.
> >> > > >
> >> > > > The error message appears during the linking step:
> >> > > >
> >> > > > Linking CXX executable ../bin/babel
> >> > > > ../src/libopenbabel.a(plugin.o): In function 
> >> > > > `OpenBabel::EnableStaticPlugins()':
> >> > > > /home/asn/Downloads/openbabel/src/plugin.cpp:245: undefined reference
> >> > > > to `OpenBabel::theChemDrawBinaryFormat'
> >> > >
> >> > >
> >> > > My first suggestion would be to try SVN trunk.
> >> > > http://openbabel.org/wiki/Subversion
> >> > >
> >> > > I know there have been multiple patches towards static compilation. 
> >> > > Not all of them can be incorporated into the v2.3 release branch.
> >> > >
> >> >
> >> > Current trunk has the same error. The ChemDrawBinaryFormat got a major
> >> > overhaul, the diff between 2.3.1 and trunk is not small.
> >> > As a temporary solution and if you do not need that format you can
> >> > comment line 245 in plugin.cpp. After that openbabel compiles fine.
> >> >
> >> > Hope that helps,
> >> > Bjoern
> >> >
> >> >
> >> > >
> >> > >
> >> > > --
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> >> > > will include endpoint s

Re: [Open Babel] Problems building OB 2.3.1 with static libs

[Igor Filippov [Contr]]

Answering my own email - it seems if I surround lines 303 and 304 in
tools/obabel.cpp with:

#if  defined(USING_DYNAMIC_LIBS)
...
#endif

I will get everything compiling nicely in MinGW.
Would it be possible to commit it to svn?

Igor



On Tue, 2012-07-31 at 17:16 -0400, Filippov, Igor (NIH/NCI) [C] wrote:
> This is very helpful - thank you!
> I was able to make a static libopenbabel on OS X 10.5 with eigen3 and
> edited plugin.cpp.
> 
> Unfortunately there seem to be more problems with MinGW build - I'm
> getting the following error - perhaps someone knows what to do:
> 
> [ 79%] Built target openbabel
> [ 79%] Built target babel
> Linking CXX executable ../bin/obabel.exe
> CMakeFiles/obabel.dir/obabel.obj: In function `main':
> c:/msys/1.0/home/igor/openbabel-svn/tools/obabel.cpp:304: undefined
> reference to
>  `DLHandler::findFiles(std::vector std::allocator >&, 
> std::string const&)'
> collect2: ld returned 1 exit status
> make[2]: *** [bin/obabel.exe] Error 1
> make[1]: *** [tools/CMakeFiles/obabel.dir/all] Error 2
> make: *** [all] Error 2
> 
> Igor
> 
> 
> 
> 
> On Tue, 2012-07-31 at 01:02 -0400, Björn Grüning wrote:
> > Am Montag, den 30.07.2012, 22:43 -0400 schrieb Geoff Hutchison:
> > > > I am having some problems to compile OpenBabel on Ubuntu with static
> > > > libs.  The compiler is GNU (GCC/G++), Eigen3, Zlib, Cairo and XML2
> > > > libraries were installed.
> > > > 
> > > > The error message appears during the linking step:
> > > > 
> > > > Linking CXX executable ../bin/babel
> > > > ../src/libopenbabel.a(plugin.o): In function 
> > > > `OpenBabel::EnableStaticPlugins()':
> > > > /home/asn/Downloads/openbabel/src/plugin.cpp:245: undefined reference
> > > > to `OpenBabel::theChemDrawBinaryFormat'
> > > 
> > > 
> > > My first suggestion would be to try SVN trunk.
> > > http://openbabel.org/wiki/Subversion
> > > 
> > > I know there have been multiple patches towards static compilation. Not 
> > > all of them can be incorporated into the v2.3 release branch.
> > > 
> > 
> > Current trunk has the same error. The ChemDrawBinaryFormat got a major
> > overhaul, the diff between 2.3.1 and trunk is not small.
> > As a temporary solution and if you do not need that format you can
> > comment line 245 in plugin.cpp. After that openbabel compiles fine.
> > 
> > Hope that helps,
> > Bjoern
> > 
> > 
> > > 
> > > 
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Re: [Open Babel] Problems building OB 2.3.1 with static libs

[Igor Filippov [Contr]]

This is very helpful - thank you!
I was able to make a static libopenbabel on OS X 10.5 with eigen3 and
edited plugin.cpp.

Unfortunately there seem to be more problems with MinGW build - I'm
getting the following error - perhaps someone knows what to do:

[ 79%] Built target openbabel
[ 79%] Built target babel
Linking CXX executable ../bin/obabel.exe
CMakeFiles/obabel.dir/obabel.obj: In function `main':
c:/msys/1.0/home/igor/openbabel-svn/tools/obabel.cpp:304: undefined
reference to
 `DLHandler::findFiles(std::vector >&, 
std::string const&)'
collect2: ld returned 1 exit status
make[2]: *** [bin/obabel.exe] Error 1
make[1]: *** [tools/CMakeFiles/obabel.dir/all] Error 2
make: *** [all] Error 2

Igor




On Tue, 2012-07-31 at 01:02 -0400, Björn Grüning wrote:
> Am Montag, den 30.07.2012, 22:43 -0400 schrieb Geoff Hutchison:
> > > I am having some problems to compile OpenBabel on Ubuntu with static
> > > libs.  The compiler is GNU (GCC/G++), Eigen3, Zlib, Cairo and XML2
> > > libraries were installed.
> > > 
> > > The error message appears during the linking step:
> > > 
> > > Linking CXX executable ../bin/babel
> > > ../src/libopenbabel.a(plugin.o): In function 
> > > `OpenBabel::EnableStaticPlugins()':
> > > /home/asn/Downloads/openbabel/src/plugin.cpp:245: undefined reference
> > > to `OpenBabel::theChemDrawBinaryFormat'
> > 
> > 
> > My first suggestion would be to try SVN trunk.
> > http://openbabel.org/wiki/Subversion
> > 
> > I know there have been multiple patches towards static compilation. Not all 
> > of them can be incorporated into the v2.3 release branch.
> > 
> 
> Current trunk has the same error. The ChemDrawBinaryFormat got a major
> overhaul, the diff between 2.3.1 and trunk is not small.
> As a temporary solution and if you do not need that format you can
> comment line 245 in plugin.cpp. After that openbabel compiles fine.
> 
> Hope that helps,
> Bjoern
> 
> 
> > 
> > 
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Re: [Open Babel] Problem call Open Babel C++ library from Java

[Igor Filippov [Contr]]

I believe your question is answered in
scripts/java/README  - 

 If you get the output "Benzene has 0 atoms", you need to preload the
OpenBabel
 library as follows:
$ LD_PRELOAD=$OB_LIBDIR/libopenbabel.so $JAVA_HOME/bin/java OBTest


Best regards,
Igor

On Wed, 2011-12-21 at 15:12 -0500, BLizzard R wrote:
> 
> 
> Hello
> 
> I just installed OpenBabel 2.3.1 on my windows vista and tried to 
> call OpenBabel 2.3.1 from a java project. 
> 
> When I tested OpenBabel's java sample: OBTest.java, I met the following 
> problem.
> 
> If I put OBTest.class in a same directory with openbabel.jar and DLL files, 
> the sample worked well.
>  
> But if they were not in same directory, it failed to call OpenBabel, output 
> is "Benzene has 0 atoms.".
> 
> I already set PATH and CLASSPATH which included DLL and jar's path.
> 
> Do I need set any other environment variables? 
> Is there anyone has experience on this problem? 
> 
> BTW: I failed to call OpenBabel in Eclipse, got same results.
> I would appreciate your advice.
> 
> Best regards
> Alex
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Re: [Open Babel] seg faults on molecules with dummy atoms

[Igor Filippov [Contr]]

Fantastic, thank you!

Igor


On Tue, 2011-10-11 at 13:07 -0400, My Th wrote:
> O , 2011-10-11 12:52 -0400, Igor Filippov [Contr] rakstīja:
> > First of - congratulations on the paper! This gives us a way to give OB
> > developers their due by citing the publication.
> > 
> > I have found a few examples of Substances from Pubchem where OB 2.3.0
> > gives segfault - my guess is due to the presence of a dummy atom - e.g.
> > 
> > 6361218
> >   -OEChem-04171109372D
> > 
> >   2  0  0 0  0  0  0  0  0999 V2000
> >-1.16660.04180. *   0  3  0  0  0  0  0  0  0  0  0  0
> > 0.37260.09290. C   0  0  0  0  0  0  0  0  0  0  0  0
> > A1
> > R
> > M  CHG  1   1   1
> > M  END
> > 
> > This particular molecule is SID 16361218.
> > 
> > While those are not real "molecules" the segfaults are quite unpleasant,
> > especially if it's one structure out of a big file of otherwise good
> > molecules. Has this been fixed already in the svn somewhere? I can share
> > a set of 5398 such structures from Pubchem substances.
> > 
> > Would it be possible to get the segfaults out of the way before 2.3.1
> > release?
> > 
> > Best regards,
> > Igor
> 
> Hi!
> 
> It is fixed in SVN. The fix should be pulled in also in 2.3.1 branch,
> but I haven't tested that.
> 
> 
> Reinis
> 



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[Open Babel] seg faults on molecules with dummy atoms

[Igor Filippov [Contr]]

First of - congratulations on the paper! This gives us a way to give OB
developers their due by citing the publication.

I have found a few examples of Substances from Pubchem where OB 2.3.0
gives segfault - my guess is due to the presence of a dummy atom - e.g.

6361218
  -OEChem-04171109372D

  2  0  0 0  0  0  0  0  0999 V2000
   -1.16660.04180. *   0  3  0  0  0  0  0  0  0  0  0  0
0.37260.09290. C   0  0  0  0  0  0  0  0  0  0  0  0
A1
R
M  CHG  1   1   1
M  END

This particular molecule is SID 16361218.

While those are not real "molecules" the segfaults are quite unpleasant,
especially if it's one structure out of a big file of otherwise good
molecules. Has this been fixed already in the svn somewhere? I can share
a set of 5398 such structures from Pubchem substances.

Would it be possible to get the segfaults out of the way before 2.3.1
release?

Best regards,
Igor


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Re: [Open Babel] Convert Molecule Structure to IUPAC

[Igor Filippov [Contr]]

6. CIR
what's wrong with CIR?

Igor

On Tue, 2011-04-05 at 11:36 -0400, qiancheng shen wrote:
> Dear Geoffrey,
>  I appreciate your help very much ! Thank you for your time.
>  At first I thought it is a very simple problem, so I am
> confident to find such a tool when a chemist friend asked me for help.
> But maybe you are right, there is no such opensource tool exists. 
>  I have tried many tools, and maybe I should give a list and
> share my experience on this problem.
> 
>  1. OPSIN , an open parser for IPUAC name. It can convert
> IUPAC name to structure but not vice versa.
>  (P.S. You can also use OPSIN with CDK to generate
> molecule images from IUPAC name.)
>  2. ChemDraw. It can generate IUPAC name from structure, but
> batch mode seems to be inavailable.(not opensource)
>  3. Openbabel.  It can convert structure to InChI name, but
> not IUPAC name.
>  4. OpenEye. Yes, it has a great tool to do this task, but not
> opensource.
>  5. Marvin Sketch. You can insert such IUPAC Name while
> drawing a molecule, but not opensource.
> 
> Thank you for all your help!!
> 
> 
> Shen
> 
> 2011/4/5 Geoffrey Hutchison 
> 
> On Apr 4, 2011, at 4:31 AM, qiancheng shen wrote:
> 
> > Thank you very much!! But all these tools are not suitable
> for me..Any other ideas?
> 
> 
> You also asked on CCL.net and several people also pointed you
> to the NIH Chemical Resolver. Noel's link pointed out that
> Cinfony and Webel can provide you with a Python solution to
> query the Resolver and get a name. It won't work for all
> molecules, only the 16 million or so in PubChem.
> 
> Put frankly, I dont expect this be solved in the open source
> space in the near term, unless the NIH or other government
> organization sponsors it. It's tedious, difficult work to code
> an IUPAC naming system. It has lots of tricky corner cases
> (even the commercial ones have problems). People are willing
> to pay money for such a solution, so there's a clear
> capitalist incentive to write something like Lexichem, sell
> it, and be financially rewarded for the work.
> 
> Name to structure has a clear benefit for OPSIN and is
> technically an easier problem: parse the chemical name into
> determining structure. There may be many names for one
> structure, but that's not a big deal. OPSIN was also used to
> solve an obvious problem -- machine parsing journal articles
> for data mining.
> 
> Structure to name has been requested for Open Babel, basically
> forever, but IMHO it's out of the scope of the project.
> 
> Cheers,
> -Geoff
> 



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Re: [Open Babel] Conversion molecule name to structure

[Igor Filippov [Contr]]

Benoit,

I don't think OpenBabel supports it out of the box.
There are other free/open solutions - OPSIN from Peter Murray-Rust,
converts IUPAC names into structures, and CIR - converts anything into
anything as long as it's one of 100 million molecules in our database:

http://cactus.nci.nih.gov/chemical/structure


Regards,
Igor

On Wed, 2011-03-23 at 06:27 -0400, Benoit Gauzere wrote:
> Hi,
> I'd would like to know if open babel is able to convert a molecule
> name, such as "butane" for example, in the related molecular
> structure ? 
> 
> This fonctionnality exists in ChemDraw but I don't find it in the open
> babel documentation.
> 
> Thanks,
> Benoit Gaüzère.
> 
> 
> -- 
> Benoît Gaüzere
> benoit.gauz...@gmail.com



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Re: [Open Babel] how to access getAlias() in perl

[Igor Filippov [Contr]]

Noel,

Thank you. I'm getting the following error though:

TypeError in method 'toSetData', argument 1 of type
'OpenBabel::OBGenericData *'

Does it mean that the argument should not be an object returned by
GetData()? What should it be then? 

Best regards,
Igor

On Tue, 2011-03-22 at 05:26 -0400, Noel O'Boyle wrote:
> You need to cast it to the specific subclass first. Try calling
> $newad = toSetData($ad)
> and then
> if ($newad && $newad->GetAlias() eq "Xx")
> 
> - Noel
> 
> On 21 March 2011 15:06, Igor Filippov [Contr]  wrote:
> > Dear Colleagues,
> >
> > I need to implement in Perl a procedure which is C++ looks like the
> > following:
> > 
> > AliasData *ad;
> > ad = (AliasData *) a->GetData(OBGenericDataType::SetData);
> > if (ad != NULL && ad->GetAlias() == "Xx")
> > 
> >
> > This is what I have at the moment and it does not work unfortunately:
> > 
> > $ad=$atom->GetData($Chemistry::OpenBabel::OBGenericDataType::SetData);
> > if ($ad && $ad->GetAlias() eq "Xx")
> > 
> >
> > It doesn't seem to work even if I replace
> > $Chemistry::OpenBabel::OBGenericDataType::SetData
> > with it's numerical value - 23.
> >
> > Any recommendations will be most welcome!
> > Igor
> >
> >
> > --
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[Open Babel] how to access getAlias() in perl

[Igor Filippov [Contr]]

Dear Colleagues,

I need to implement in Perl a procedure which is C++ looks like the
following:

AliasData *ad;
ad = (AliasData *) a->GetData(OBGenericDataType::SetData);
if (ad != NULL && ad->GetAlias() == "Xx")


This is what I have at the moment and it does not work unfortunately:

$ad=$atom->GetData($Chemistry::OpenBabel::OBGenericDataType::SetData);
if ($ad && $ad->GetAlias() eq "Xx") 


It doesn't seem to work even if I replace
$Chemistry::OpenBabel::OBGenericDataType::SetData
with it's numerical value - 23.

Any recommendations will be most welcome!
Igor


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Re: [Open Babel] openbabel library prints out warning messages

[Igor Filippov [Contr]]

Works like a charm, this is exactly what I needed!

Thanks,
Igor


On Wed, 2010-12-15 at 10:27 -0500, Geoffrey Hutchison wrote:
> > I've never seen this before, but it looks like libopenbabel is now
> > printing warning messages on stderr:
> > ==
> > *** Open Babel Warning  in CreateCisTrans
> >  Error in cis/trans stereochemistry specified for the double bond
> 
> If you don't like to see warnings, you can easily turn it off, redirect it, 
> or otherwise go through the output. This is covered by OBMessageHandler and 
> the global log obErrorLog:
> 
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMessageHandler.shtml
> 
> For example, you may want:
> 
> obErrorLog.StopLogging();
> 
> Cheers,
> -Geoff



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[Open Babel] openbabel library prints out warning messages

[Igor Filippov [Contr]]

I've never seen this before, but it looks like libopenbabel is now
printing warning messages on stderr:

==
*** Open Babel Warning  in CreateCisTrans
  Error in cis/trans stereochemistry specified for the double bond

I think this is wrong - a library should not spit out any unsolicited
output on stderr or stdout.

Igor


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Re: [Open Babel] cmake error in source install

[Igor Filippov [Contr]]

John,

Did you run "make install"?
If you have babel installed and it still doesn't recognize formats, or
if you don't want to install it set BABEL_DATADIR=~/src/openbabel/data
and BABEL_LIBDIR=~/build/openbabel/lib before running.

(substitute your own location);

Igor

On Thu, 2010-12-09 at 16:02 -0500, John Merle wrote:
> Thank you Noel and Igor,
> 
> That seemed to work. I saw no fatal errors. Cmake couldn't find my wxwidget
> files but I'm not interested in GUI. I attatched the cmake output. I
> completed the install process and the program is not working.
> 
> [jme...@n1 183]$ babel -igamout output.log -opdb
> babel: cannot read input format!
> Open Babel 2.3.0 -- Dec  9 2010 -- 15:16:34
> Usage: babel [-i]  [-o] 
> Try  -H option for more information.
> 
> Also, it appears that I can only read one file format.
> 
> [jme...@n1 183]$ babel -L formats
> csr -- Accelrys/MSI Quanta CSR format [Write-only]
> [jme...@n1 183]$ 
> 
> 
> Thanks,
> 
> John
> 
> 
> On 12/9/10 3:00 PM, "Igor Filippov [Contr]"  wrote:
> 
> > 
> > True, but  it's still out of source even if build directory is in
> > openbabel-2.3.0 - all the object files and CMakeCache.txt are in "build"
> > and not intermingled with the source code.
> > 
> > On Thu, 2010-12-09 at 15:00 -0500, Noel O'Boyle wrote:
> >> CMake recommends out-of-source builds.
> >> (http://www.cmake.org/Wiki/CMake_FAQ#Out-of-source_build_trees)
> >> 
> >> - Noel
> >> 
> >> On 9 December 2010 19:48, Igor Filippov [Contr] 
> >> wrote:
> >>> Hmmm, looks like the instructions published on that website are a bit
> >>> tricky:
> >>> tar zxf openbabel-2.3.0.tar.gz
> >>> mv openbabel-2.3.0 src
> >>> mkdir build
> >>> cmake ../src
> >>> 
> >>> While this is correct, I believe the more common route (as usually 
> >>> described
> >>> for other packages) would be:
> >>> tar -xzf openbabel-2.3.0.tar.gz
> >>> cd openbabel-2.3.0
> >>> mkdir build
> >>> cd build
> >>> cmake ../
> >>> 
> >>> Igor
> >>> 
> >>> On Thu, 2010-12-09 at 14:37 -0500, John Merle wrote:
> >>>> Noel,
> >>>> 
> >>>> When I run "cmake ../src" I am in the build folder inside the openbabel
> >>>> folder. So, the "../src" IS referring to the src directory in the source
> >>>> distribution.
> >>>> 
> >>>> If this is wrong should I run "cmake .."?
> >>>> 
> >>>> Thanks
> >>>> 
> >>>> John
> >>>> 
> >>>> 
> >>>> On 12/9/10 2:25 PM, "Noel O'Boyle"  wrote:
> >>>> 
> >>>>> Hi John, (Please cc to the list)
> >>>>> 
> >>>>> You're not alone - someone else just filed the same bug on our bug
> >>>>> tracker.
> >>>>> 
> >>>>> When you run "cmake ../src", which directory is this exactly? It
> >>>>> should be the directory containing INSTALL, THANKS, etc. Just to be
> >>>>> clear, it is not the "src" directory included in the openbabel source
> >>>>> distribution.
> >>>>> 
> >>>>> - Noel
> >>>>> 
> >>>>> On 9 December 2010 15:37, Merle, John  wrote:
> >>>>>> Dear Noel,
> >>>>>> 
> >>>>>> Thanks for the reply.
> >>>>>> 
> >>>>>> I am using the latest release OpenBabel 2.3 source distrubution and
> >>>>>> Cmake-2.6.4-5.el5.2.x86_64 (recently downloaded and installed).
> >>>>>> I executed the command: cmake ../src 2>&1 | tee cmake.out
> >>>>>> 
> >>>>>> The requested output file is attached.
> >>>>>> 
> >>>>>> Thank you,
> >>>>>> 
> >>>>>> John
> >>>>>> ---
> >>>>>>  Dr. John K. Merle
> >>>>>>  Assistant Professor of Chemistry
> >>>>>>  Winston-Salem State University
> >>>>>>  601 Martin Luther King Jr. Drive
> >>>>>>  W. B. Atkinson Building
> >>>>>>  Winston-Salem, NC 27110
&

Re: [Open Babel] cmake error in source install

[Igor Filippov [Contr]]

True, but  it's still out of source even if build directory is in
openbabel-2.3.0 - all the object files and CMakeCache.txt are in "build"
and not intermingled with the source code.

On Thu, 2010-12-09 at 15:00 -0500, Noel O'Boyle wrote:
> CMake recommends out-of-source builds.
> (http://www.cmake.org/Wiki/CMake_FAQ#Out-of-source_build_trees)
> 
> - Noel
> 
> On 9 December 2010 19:48, Igor Filippov [Contr]  
> wrote:
> > Hmmm, looks like the instructions published on that website are a bit
> > tricky:
> > tar zxf openbabel-2.3.0.tar.gz
> > mv openbabel-2.3.0 src
> > mkdir build
> > cmake ../src
> >
> > While this is correct, I believe the more common route (as usually 
> > described for other packages) would be:
> > tar -xzf openbabel-2.3.0.tar.gz
> > cd openbabel-2.3.0
> > mkdir build
> > cd build
> > cmake ../
> >
> > Igor
> >
> > On Thu, 2010-12-09 at 14:37 -0500, John Merle wrote:
> >> Noel,
> >>
> >> When I run "cmake ../src" I am in the build folder inside the openbabel
> >> folder. So, the "../src" IS referring to the src directory in the source
> >> distribution.
> >>
> >> If this is wrong should I run "cmake .."?
> >>
> >> Thanks
> >>
> >> John
> >>
> >>
> >> On 12/9/10 2:25 PM, "Noel O'Boyle"  wrote:
> >>
> >> > Hi John, (Please cc to the list)
> >> >
> >> > You're not alone - someone else just filed the same bug on our bug 
> >> > tracker.
> >> >
> >> > When you run "cmake ../src", which directory is this exactly? It
> >> > should be the directory containing INSTALL, THANKS, etc. Just to be
> >> > clear, it is not the "src" directory included in the openbabel source
> >> > distribution.
> >> >
> >> > - Noel
> >> >
> >> > On 9 December 2010 15:37, Merle, John  wrote:
> >> >> Dear Noel,
> >> >>
> >> >> Thanks for the reply.
> >> >>
> >> >> I am using the latest release OpenBabel 2.3 source distrubution and
> >> >> Cmake-2.6.4-5.el5.2.x86_64 (recently downloaded and installed).
> >> >> I executed the command: cmake ../src 2>&1 | tee cmake.out
> >> >>
> >> >> The requested output file is attached.
> >> >>
> >> >> Thank you,
> >> >>
> >> >> John
> >> >> ---
> >> >>  Dr. John K. Merle
> >> >>  Assistant Professor of Chemistry
> >> >>  Winston-Salem State University
> >> >>  601 Martin Luther King Jr. Drive
> >> >>  W. B. Atkinson Building
> >> >>  Winston-Salem, NC 27110
> >> >>  Office:  (336) 750-2237
> >> >>  Fax: (336) 750-2549
> >> >>  Email: merl...@wssu.edu
> >> >>  ---
> >> >>
> >> >>
> >> >>
> >> >> -Original Message-
> >> >> From: Noel O'Boyle [mailto:baoille...@gmail.com]
> >> >> Sent: Fri 12/3/2010 6:51 AM
> >> >> To: Merle, John
> >> >> Cc: openbabel-discuss@lists.sourceforge.net
> >> >> Subject: Re: [Open Babel] cmake error in source install
> >> >>
> >> >> Hi John,
> >> >>
> >> >> Can you provide some more background?
> >> >>
> >> >> What command line did you use? What version of CMake? Is this the Open
> >> >> Babel 2.3.0 official release you are compiling? Can you delete
> >> >> CMakeCache.txt and rerun CMake attaching the complete output (you
> >> >> should pipe it all to a file).
> >> >>
> >> >> - Noel
> >> >>
> >> >> On 2 December 2010 16:35, Merle, John  wrote:
> >> >>> Hello,
> >> >>>
> >> >>> I get the following errors from the cmake portion of the openbabel 
> >> >>> source
> >> >>> installation on Centos5.5 machine.
> >> >>>
> >> >>> Thanks
> >> >>>
> >> >>> CMake Error at formats/inchi103/CMakeLists.txt:21 (export):
> >> >>>   export FILE option given filename "" which does not have an 
> >

Re: [Open Babel] cmake error in source install

[Igor Filippov [Contr]]

Hmmm, looks like the instructions published on that website are a bit
tricky:
tar zxf openbabel-2.3.0.tar.gz
mv openbabel-2.3.0 src
mkdir build
cmake ../src

While this is correct, I believe the more common route (as usually described 
for other packages) would be:
tar -xzf openbabel-2.3.0.tar.gz
cd openbabel-2.3.0
mkdir build
cd build
cmake ../

Igor

On Thu, 2010-12-09 at 14:37 -0500, John Merle wrote:
> Noel,
> 
> When I run "cmake ../src" I am in the build folder inside the openbabel
> folder. So, the "../src" IS referring to the src directory in the source
> distribution.
> 
> If this is wrong should I run "cmake .."?
> 
> Thanks
> 
> John 
> 
> 
> On 12/9/10 2:25 PM, "Noel O'Boyle"  wrote:
> 
> > Hi John, (Please cc to the list)
> > 
> > You're not alone - someone else just filed the same bug on our bug tracker.
> > 
> > When you run "cmake ../src", which directory is this exactly? It
> > should be the directory containing INSTALL, THANKS, etc. Just to be
> > clear, it is not the "src" directory included in the openbabel source
> > distribution.
> > 
> > - Noel
> > 
> > On 9 December 2010 15:37, Merle, John  wrote:
> >> Dear Noel,
> >> 
> >> Thanks for the reply.
> >> 
> >> I am using the latest release OpenBabel 2.3 source distrubution and
> >> Cmake-2.6.4-5.el5.2.x86_64 (recently downloaded and installed).
> >> I executed the command: cmake ../src 2>&1 | tee cmake.out
> >> 
> >> The requested output file is attached.
> >> 
> >> Thank you,
> >> 
> >> John
> >> ---
> >>  Dr. John K. Merle
> >>  Assistant Professor of Chemistry
> >>  Winston-Salem State University
> >>  601 Martin Luther King Jr. Drive
> >>  W. B. Atkinson Building
> >>  Winston-Salem, NC 27110
> >>  Office:  (336) 750-2237
> >>  Fax: (336) 750-2549
> >>  Email: merl...@wssu.edu
> >>  ---
> >> 
> >> 
> >> 
> >> -Original Message-
> >> From: Noel O'Boyle [mailto:baoille...@gmail.com]
> >> Sent: Fri 12/3/2010 6:51 AM
> >> To: Merle, John
> >> Cc: openbabel-discuss@lists.sourceforge.net
> >> Subject: Re: [Open Babel] cmake error in source install
> >> 
> >> Hi John,
> >> 
> >> Can you provide some more background?
> >> 
> >> What command line did you use? What version of CMake? Is this the Open
> >> Babel 2.3.0 official release you are compiling? Can you delete
> >> CMakeCache.txt and rerun CMake attaching the complete output (you
> >> should pipe it all to a file).
> >> 
> >> - Noel
> >> 
> >> On 2 December 2010 16:35, Merle, John  wrote:
> >>> Hello,
> >>> 
> >>> I get the following errors from the cmake portion of the openbabel source
> >>> installation on Centos5.5 machine.
> >>> 
> >>> Thanks
> >>> 
> >>> CMake Error at formats/inchi103/CMakeLists.txt:21 (export):
> >>>   export FILE option given filename "" which does not have an extension of
> >>>   ".cmake".
> >>> 
> >>> 
> >>> 
> >>> CMake Error at formats/inchi103/CMakeLists.txt:23 (install):
> >>>   install TARGETS given no ARCHIVE DESTINATION for static library target
> >>>   "inchi".
> >>> 
> >>> 
> >>> CMake Error at CMakeLists.txt:232 (export):
> >>>   export FILE option given filename "" which does not have an extension of
> >>>   ".cmake".
> >>> 
> >>> 
> >>> 
> >>> CMake Error at CMakeLists.txt:234 (install):
> >>>   install TARGETS given no ARCHIVE DESTINATION for static library target
> >>>   "openbabel".
> >>> 
> >>> 
> >>> -- Configuring incomplete, errors occurred!
> >>> 
> >>> 
> >>> ---
> >>>  Dr. John K. Merle
> >>>  Assistant Professor of Chemistry
> >>>  Winston-Salem State University
> >>>  601 Martin Luther King Jr. Drive
> >>>  W. B. Atkinson Building
> >>>  Winston-Salem, NC 27110
> >>>  Office:  (336) 750-2237
> >>>  Fax: (336) 750-2549
> >>>  Email: merl...@wssu.edu
> >>>  ---
> >>> 
> >>> 
> >>> 
> >>> 
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> >>> 
> >> 
> >> 
> >> 
> 
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Re: [Open Babel] cmake error in source install

[Igor Filippov [Contr]]

I was just going to say RTFM, but to my shock and surprise the manual
actually does say "cmake ../src"!!!
http://openbabel.org/docs/2.3.0/Installation/install.html#compiling-open-babel

John, you should use "cmake ../" I have no slightest idea who put
"cmake ../src" on the above page, it's just plain wrong.

There were several other places with compilation instructions, not sure
where they are now. Some of those instructions have been correct for
some of the OSes.

Best,
Igor

On Thu, 2010-12-09 at 14:37 -0500, John Merle wrote:
> Noel,
> 
> When I run "cmake ../src" I am in the build folder inside the openbabel
> folder. So, the "../src" IS referring to the src directory in the source
> distribution.
> 
> If this is wrong should I run "cmake .."?
> 
> Thanks
> 
> John 
> 
> 
> On 12/9/10 2:25 PM, "Noel O'Boyle"  wrote:
> 
> > Hi John, (Please cc to the list)
> > 
> > You're not alone - someone else just filed the same bug on our bug tracker.
> > 
> > When you run "cmake ../src", which directory is this exactly? It
> > should be the directory containing INSTALL, THANKS, etc. Just to be
> > clear, it is not the "src" directory included in the openbabel source
> > distribution.
> > 
> > - Noel
> > 
> > On 9 December 2010 15:37, Merle, John  wrote:
> >> Dear Noel,
> >> 
> >> Thanks for the reply.
> >> 
> >> I am using the latest release OpenBabel 2.3 source distrubution and
> >> Cmake-2.6.4-5.el5.2.x86_64 (recently downloaded and installed).
> >> I executed the command: cmake ../src 2>&1 | tee cmake.out
> >> 
> >> The requested output file is attached.
> >> 
> >> Thank you,
> >> 
> >> John
> >> ---
> >>  Dr. John K. Merle
> >>  Assistant Professor of Chemistry
> >>  Winston-Salem State University
> >>  601 Martin Luther King Jr. Drive
> >>  W. B. Atkinson Building
> >>  Winston-Salem, NC 27110
> >>  Office:  (336) 750-2237
> >>  Fax: (336) 750-2549
> >>  Email: merl...@wssu.edu
> >>  ---
> >> 
> >> 
> >> 
> >> -Original Message-
> >> From: Noel O'Boyle [mailto:baoille...@gmail.com]
> >> Sent: Fri 12/3/2010 6:51 AM
> >> To: Merle, John
> >> Cc: openbabel-discuss@lists.sourceforge.net
> >> Subject: Re: [Open Babel] cmake error in source install
> >> 
> >> Hi John,
> >> 
> >> Can you provide some more background?
> >> 
> >> What command line did you use? What version of CMake? Is this the Open
> >> Babel 2.3.0 official release you are compiling? Can you delete
> >> CMakeCache.txt and rerun CMake attaching the complete output (you
> >> should pipe it all to a file).
> >> 
> >> - Noel
> >> 
> >> On 2 December 2010 16:35, Merle, John  wrote:
> >>> Hello,
> >>> 
> >>> I get the following errors from the cmake portion of the openbabel source
> >>> installation on Centos5.5 machine.
> >>> 
> >>> Thanks
> >>> 
> >>> CMake Error at formats/inchi103/CMakeLists.txt:21 (export):
> >>>   export FILE option given filename "" which does not have an extension of
> >>>   ".cmake".
> >>> 
> >>> 
> >>> 
> >>> CMake Error at formats/inchi103/CMakeLists.txt:23 (install):
> >>>   install TARGETS given no ARCHIVE DESTINATION for static library target
> >>>   "inchi".
> >>> 
> >>> 
> >>> CMake Error at CMakeLists.txt:232 (export):
> >>>   export FILE option given filename "" which does not have an extension of
> >>>   ".cmake".
> >>> 
> >>> 
> >>> 
> >>> CMake Error at CMakeLists.txt:234 (install):
> >>>   install TARGETS given no ARCHIVE DESTINATION for static library target
> >>>   "openbabel".
> >>> 
> >>> 
> >>> -- Configuring incomplete, errors occurred!
> >>> 
> >>> 
> >>> ---
> >>>  Dr. John K. Merle
> >>>  Assistant Professor of Chemistry
> >>>  Winston-Salem State University
> >>>  601 Martin Luther King Jr. Drive
> >>>  W. B. Atkinson Building
> >>>  Winston-Salem, NC 27110
> >>>  Office:  (336) 750-2237
> >>>  Fax: (336) 750-2549
> >>>  Email: merl...@wssu.edu
> >>>  ---
> >>> 
> >>> 
> >>> 
> >>> 
> >>> --
> >>> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> >>> Tap into the largest installed PC base & get more eyes on your game by
> >>> optimizing for Intel(R) Graphics Technology. Get started today with the
> >>> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> >>> http://p.sf.net/sfu/intelisp-dev2dev
> >>> ___
> >>> OpenBabel-discuss mailing list
> >>> OpenBabel-discuss@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >>> 
> >>> 
> >> 
> >> 
> >> 
> 
> 
> --
> ___
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> https://lists.sourceforge.net/lists/listinfo/openbabel-d

Re: [Open Babel] Retrieving both Kekule structures?

[Igor Filippov [Contr]]

I would be very interested in this too, if it's possible in a general
case.

Best regards,
Igor

On Tue, 2010-11-30 at 05:48 -0500, Hans De Winter wrote:
> All,
> 
> I'm using the OB C++ API and I wwas wondering whether there is a way  
> to retrieve bot Kekule structure from an aromatic system (if there are  
> two Kekule's)? For example, I would like to get access to both Kekule  
> forms of the aromatic indole ( c1ccc2c(c1)[nH]cc2 ), hence  
> [NH]1C=CC2=CC=CC=C12 and [NH]1C=CC2=C1C=CC=C2
> 
> Any C++ API methods available or alternative ideas?
> 
> Thank you,
> Hans
> 
> 
> 
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Re: [Open Babel] problem with installation of openbabel_2.3.0

[Igor Filippov [Contr]]

Duan,

Looks like you need to install boost. On my Fedora 13 system the
necessary package is boost-devel.


Hope this helps,
Igor


On Fri, 2010-11-12 at 03:18 -0500, 段宝根 wrote:
>  
> Hi,
>
>I want to install openbabel_2.3.0 in linux OS, but some errors are
> found in the course of compiling. The attachments are cmake.out and
> make.out files.
>  
>   Thanks you for  your great help.
>  
> Duan baogen
>  



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Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

Tim,

The "cmake" step now requires static libxml2 installed, otherwise it
fails - not a problem, just something people should be aware of. The
output when lixml2.a is absent is attached  - cmake.out;

The bigger problem is, even after I install static libxml2 the
compilation step fails for me. I'm attaching make.out output of "make".

Igor


On Thu, 2010-10-21 at 20:25 -0400, Tim Vandermeersch wrote:
> On Thu, Oct 21, 2010 at 1:35 AM, Tim Vandermeersch
>  wrote:
> > On Wed, Oct 20, 2010 at 4:29 PM, Igor Filippov [Contr]
> >  wrote:
> >> Tim,
> >>
> >>> I'll take a look since it is an important format to support. This
> >>> should be the last major issue for static building though.
> >>>
> >>
> >> Great - thank you! Could the static_plugins.o be also compiled into
> >> libopenbabel.a by default? I think this would make sense...
> >
> > Yes, but this would require the -u flags again... The plugins are
> > compiled into libopenbabel.a but the symbols are not taken from the
> > libopenbabel.a archive when linking your executable since they are not
> > referenced. There are two solutions:
> >
> > * Include the plugins inside the executable (or include
> > static_plugin.o when linking)
> > * Undefine the symbols explicitly at link time using the -u flag to
> > ensure the symbols are taken from libopenbabel.a
> >
> > However, I just pushed the changes to include inchi in the static
> > builds and you could use this command line to create a
> > static_plugins.o that contains all plugins: (run this after compiling)
> >
> > tim...@timvdm-desktop:~/openbabel-gitsvn/build_static$ g++ -Wl,-r -o
> > static_plugins.o -nostdlib  src/CMakeFiles/openbabel.dir/charges/*.o
> > src/CMakeFiles/openbabel.dir/descriptors/*.o
> > src/CMakeFiles/openbabel.dir/fingerprints/*.o
> > src/CMakeFiles/openbabel.dir/forcefields/*.o
> > src/CMakeFiles/openbabel.dir/formats/*.o
> > src/CMakeFiles/openbabel.dir/formats/xml/*.o
> > src/CMakeFiles/openbabel.dir/ops/*.o
> >
> > tim...@timvdm-desktop:~/openbabel-gitsvn/build_static$ ls static_plugins.o 
> > -lh
> > -rw-r--r-- 1 timvdm timvdm 65M 2010-10-21 01:16 static_plugins.o
> >
> > tim...@timvdm-desktop:~/openbabel-gitsvn/build_static$ objdump -t
> > static_plugins.o | grep _ZTVN9OpenBabel11InChIFormatE
> >  ld
> > .rodata._ZTVN9OpenBabel11InChIFormatE   
> > .rodata._ZTVN9OpenBabel11InChIFormatE
> >   wO
> > .rodata._ZTVN9OpenBabel11InChIFormatE   00a8 .hidden
> > _ZTVN9OpenBabel11InChIFormatE
> >
> > tim...@timvdm-desktop:~/openbabel-gitsvn/build_static$ g++ -Iinclude
> > -I../include -static  ../doc/examples/static_executable/myexe.cpp
> > static_plugins.o -o myexe  src/libopenbabel.a
> > src/formats/inchi103/libinchi.a -Wl,-Bstatic -lxml2 -lz
> > ...
> > tim...@timvdm-desktop:~/openbabel-gitsvn/build_static$ ./myexe
> > ... lists all plugins ...
> >
> > The command first line "merges" all the object files in a single
> > static_plugins.o. There is probably a better way but at least you
> > should now be able to make a static executable with all plugins.
> 
> With r4240, plugins are now included in an executable without any
> additional hacks. It's all done in C++ which means it is also easier
> to maintain for different compilers. This also means that the tests
> can now be executed for static builds. This helped me identify some
> missing plugins.
> 
> Tim
> 
> > Tim
> >
> >> Igor
> >>
> >>
> >



make.out
Description: chemical/gulp


cmake.out
Description: chemical/gulp
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Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

Tim,

> 
> With r4240, plugins are now included in an executable without any
> additional hacks. It's all done in C++ which means it is also easier
> to maintain for different compilers. This also means that the tests
> can now be executed for static builds. This helped me identify some
> missing plugins.

This is great! Will there be an RC2 to test the newest
additions/changes?


Igor


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Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

Tim,

> I'll take a look since it is an important format to support. This
> should be the last major issue for static building though.
> 

Great - thank you! Could the static_plugins.o be also compiled into
libopenbabel.a by default? I think this would make sense...

Igor


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Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

> 
> static_plugins.cpp only contains a few formats since including all
> formats in a single cpp file can take a long time/memory to compile.
True, but piece-meal inclusion with flags such as WITH_COMMON_FORMATS seems a 
very reasonable approach.
It would be great if a set of such flags covered the whole total of 147
formats available.

> 
> I have not yet attempted to include InChI in the static build.
> However, if you have a static inchi library, you should be able to
> include the inchi OB formats and link against it.

Are you planning to do it for the release?

I am trying to make a static InChI library but as I know exactly zero
about cmake I'm not very successful so far...


Igor


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Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

These are the formats recognized by statically linked OB:

$ bin/babel -L formats
can -- Canonical SMILES format
copy -- Copy raw text [Write-only]
ent -- Protein Data Bank format
fix -- SMILES FIX format [Write-only]
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
molreport -- Open Babel molecule report [Write-only]
pdb -- Protein Data Bank format
pov -- POV-Ray input format [Write-only]
report -- Open Babel report format [Write-only]
sd -- MDL MOL format
sdf -- MDL MOL format
smi -- SMILES format
smiles -- SMILES format
sy2 -- Sybyl Mol2 format
txt -- Title format

The formats recognized by "regular" (dynamical) OB are numbered 147 so I
won't quote them all here, but clearly a lot are missing. Most important
for me is InChI.

Igor




On Mon, 2010-10-18 at 16:09 -0400, Tim Vandermeersch wrote:
> On Mon, Oct 18, 2010 at 9:49 PM, Igor Filippov [Contr]
>  wrote:
> > Tim,
> >
> > Something still not working for me -
> >
> > Here is what I do:
> >
> > g++ -fopenmp -g -O3 -g -O2  -I/usr/local/  -D_LIB -D_MT   -Wall
> > -I/usr/local//src/ -I/usr/local//src/ -I/usr/local//include/
> > -I../openbabel-2.3.0rc1//include/
> > -I../openbabel-2.3.0rc1//build/include/ -I/usr/local/include/
> > -I/usr/include/GraphicsMagick -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> > -mtune=generic -pthread   -u _ZTVN9OpenBabel9SMIFormatE
> > -u_ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9CanSmilesE -c
> > osra.cpp
> >
> > .
> >
> > g++ -fopenmp -g -O3  -u _ZTVN9OpenBabel9SMIFormatE
> > -u_ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9CanSmilesE  -o osra
> > osra.o osra_anisotropic.o osra_ocr.o osra_openbabel.o mcdlutil.o
> > unpaper.o -L/usr/local//src/ -lpotrace -L/usr/local/ -locrad -lm
> > -lGraphicsMagick++ -lGraphicsMagick -llcms -lfreetype -lXext -lSM -lICE
> > -lX11 -lbz2 -lz -lm -lgomp -lpthread  -L/usr/lib64 -L/usr/lib -L/usr/lib
> > -L/usr/local//src/ -lPgm2asc
> > -lnetpbm ../openbabel-2.3.0rc1//build/src/libopenbabel.a
> >
> > The resulting executable does not produce SMILES.
> 
> You can verify that the symbols are in the executable using:
> 
> objdump -t myexe | grep CanSmi
> 
> > Moreover, when I try to do "make test" on statically linked babel I get
> > the following:
> >
> > 27% tests passed, 41 tests failed out of 56
> >
> > Far cry from 100% "PASS" on dynamically linked babel.
> 
> No, the tests don't work for static builds yet. Only the babel
> executable with all plugins.
> 
> > Igor
> >
> > On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wrote:
> >> Hi,
> >>
> >> On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr]
> >>  wrote:
> >> > Tim,
> >> >
> >> > Thanks, I can build my executable per your instructions and it runs
> >> > without segfaults, but doesn't seem to get the format plugins yet - the
> >> > output when I want to get SMILES for example is empty.
> >> >
> >> > I'm also looking at the page "Plugins -> Creating custom static
> >> > libraries" at http://openbabel.org/wiki/CMake
> >> > but it's so terse I cannot figure out how to use this information for a
> >> > project that does not use cmake itself. And I'm not a cmake expert at
> >> > all unfortunately...
> >>
> >> You can build the doc/examples/static_executable exe using cmake and
> >> "make VERBOSE=1". This will print the commands used for compiling.
> >>
> >> For example:
> >>
> >> [100%] Building CXX object CMakeFiles/myexe.dir/myexe.cpp.o
> >> /usr/bin/c++-u _ZTVN9OpenBabel9ACRFormatE -u
> >> _ZTVN9OpenBabel15ADFOutputFormatE -u _ZTVN9OpenBabel14ADFInputFormatE
> >> -u _ZTVN9OpenBabel11OBT41FormatE -u _ZTVN9OpenBabel13AlchemyFormatE -u
> >> _ZTVN9OpenBabel15AmberPrepFormatE -u _ZTVN9OpenBabel14OBAPIInterfaceE
> >> -u _ZTVN9OpenBabel15BallStickFormatE -u _ZTVN9OpenBabel9BGFFormatE -u
> >> _ZTVN9OpenBabel9BoxFormatE -u _ZTVN9OpenBabel11CacaoFormatE -u
> >> _ZTVN9OpenBabel11CacheFormatE -u _ZTVN9OpenBabel9CARFormatE -u
> >> _ZTVN9OpenBabel9CCCFormatE -u _ZTVN9OpenBabel13CHEM3D1FormatE -u
> >> _ZTVN9OpenBabel13CHEM3D2FormatE -u
> >> _ZTVN9OpenBabel20ChemDrawBinaryFormatE -u
> >> _ZTVN9OpenBabel14ChemDrawFormatE -u _ZTVN9OpenBabel13ChemKinFormatE -u
> >> _ZTVN9OpenBabel9CHTFormatE -u _ZTVN9OpenBabel9CIFFormatE -u
> >>

Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

Replying to my own message - I can happily report some progress:
I was able to get a functioning executable by linking with
libopenbabel.a AND static_plugins.o:

g++ -fopenmp -g -O3 -fPIC   -o osra osra.o osra_anisotropic.o osra_ocr.o
osra_openbabel.o mcdlutil.o unpaper.o -L/usr/local//src/ -lpotrace
-L/usr/local/ -locrad -lm  -lGraphicsMagick++ -lGraphicsMagick -llcms
-lfreetype -lXext -lSM -lICE -lX11 -lbz2 -lz -lm -lgomp -lpthread
-L/usr/lib64 -L/usr/lib -L/usr/lib  -L/usr/local//src/ -lPgm2asc
-lnetpbm 
../openbabel-2.3.0rc1//build/tools/CMakeFiles/babel.dir/static_plugins.o 
../openbabel-2.3.0rc1//build/src/libopenbabel.a  

The executable produced in this way (no -u... options were necessary) is
generating SMILES and SDF output. However InChI output is still missing
for some reason, so we're 95% there for me.

Igor


On Mon, 2010-10-18 at 15:49 -0400, Filippov, Igor (NIH/NCI) [C] wrote:
> Tim,
> 
> Something still not working for me -
> 
> Here is what I do:
> 
> g++ -fopenmp -g -O3 -g -O2  -I/usr/local/  -D_LIB -D_MT   -Wall
> -I/usr/local//src/ -I/usr/local//src/ -I/usr/local//include/
> -I../openbabel-2.3.0rc1//include/
> -I../openbabel-2.3.0rc1//build/include/ -I/usr/local/include/
> -I/usr/include/GraphicsMagick -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> -mtune=generic -pthread   -u _ZTVN9OpenBabel9SMIFormatE
> -u_ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9CanSmilesE -c
> osra.cpp
> 
> .
> 
> g++ -fopenmp -g -O3  -u _ZTVN9OpenBabel9SMIFormatE
> -u_ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9CanSmilesE  -o osra
> osra.o osra_anisotropic.o osra_ocr.o osra_openbabel.o mcdlutil.o
> unpaper.o -L/usr/local//src/ -lpotrace -L/usr/local/ -locrad -lm
> -lGraphicsMagick++ -lGraphicsMagick -llcms -lfreetype -lXext -lSM -lICE
> -lX11 -lbz2 -lz -lm -lgomp -lpthread  -L/usr/lib64 -L/usr/lib -L/usr/lib
> -L/usr/local//src/ -lPgm2asc
> -lnetpbm ../openbabel-2.3.0rc1//build/src/libopenbabel.a
> 
> The resulting executable does not produce SMILES.
> 
> Moreover, when I try to do "make test" on statically linked babel I get
> the following:
> 
> 27% tests passed, 41 tests failed out of 56
> 
> Far cry from 100% "PASS" on dynamically linked babel.
> 
> Igor
> 
> On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wrote:
> > Hi,
> >
> > On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr]
> >  wrote:
> > > Tim,
> > >
> > > Thanks, I can build my executable per your instructions and it runs
> > > without segfaults, but doesn't seem to get the format plugins yet - the
> > > output when I want to get SMILES for example is empty.
> > >
> > > I'm also looking at the page "Plugins -> Creating custom static
> > > libraries" at http://openbabel.org/wiki/CMake
> > > but it's so terse I cannot figure out how to use this information for a
> > > project that does not use cmake itself. And I'm not a cmake expert at
> > > all unfortunately...
> >
> > You can build the doc/examples/static_executable exe using cmake and
> > "make VERBOSE=1". This will print the commands used for compiling.
> >
> > For example:
> >
> > [100%] Building CXX object CMakeFiles/myexe.dir/myexe.cpp.o
> > /usr/bin/c++-u _ZTVN9OpenBabel9ACRFormatE -u
> > _ZTVN9OpenBabel15ADFOutputFormatE -u _ZTVN9OpenBabel14ADFInputFormatE
> > -u _ZTVN9OpenBabel11OBT41FormatE -u _ZTVN9OpenBabel13AlchemyFormatE -u
> > _ZTVN9OpenBabel15AmberPrepFormatE -u _ZTVN9OpenBabel14OBAPIInterfaceE
> > -u _ZTVN9OpenBabel15BallStickFormatE -u _ZTVN9OpenBabel9BGFFormatE -u
> > _ZTVN9OpenBabel9BoxFormatE -u _ZTVN9OpenBabel11CacaoFormatE -u
> > _ZTVN9OpenBabel11CacheFormatE -u _ZTVN9OpenBabel9CARFormatE -u
> > _ZTVN9OpenBabel9CCCFormatE -u _ZTVN9OpenBabel13CHEM3D1FormatE -u
> > _ZTVN9OpenBabel13CHEM3D2FormatE -u
> > _ZTVN9OpenBabel20ChemDrawBinaryFormatE -u
> > _ZTVN9OpenBabel14ChemDrawFormatE -u _ZTVN9OpenBabel13ChemKinFormatE -u
> > _ZTVN9OpenBabel9CHTFormatE -u _ZTVN9OpenBabel9CIFFormatE -u
> > _ZTVN9OpenBabel10CopyFormatE -u _ZTVN9OpenBabel11CRK2DFormatE -u
> > _ZTVN9OpenBabel11CRK3DFormatE -u _ZTVN9OpenBabel9CSRFormatE -u
> > _ZTVN9OpenBabel10CSSRFormatE -u _ZTVN9OpenBabel18DlpolyConfigFormatE
> > -u _ZTVN9OpenBabel19DlpolyHISTORYFormatE -u
> > _ZTVN9OpenBabel10DMolFormatE -u _ZTVN9OpenBabel9XXXFormatE -u
> > _ZTVN9OpenBabel11FASTAFormatE -u _ZTVN9OpenBabel16FastSearchFormatE -u
> > _ZTVN9OpenBabel10FCHKFormatE -u _ZTVN9OpenBabel10FEATFormatE -u
> > _ZTVN9OpenBabel16FenskeZmatFormatE -u _ZTVN9OpenBa

Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

Tim, 

Something still not working for me - 

Here is what I do:

g++ -fopenmp -g -O3 -g -O2  -I/usr/local/  -D_LIB -D_MT   -Wall
-I/usr/local//src/ -I/usr/local//src/ -I/usr/local//include/
-I../openbabel-2.3.0rc1//include/
-I../openbabel-2.3.0rc1//build/include/ -I/usr/local/include/
-I/usr/include/GraphicsMagick -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -pthread   -u _ZTVN9OpenBabel9SMIFormatE
-u_ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9CanSmilesE -c
osra.cpp

.

g++ -fopenmp -g -O3  -u _ZTVN9OpenBabel9SMIFormatE
-u_ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9CanSmilesE  -o osra
osra.o osra_anisotropic.o osra_ocr.o osra_openbabel.o mcdlutil.o
unpaper.o -L/usr/local//src/ -lpotrace -L/usr/local/ -locrad -lm
-lGraphicsMagick++ -lGraphicsMagick -llcms -lfreetype -lXext -lSM -lICE
-lX11 -lbz2 -lz -lm -lgomp -lpthread  -L/usr/lib64 -L/usr/lib -L/usr/lib
-L/usr/local//src/ -lPgm2asc
-lnetpbm ../openbabel-2.3.0rc1//build/src/libopenbabel.a   

The resulting executable does not produce SMILES.

Moreover, when I try to do "make test" on statically linked babel I get
the following:

27% tests passed, 41 tests failed out of 56

Far cry from 100% "PASS" on dynamically linked babel.

Igor

On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wrote:
> Hi,
> 
> On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr]
>  wrote:
> > Tim,
> >
> > Thanks, I can build my executable per your instructions and it runs
> > without segfaults, but doesn't seem to get the format plugins yet - the
> > output when I want to get SMILES for example is empty.
> >
> > I'm also looking at the page "Plugins -> Creating custom static
> > libraries" at http://openbabel.org/wiki/CMake
> > but it's so terse I cannot figure out how to use this information for a
> > project that does not use cmake itself. And I'm not a cmake expert at
> > all unfortunately...
> 
> You can build the doc/examples/static_executable exe using cmake and
> "make VERBOSE=1". This will print the commands used for compiling.
> 
> For example:
> 
> [100%] Building CXX object CMakeFiles/myexe.dir/myexe.cpp.o
> /usr/bin/c++-u _ZTVN9OpenBabel9ACRFormatE -u
> _ZTVN9OpenBabel15ADFOutputFormatE -u _ZTVN9OpenBabel14ADFInputFormatE
> -u _ZTVN9OpenBabel11OBT41FormatE -u _ZTVN9OpenBabel13AlchemyFormatE -u
> _ZTVN9OpenBabel15AmberPrepFormatE -u _ZTVN9OpenBabel14OBAPIInterfaceE
> -u _ZTVN9OpenBabel15BallStickFormatE -u _ZTVN9OpenBabel9BGFFormatE -u
> _ZTVN9OpenBabel9BoxFormatE -u _ZTVN9OpenBabel11CacaoFormatE -u
> _ZTVN9OpenBabel11CacheFormatE -u _ZTVN9OpenBabel9CARFormatE -u
> _ZTVN9OpenBabel9CCCFormatE -u _ZTVN9OpenBabel13CHEM3D1FormatE -u
> _ZTVN9OpenBabel13CHEM3D2FormatE -u
> _ZTVN9OpenBabel20ChemDrawBinaryFormatE -u
> _ZTVN9OpenBabel14ChemDrawFormatE -u _ZTVN9OpenBabel13ChemKinFormatE -u
> _ZTVN9OpenBabel9CHTFormatE -u _ZTVN9OpenBabel9CIFFormatE -u
> _ZTVN9OpenBabel10CopyFormatE -u _ZTVN9OpenBabel11CRK2DFormatE -u
> _ZTVN9OpenBabel11CRK3DFormatE -u _ZTVN9OpenBabel9CSRFormatE -u
> _ZTVN9OpenBabel10CSSRFormatE -u _ZTVN9OpenBabel18DlpolyConfigFormatE
> -u _ZTVN9OpenBabel19DlpolyHISTORYFormatE -u
> _ZTVN9OpenBabel10DMolFormatE -u _ZTVN9OpenBabel9XXXFormatE -u
> _ZTVN9OpenBabel11FASTAFormatE -u _ZTVN9OpenBabel16FastSearchFormatE -u
> _ZTVN9OpenBabel10FCHKFormatE -u _ZTVN9OpenBabel10FEATFormatE -u
> _ZTVN9OpenBabel16FenskeZmatFormatE -u _ZTVN9OpenBabel13FHIainsFormatE
> -u _ZTVN9OpenBabel17FingerprintFormatE -u
> _ZTVN9OpenBabel24FreeFormFractionalFormatE -u
> _ZTVN9OpenBabel18GAMESSOutputFormatE -u
> _ZTVN9OpenBabel17GAMESSInputFormatE -u
> _ZTVN9OpenBabel14GAMESSUKFormatE -u
> _ZTVN9OpenBabel19GAMESSUKInputFormatE -u
> _ZTVN9OpenBabel20GAMESSUKOutputFormatE -u
> _ZTVN9OpenBabel20OBGaussianCubeFormatE -u
> _ZTVN9OpenBabel20GaussianOutputFormatE -u
> _ZTVN9OpenBabel19GaussianInputFormatE -u
> _ZTVN9OpenBabel26GaussianZMatrixInputFormatE -u
> _ZTVN9OpenBabel13GenBankFormatE -u _ZTVN9OpenBabel14GhemicalFormatE -u
> _ZTVN9OpenBabel14GROMOS96FormatE -u _ZTVN9OpenBabel10GULPFormatE -u
> _ZTVN9OpenBabel9HINFormatE -u _ZTVN9OpenBabel18JaguarOutputFormatE -u
> _ZTVN9OpenBabel17JaguarInputFormatE -u _ZTVN9OpenBabel10MCDLFormatE -u
> _ZTVN9OpenBabel9MDLFormatE -u _ZTVN9OpenBabel9MOLFormatE -u
> _ZTVN9OpenBabel9SDFFormatE -u _ZTVN9OpenBabel11mmCIFFormatE -u
> _ZTVN9OpenBabel14MacroModFormatE -u _ZTVN9OpenBabel9MNAFormatE -u
> _ZTVN9OpenBabel10MOL2FormatE -u _ZTVN9OpenBabel14OBMoldenFormatE -u
> _ZTVN9OpenBabel18MolproOutputFormatE -u
> _ZTVN9OpenBabel17MolproInputFormatE -u
> _ZTVN9OpenBabel15MolReportFormatE -u _ZTVN9OpenBabel11MOPACFormatE -u
> _ZTVN9OpenBabel15MOPACCARTFormatE -u _ZTVN9OpenBabel14MOPACINTF

Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

Tim,

Thanks, I can build my executable per your instructions and it runs
without segfaults, but doesn't seem to get the format plugins yet - the
output when I want to get SMILES for example is empty.

I'm also looking at the page "Plugins -> Creating custom static
libraries" at http://openbabel.org/wiki/CMake
but it's so terse I cannot figure out how to use this information for a
project that does not use cmake itself. And I'm not a cmake expert at
all unfortunately...

Igor


On Sat, 2010-10-16 at 10:23 -0400, Tim Vandermeersch wrote:
> On Fri, Oct 15, 2010 at 11:40 PM, Igor Filippov [Contr]
>  wrote:
> > It builds nicely on Fedora 12, x64 system.
> > Some points:
> >
> > 1) When building with -DBUILD_SHARED=no one needs to make sure static
> > zlib exists somewhere (libz.a) otherwise the error message which cmake
> > gives is somewhat confusing.
> >
> > 2) build/lib is full of dynamic libs (.so) even with BUILD_SHARED=no.
> > There is a static libopenbabel.a is build/src, which is great, but
> > linking against it gives the following error:
> > undefined reference to `OpenBabel::OBMol::FindChiralCenters()'
> > collect2: ld returned 1 exit status
> >
> > babel executable seems to be linked statically though so perhaps I'm not
> > linking correctly?
> 
> Something like this should work:
> 
> g++ -static myexe.cpp.o  -o myexe  /usr/local/lib/libopenbabel.a
> -Wl,-Bstatic -lm -lz
> 
> I'll reply in a separate thread with more details on static building.
> The MinGW page (http://openbabel.org/wiki/Install_%28MinGW%29) is
> updated but it doesn't address handling plugins yet.
> 
> Tim
> 
> > 3) The version is still set at 2.2.99 not 2.3.0 :)
> >
> > Thanks!
> > Igor
> >
> >
> > On Fri, 2010-10-15 at 16:56 -0400, Geoffrey Hutchison wrote:
> >> I have uploaded a source-code only version of the 2.3.0 release candidate 
> >> 1.
> >> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-10-15/openbabel-2.3.0rc1-20101015-r4206.tar.gz/download
> >>
> >> Please give this a try and see if there are glaring bugs, issues, etc. 
> >> Over the next week, we will be working on fixing up the documentation the 
> >> website, etc.
> >>
> >> Let us know what you think -- we look forward to a good release on Oct. 
> >> 23rd.
> >>
> >> Thanks,
> >> -Geoff
> >>
> >> ---
> >> Prof. Geoffrey Hutchison
> >> Department of Chemistry
> >> University of Pittsburgh
> >> tel: (412) 648-0492
> >> email: geo...@pitt.edu
> >> web: http://hutchison.chem.pitt.edu/
> >>
> >>
> >> --
> >> Download new Adobe(R) Flash(R) Builder(TM) 4
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> >> ___
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> >> openbabel-de...@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
> >
> >
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> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >



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Re: [Open Babel] [OpenBabel-Devel] Version 2.3.0 Release Candidate 1

[Igor Filippov [Contr]]

It builds nicely on Fedora 12, x64 system.
Some points:

1) When building with -DBUILD_SHARED=no one needs to make sure static
zlib exists somewhere (libz.a) otherwise the error message which cmake
gives is somewhat confusing.

2) build/lib is full of dynamic libs (.so) even with BUILD_SHARED=no.
There is a static libopenbabel.a is build/src, which is great, but
linking against it gives the following error:
undefined reference to `OpenBabel::OBMol::FindChiralCenters()'
collect2: ld returned 1 exit status

babel executable seems to be linked statically though so perhaps I'm not
linking correctly?

3) The version is still set at 2.2.99 not 2.3.0 :)

Thanks!
Igor


On Fri, 2010-10-15 at 16:56 -0400, Geoffrey Hutchison wrote:
> I have uploaded a source-code only version of the 2.3.0 release candidate 1.
> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-10-15/openbabel-2.3.0rc1-20101015-r4206.tar.gz/download
> 
> Please give this a try and see if there are glaring bugs, issues, etc. Over 
> the next week, we will be working on fixing up the documentation the website, 
> etc.
> 
> Let us know what you think -- we look forward to a good release on Oct. 23rd.
> 
> Thanks,
> -Geoff
> 
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu
> web: http://hutchison.chem.pitt.edu/
> 
> 
> --
> Download new Adobe(R) Flash(R) Builder(TM) 4
> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly 
> Flex(R) Builder(TM)) enable the development of rich applications that run
> across multiple browsers and platforms. Download your free trials today!
> http://p.sf.net/sfu/adobe-dev2dev
> ___
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> openbabel-de...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel



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Re: [Open Babel] markush structures in openbabel

[Igor Filippov [Contr]]

Tim,

You are absolutely right. As soon as I removed openbabel rpm which came
with my Fedora 12 installation I could compile and link things properly
with the svn snapshot libopenbabel.

Thank you,
Igor

P.S. Chris the fix for atomic aliases works like a charm, thanks once
again!


On Mon, 2010-08-09 at 12:11 -0400, Tim Vandermeersch wrote:
> On Mon, Aug 9, 2010 at 5:50 PM, Igor Filippov [Contr]
>  wrote:
> > Chris,
> >
> > Thank you. I'm trying to test it with the latest trunk (r3955) but even
> > though OB itself compiled fine I'm getting the following error when
> > trying to link libopenbabel to my program:
> >
> > undefined reference to `OpenBabel::AliasData::GetAlias(bool) const'
> > collect2: ld returned 1 exit status
> >
> > Was there some significant change in how libopenbabel should be linked?
> > It was working fine with 2.2.3 release.
> 
> No, the API and "linking method" is unchanged. However, the ABI will
> be changed for the 2.3 release and the GetAlias function changed from:
> 
> std::string GetAlias() const;
> 
> to:
> 
> std::string GetAlias(bool rightAligned = false) const;
> 
> Since the linker complains about this symbol being undefined you are
> probably using the new headers but link to the old library.
> 
> Tim
> 
> > Igor
> >
> > On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote:
> >> Thanks. Corrected in r3897.
> >> Chris
> >>
> >> On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
> >> > I've run into a problem with an SD file generated by OB with atomic
> >> > aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
> >> > displayed correctly by ChemAxxon MarvinSketch.
> >> > CamridgeSoft support tells me the atom numbers should be
> >> > right-justified, where they are left-justified in OB output. Akos Papp
> >> > from ChemAxxon says that there is not enough white space between "A" and
> >> > the atom number. Here is an example of OB output and what Akos
> >> > corrected:
> >> > OB output -
> >> >
> >> > A  8
> >> > R5
> >> > A  10
> >> > R4
> >> > A  11
> >> > R3
> >> > A  14
> >> > R2
> >> > A  16
> >> > R1
> >> >
> >> > Corrected -
> >> >
> >> > A8
> >> > R5
> >> > A   10
> >> > R4
> >> > A   11
> >> > R3
> >> > A   14
> >> > R2
> >> > A   16
> >> > R1
> >> >
> >> > the corrected file can be opened by ChemDraw, MarvinSketch, as well as
> >> > Symyx Draw and CACTVS csbr. Could we correct the output of atomic
> >> > aliases in the next OB release?
> >> >
> >> > Igor
> >> >
> >> >
> >> > On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> >> >> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
> >> >>
> >> >>>> So far I see only SetAtomicNum to specify atom type, but nothing to
> >> > set
> >> >>>> the atomic label to something like "R1".
> >> >>>
> >> >>> You can use AliasData for this.
> >> >>
> >> >> See src/formats/mdlformat.cpp for an exact example.
> >> >>
> >> >> Hope that helps,
> >> >> -Geoff
> >> >
> >> >
> >> >
> >> > --
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> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >> >
> >> >
> >> >
> >> >
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Re: [Open Babel] markush structures in openbabel

[Igor Filippov [Contr]]

Chris,

Thank you. I'm trying to test it with the latest trunk (r3955) but even
though OB itself compiled fine I'm getting the following error when
trying to link libopenbabel to my program:

undefined reference to `OpenBabel::AliasData::GetAlias(bool) const'
collect2: ld returned 1 exit status

Was there some significant change in how libopenbabel should be linked?
It was working fine with 2.2.3 release.

Igor

On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote:
> Thanks. Corrected in r3897.
> Chris
> 
> On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
> > I've run into a problem with an SD file generated by OB with atomic
> > aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
> > displayed correctly by ChemAxxon MarvinSketch.
> > CamridgeSoft support tells me the atom numbers should be
> > right-justified, where they are left-justified in OB output. Akos Papp
> > from ChemAxxon says that there is not enough white space between "A" and
> > the atom number. Here is an example of OB output and what Akos
> > corrected:
> > OB output -
> >
> > A  8
> > R5
> > A  10
> > R4
> > A  11
> > R3
> > A  14
> > R2
> > A  16
> > R1
> >
> > Corrected -
> >
> > A8
> > R5
> > A   10
> > R4
> > A   11
> > R3
> > A   14
> > R2
> > A   16
> > R1
> >
> > the corrected file can be opened by ChemDraw, MarvinSketch, as well as
> > Symyx Draw and CACTVS csbr. Could we correct the output of atomic
> > aliases in the next OB release?
> >
> > Igor
> >
> >
> > On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> >> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
> >>
> >>>> So far I see only SetAtomicNum to specify atom type, but nothing to
> > set
> >>>> the atomic label to something like "R1".
> >>>
> >>> You can use AliasData for this.
> >>
> >> See src/formats/mdlformat.cpp for an exact example.
> >>
> >> Hope that helps,
> >> -Geoff
> >
> >
> >
> > --
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> >
> >
> >
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> > 19:36:00
> >
> 
> 
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[Open Babel] markush structures in openbabel

[Igor Filippov [Contr]]

I've run into a problem with an SD file generated by OB with atomic
aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
displayed correctly by ChemAxxon MarvinSketch.
CamridgeSoft support tells me the atom numbers should be
right-justified, where they are left-justified in OB output. Akos Papp
from ChemAxxon says that there is not enough white space between "A" and
the atom number. Here is an example of OB output and what Akos
corrected:
OB output - 

A  8
R5
A  10
R4
A  11
R3
A  14
R2
A  16
R1

Corrected - 

A8
R5
A   10
R4
A   11
R3
A   14
R2
A   16
R1

the corrected file can be opened by ChemDraw, MarvinSketch, as well as
Symyx Draw and CACTVS csbr. Could we correct the output of atomic
aliases in the next OB release?

Igor


On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
> 
> >> So far I see only SetAtomicNum to specify atom type, but nothing to
set
> >> the atomic label to something like "R1".
> > 
> > You can use AliasData for this.
> 
> See src/formats/mdlformat.cpp for an exact example.
> 
> Hope that helps,
> -Geoff



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