[Open Babel] Windows 7 (64 bit) compatibility

2011-06-28 Thread Richard V. Williams 
Are there any known compatibility issues of Babel 2.3.0a with Windows 7 
(64 bit).  I have been unable to get Babel to work on my new Windows 
machine.  Thanks.

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Phone 208-885-6775
FAX 208-885-6173

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[Open Babel] Help: everything compile well... But no results

2011-06-28 Thread Marianne 
Hello

I am new to using the openbabel API and really exciting to use OB. I have an
existing C++ program in MSVC2008, I would like to use some of the functions
in Openbabel (Isomorphism).

I followed the instructions on the website and built the windows-vc2008 and
then tried to add the sample code in C++  to make test of the results first:

--
*#include 
#include 

using namespace std;
using namespace OpenBabel;

int _tmain(int argc,char **argv) {
   // Read molecule from SMILES string

   OBConversion conv;
   OBMol mol;
   conv.SetInFormat("smi");
   conv.ReadString(&mol, "C(Cl)(=O)CCC(=O)Cl");



   // Print out some general information

   conv.SetOutFormat("can");
   cout<<"Canonical SMILES:
"<
---

Everything compile fine but when I execute the code, I obtain

---
*Canonical SMILES:
The molecular weight is 0*

---

I link this small program with
1) Include files:
openbabel-2.3.0\windows-vc2008\build\include
openbabel-2.3.0\windows-vc2008\include
openbabel-2.3.0\include

2) Source file:
openbabel-2.3.0\src

3) Lib file:
openbabel-2.3.0\windows-vc2008\build\src\Release\openbabel-2.lib


openbabel-2.dll is added  in the exe folder.


Help will be really appreciate. Thank you


Marianne

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Re: [Open Babel] Windows 7 (64 bit) compatibility

2011-06-28 Thread Noel O'Boyle 
There are no known issues, but it may be a good idea to uninstall any
existing installations of Open Babel, before installing.

What is the specific problem?

- Noel

On 23 June 2011 19:37, Richard V. Williams  wrote:
> Are there any known compatibility issues of Babel 2.3.0a with Windows 7
> (64 bit).  I have been unable to get Babel to work on my new Windows
> machine.  Thanks.
>
> --
> Dr. Richard V. Williams
> Professor of Chemistry
> Department of Chemistry
> University of Idaho
> PO Box 442343
> Moscow, ID 83844-2343
> USA
>
> Phone 208-885-6775
> FAX 208-885-6173
>
> http://neon.chem.uidaho.edu/~williams/
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
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Re: [Open Babel] Segfault cause?

2011-06-28 Thread Chris Morley 
On 28/06/2011 01:02, A. Heifets wrote:
> Any obvious idea why the following file causes a segfault with "obabel
> -isdf junk.sdf -osdf -Ofoo.sdf"?  It's something to do with the R
> groups because, if I replace them with 'C', the file works.  Is there
> a way to skip generating output instead of making OpenBabel segfault?

This is related to your bug report #3325452. The comments I made on it 
do not seem to made it on to SourceForge. I'll try again, but the gist 
is that the development code no longer segfaults with R groups.

I can see why your file has the name "junk.sdf". You could try the -r 
option - Remove all but the largest contiguous fragment. With this file 
the 5 fragments with R groups (one of them miles away) would be 
eliminated. But I don't think this prevents the segfault and neither 
does using -o nul. You would probably have to build the development 
code. For Windows, I could provide a compiled version.

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Re: [Open Babel] Segfault cause?

2011-06-28 Thread A. Heifets 
Based on Chris Morley's response to a previous question [1], I checked
out the latest SVN build and tested it on this file.  The files *does
not* cause segfault with the latest checkout, so please ignore my
question.  It's already handled.  Thank you!

[1] 
https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3325452&group_id=40728

On Mon, Jun 27, 2011 at 8:02 PM, A. Heifets  wrote:
> Any obvious idea why the following file causes a segfault with "obabel
> -isdf junk.sdf -osdf -Ofoo.sdf"?  It's something to do with the R
> groups because, if I replace them with 'C', the file works.  Is there
> a way to skip generating output instead of making OpenBabel segfault?
>
>  OpenBabel06261100152D
>
>  13  8  0  0  0  0  0  0  0  0999 V2000
>    3.6440    1.8715    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    3.1123    3.5077    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    1.3919    3.5077    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.8602    1.8715    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    2.2521 0.8602    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    7.0849 0.8602    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    5.3644    0.8602    0. *   0  0  0  0  0  0  0  0  0  0  0  0
>    1.2717  -82.4145    0. *   0  0  0  0  0  0  0  0  0  0  0  0
>    8.8849 0.8602    0. *   0  0  0  0  0  0  0  0  0  0  0  0
>   10.0278    5.2282    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>   10.0278    5.2282    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    7.1645 5.2282    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>    5.4440 5.2282    0. C   0  0  0  0  0  0  0  0  0  0  0  0
>  1  2  1  0  0  0  0
>  1  5  1  0  0  0  0
>  2  3  1  0  0  0  0
>  3  4  1  0  0  0  0
>  4  5  1  0  0  0  0
>  6  7  1  0  0  0  0
>  10 11  1  0  0  0  0
>  12 13  1  0  0  0  0
> A    7
> R
> A    8
> R
> A    9
> R
> M  END
>
> 
>
>
> --
> A. Heifets
> http://www.cs.toronto.edu/~aheifets/
>



-- 
A. Heifets
http://www.cs.toronto.edu/~aheifets/

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Re: [Open Babel] problems compiling openbabel on 64bit RHEL5

2011-06-28 Thread Geoffrey Hutchison 
> Sorry if this problem is obvious to the experts but I can’t get OB to compile

Well, you got it to compile, but as you noticed, the tests didn't all pass.

What version of gcc are you using?

"gcc -v"

CentOS has had a buggy version of g++.

-Geoff
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Re: [Open Babel] Segfault cause?

2011-06-28 Thread Geoffrey Hutchison 
> The files *does
> not* cause segfault with the latest checkout, so please ignore my
> question.  It's already handled.  Thank you!

No sweat. Obviously, we like to track down every crash.

-Geoff

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Re: [Open Babel] problems compiling openbabel on 64bit RHEL5

2011-06-28 Thread Noel O'Boyle 
It seems like it compiled fine. Try "make install", and away you go.

- Noel

On 27 June 2011 17:05, Mike Lipkin, BioFocus  wrote:
> Hi,
>
>
>
> Sorry if this problem is obvious to the experts but I can’t get OB to
> compile
>
>
>
> Here are the messages from cmake
>
>
>
> mlip...@cpwork6.glpg.com 952% cmake ../
>
> -- The C compiler identification is GNU
>
> -- The CXX compiler identification is GNU
>
> -- Check for working C compiler: /usr/bin/gcc
>
> -- Check for working C compiler: /usr/bin/gcc -- works
>
> -- Detecting C compiler ABI info
>
> -- Detecting C compiler ABI info - done
>
> -- Check for working CXX compiler: /usr/bin/c++
>
> -- Check for working CXX compiler: /usr/bin/c++ -- works
>
> -- Detecting CXX compiler ABI info
>
> -- Detecting CXX compiler ABI info - done
>
> Using included inchi library.
>
> -- checking for module 'libxml-2.0'
>
> --   found libxml-2.0, version 2.6.26
>
> -- Found LibXml2: /usr/lib64/libxml2.so
>
> -- Found ZLIB: /usr/lib64/libz.so
>
> -- Could NOT find wxWidgets  (missing:  wxWidgets_FOUND)
>
> -- Looking for conio.h
>
> -- Looking for conio.h - not found
>
> -- Looking for sys/time.h
>
> -- Looking for sys/time.h - found
>
> -- Looking for time.h
>
> -- Looking for time.h - found
>
> -- Looking for strings.h
>
> -- Looking for strings.h - found
>
> -- Looking for rpc/xdr.h
>
> -- Looking for rpc/xdr.h - found
>
> -- Looking for regex.h
>
> -- Looking for regex.h - found
>
> -- Looking for C++ include sstream
>
> -- Looking for C++ include sstream - found
>
> -- Looking for rint
>
> -- Looking for rint - not found.
>
> -- Looking for snprintf
>
> -- Looking for snprintf - found
>
> -- Looking for sranddev
>
> -- Looking for sranddev - not found.
>
> -- Looking for strcasecmp
>
> -- Looking for strcasecmp - found
>
> -- Looking for strncasecmp
>
> -- Looking for strncasecmp - found
>
> -- Looking for dlopen in dl
>
> -- Looking for dlopen in dl - found
>
> -- Looking for sys/types.h
>
> -- Looking for sys/types.h - found
>
> -- Looking for stdint.h
>
> -- Looking for stdint.h - found
>
> -- Looking for stddef.h
>
> -- Looking for stddef.h - found
>
> -- Check size of clock_t
>
> -- Check size of clock_t - done
>
> -- Performing Test SCANDIR_NEEDS_CONST
>
> -- Performing Test SCANDIR_NEEDS_CONST - Failed
>
> -- Performing Test HAVE_GCC_VISIBILITY
>
> -- Performing Test HAVE_GCC_VISIBILITY - Success
>
> -- Found Eigen2: /usr/local/include/eigen2
>
> -- Looking for getopt
>
> -- Looking for getopt - found
>
> Attempting to build the GUI
>
>    wxWidgets not found => GUI will not be built
>
> -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs'
> or 'svn'. CTest update will not work.
>
> -- Found PythonInterp:
> /bfhome/freesoftware/coot/coot-Linux-x86_64-centos-5-gtk2-python/bin/python2.6
>
> -- Configuring done
>
> -- Generating done
>
> -- Build files have been written to:
> /bfhome/mlipkin/Projects/Development/Scripts/mlipkin/openbabel_new/new_version/openbabel-2.3.0/build
>
>
>
> And here are the messages from make test
>
>
>
> mlip...@cpwork6.glpg.com 957% make test
>
> make: Warning: File `Makefile' has modification time 5.3e+02 s in the future
>
> Running tests...
>
> Start processing tests
>
> Test project
> /bfhome/mlipkin/Projects/Development/Scripts/mlipkin/openbabel_new/new_version/openbabel-2.3.0/build
>
>   1/ 57 Testing align_Test   Passed
>
>   2/ 57 Testing automorphism_Test    Passed
>
>   3/ 57 Testing builder_Test  ***Failed Error regular
> expression found in output. Regex=[FAIL]
>
>   4/ 57 Testing canonconsistent_Test Passed
>
>   5/ 57 Testing canonstable_Test Passed
>
>   6/ 57 Testing cistrans_Test    Passed
>
>   7/ 57 Testing graphsym_Test    Passed
>
>   8/ 57 Testing implicitH_Test   Passed
>
>   9/ 57 Testing lssr_Test    Passed
>
>  10/ 57 Testing isomorphism_Test Passed
>
>  11/ 57 Testing rotor_Test   Passed
>
>  12/ 57 Testing shuffle_Test Passed
>
>  13/ 57 Testing smiles_Test  Passed
>
>  14/ 57 Testing spectrophore_Test    Passed
>
>  15/ 57 Testing squareplanar_Test    Passed
>
>  16/ 57 Testing stereo_Test  Passed
>
>  17/ 57 Testing stereoperception_Test    Passed
>
>  18/ 57 Testing tetrahedral_Test Passed
>
>  19/ 57 Testing tetranonplanar_Test  Passed
>
>  20/ 57 Testing tetraplanar_Test Passed
>
>  21/ 57 Testing uniqueid_Test    Passed
>
>  22/ 57 Testing inchiSamples_Test ***Failed
>
>  23/ 57 Testing inchiSamplesTechMan_Test Passed
>
>  24/ 57 Testing aromatest_Test   Passed
>
>  25/ 57 Testing atom_Test    Passed
>
>  26/ 57 Testing bond_Test    Passed
>
>  27/ 57 Testing cansmi_Test 

Re: [Open Babel] problems compiling openbabel on 64bit RHEL5

2011-06-28 Thread Geoffrey Hutchison 
Yes, you have the infamous buggy gcc-4.1.

Try:

yum install gcc44 gcc44-c++

Hope that helps,
-Geoff

On Jun 28, 2011, at 11:27 AM, Mike Lipkin, BioFocus wrote:

> Thanks for the reply,
> 
> I am using gcc 4.1.2
> 
> Currently I have openbabel 2.2.3 installed and two programs using it 
> (I don't mind recompiling them, I am the only OB user here)
> 
> I've been round the block a couple of times, installing it and not
> getting it to work, so I assumed the errors in the tests must be
> important!
> 
> I don't need the gui and python is not essential
> 
> Is this the buggy gcc ?


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Re: [Open Babel] Windows 7 (64 bit) compatibility

2011-06-28 Thread Noel O'Boyle 
I don't recommend that you use 2.1.1 instead of 2.3.0, so let us know
if you want to track down the problem...

- Noel

On 28 June 2011 17:01, Richard V. Williams  wrote:
> Noel,
>
>    Thanks for your message.  I was starting from a new machine - no previous
> installations.  The problem, could read files but not convert them.  I have
> subsequently removed 2.3.0a and installed 2.1.1 which works flawlessly as it
> did on my previous machine.
>
> Richard.
>
> On 6/28/2011 2:05 AM, Noel O'Boyle wrote:
>>
>> There are no known issues, but it may be a good idea to uninstall any
>> existing installations of Open Babel, before installing.
>>
>> What is the specific problem?
>>
>> - Noel
>>
>> On 23 June 2011 19:37, Richard V. Williams  wrote:
>>
>>>
>>> Are there any known compatibility issues of Babel 2.3.0a with Windows 7
>>> (64 bit).  I have been unable to get Babel to work on my new Windows
>>> machine.  Thanks.
>>>
>>> --
>>> Dr. Richard V. Williams
>>> Professor of Chemistry
>>> Department of Chemistry
>>> University of Idaho
>>> PO Box 442343
>>> Moscow, ID 83844-2343
>>> USA
>>>
>>> Phone 208-885-6775
>>> FAX 208-885-6173
>>>
>>> http://neon.chem.uidaho.edu/~williams/
>>>
>>>
>>>
>>> --
>>> All of the data generated in your IT infrastructure is seriously
>>> valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>
> --
> Dr. Richard V. Williams
> Professor of Chemistry
> Department of Chemistry
> University of Idaho
> PO Box 442343
> Moscow, ID 83844-2343
> USA
>
> Phone 208-885-6775
> FAX 208-885-6173
>
> http://neon.chem.uidaho.edu/~williams/
>
>

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