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[OpenBabel-scripting] [openbabel-scripting] [OpenBabel & Pybel] Atomic Types Automatically Changed

[laurent.personal <lau...@gm...>]

Hello

I am using openbabel for a project (convert molec in different formats ...).
Besides, I have to do some scripts in order to modify some molecules of my
DB. I use pybel to do this.

My problem is that pybel automatically changes some atomic types in molecule
of my DB ... and it shouldn't do it. It replaces some carbons (C2 or others)
by the type C.cat. The last is for the guanidium group but I don't have a
such group in my DB.

I did a basic script in order to verify this :

[quote]
#!/usr/bin/python
import openbabel
import pybel
for mol in pybel.readfile("mol2", "molec_test.mol2"):
	outputfile = pybel.Outputfile("mol2", "molec_pybel.mol2", overwrite=True)
	outputfile.write(mol)
	outputfile.close()
[/quote]

The input/output structure files are uploaded here.
http://www.nabble.com/file/p22574797/molec_pybel.mol2 molec_pybel.mol2 
http://www.nabble.com/file/p22574797/molec_test.mol2 molec_test.mol2 

Can we read a molecule with pybel with an option "read only the mol2 file
without changing anything" ?

TIA for your answer,

Cheers,

Laurent
-- 
View this message in context: http://www.nabble.com/-OpenBabel---Pybel--Atomic-Types-Automatically-Changed-tp22574797p22574797.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] Can OpenBabel calculate intermolecular hydrogen bonds?

[Noel O'B. <bao...@gm...>]

Assuming that you already have the coordinates of the ligand in
relation to the protein, you can script this quite easily. You just
need to write a loop over the atoms of the ligand, and another loop
over the atoms of the protein, see if they have the right atom types
for hydrogen bonding (atom types are available from OB), and see if
the heavy atom distance is < 3.0 or 3.1 Ang distance.

In fact, I'd like to have a script that does this too, so if you send
me (off list) an example PDB and ligand file, I will throw a prototype
script together and report back to the list.

An alternative is PyMol, which I guess has automatic hydrogen bond
detection or so (I have never used PyMol so I'm not sure).

Regards,
   Noel

2009/3/12 Steven Platt <Ste...@hp...>:
> Hi,
>
> Given a small carbohydrate ligand and a relatively large protein, can
> OpenBabel calculate the hydrogen bonds between these two molecules and
> report them to a file?
>
> I realise that there are GUIs that will do this, but I’ve got dozens of
> ligand/protein combinations and would like to script the process.
>
> It’s worth saying that I’ve got no experience with OB, so simple answers
> please.
>
> Thanks
>
> Steve
>
> Dr Steven Platt
>
> Bioinformatics Support Coordinator
>
> Statistics, Modelling and Bioinformatics
>
> Health Protection Agency
>
> Centre for Infections
>
> 61 Colindale Avenue
>
> London
>
> NW9 5EQ
>
> 0208 327 6618
>
> www.hpa.org.uk/bioinformatics
>
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[OpenBabel-scripting] Can OpenBabel calculate intermolecular hydrogen bonds?

[Steven P. <Ste...@HP...>]

Hi,

Given a small carbohydrate ligand and a relatively large protein, can
OpenBabel calculate the hydrogen bonds between these two molecules and
report them to a file?
I realise that there are GUIs that will do this, but I've got dozens of
ligand/protein combinations and would like to script the process.

It's worth saying that I've got no experience with OB, so simple answers
please.

Thanks

Steve

Dr Steven Platt
Bioinformatics Support Coordinator
Statistics, Modelling and Bioinformatics
Health Protection Agency
Centre for Infections
61 Colindale Avenue
London
NW9 5EQ
0208 327 6618
www.hpa.org.uk/bioinformatics



-----------------------------------------
**************************************************************************
The information contained in the EMail and any attachments is
confidential and intended solely and for the attention and use of
the named addressee(s). It may not be disclosed to any other person
without the express authority of the HPA, or the intended
recipient, or both. If you are not the intended recipient, you must
not disclose, copy, distribute or retain this message or any part
of it. This footnote also confirms that this EMail has been swept
for computer viruses, but please re-sweep any attachments before
opening or saving. HTTP://www.HPA.org.uk
**************************************************************************

Re: [OpenBabel-scripting] Problems with OBDotNet

[Noel O'B. <bao...@gm...>]

Hello Bob,

I've just written some installation instructions for OBDotNet. Please
find them at http://openbabel.org/wiki/OBDotNet

Let us know if you have any further problems.

- Noel

2009/2/20 Bob Trucchi <Bob...@co...>:
> I'm having some troubles with getting OBDotNet to work and am hoping for
> some help. I have OpenBable-2.2.0 installed and am using VS 2008 sp1. I made
> the simplest program
>
> using System;
> using OpenBabel;
>
> namespace OpenBabelTesting
> {
> class Program
> {
> static void Main(string[] args)
> {
> OBConversion obc = new OBConversion();
> }
>
> }
> }
> and when I run it I get this exception:
> System.TypeInitializationException was unhandled
> Message="The type initializer for 'OpenBabel.openbabelPINVOKE' threw an
> exception."
> Source="OBDotNet"
> TypeName="OpenBabel.openbabelPINVOKE"
> StackTrace:
> at OpenBabel.openbabelPINVOKE.new_OBConversion__SWIG_2()
> at OpenBabel.OBConversion..ctor()
> at OpenBabelTesting.Program.Main(String[] args) in
> C:\Projects\Constellation.HTS\ChemRegistration\OpenBabelTesting\Program.cs:line
> 10
> at System.AppDomain._nExecuteAssembly(Assembly assembly, String[] args)
> at System.AppDomain.ExecuteAssembly(String assemblyFile, Evidence
> assemblySecurity, String[] args)
> at Microsoft.VisualStudio.HostingProcess.HostProc.RunUsersAssembly()
> at System.Threading.ThreadHelper.ThreadStart_Context(Object state)
> at System.Threading.ExecutionContext.Run(ExecutionContext executionContext,
> ContextCallback callback, Object state)
> at System.Threading.ThreadHelper.ThreadStart()
> InnerException: System.TypeInitializationException
> Message="The type initializer for 'SWIGExceptionHelper' threw an exception."
> Source="OBDotNet"
> TypeName="SWIGExceptionHelper"
> StackTrace:
> at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..ctor()
> at OpenBabel.openbabelPINVOKE..cctor()
> InnerException: System.DllNotFoundException
> Message="Unable to load DLL 'openbabel': The specified module could not be
> found. (Exception from HRESULT: 0x8007007E)"
> Source="OBDotNet"
> TypeName=""
> StackTrace:
> at
> OpenBabel.openbabelPINVOKE.SWIGExceptionHelper.SWIGRegisterExceptionCallbacks_openbabel(ExceptionDelegate
> applicationDelegate, ExceptionDelegate arithmeticDelegate, ExceptionDelegate
> divideByZeroDelegate, ExceptionDelegate indexOutOfRangeDelegate,
> ExceptionDelegate invalidCastDelegate, ExceptionDelegate
> invalidOperationDelegate, ExceptionDelegate ioDelegate, ExceptionDelegate
> nullReferenceDelegate, ExceptionDelegate outOfMemoryDelegate,
> ExceptionDelegate overflowDelegate, ExceptionDelegate
> systemExceptionDelegate)
> at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..cctor()
> InnerException:
>
> I thought it had something to do with openbabel.dll but I could not add it
> as a reference to my project or the GAC. Any ideas?
>
> Thanks in advance,
> Bob
>
>
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
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>
>

Re: [OpenBabel-scripting] Problems with OBDotNet

[Geoffrey H. <ge...@ge...>]

On Feb 20, 2009, at 10:35 AM, Bob Trucchi wrote:

> I'm having some troubles with getting OBDotNet to work and am hoping  
> for some help. I have OpenBable-2.2.0 installed and am using VS 2008  
> sp1. I made the simplest program


Have you tried 2.2.1? The OBDotNet code has been significantly improved.

Cheers,
-Geoff

[OpenBabel-scripting] Problems with OBDotNet

[Bob T. <Bob...@co...>]

I'm having some troubles with getting OBDotNet to work and am hoping for some help. I have OpenBable-2.2.0 installed and am using VS 2008 sp1. I made the simplest program

using System;
using OpenBabel;

namespace OpenBabelTesting
{
class Program
{
static void Main(string[] args)
{
OBConversion obc = new OBConversion();
}

}
}
and when I run it I get this exception:
System.TypeInitializationException was unhandled
Message="The type initializer for 'OpenBabel.openbabelPINVOKE' threw an exception."
Source="OBDotNet"
TypeName="OpenBabel.openbabelPINVOKE"
StackTrace:
at OpenBabel.openbabelPINVOKE.new_OBConversion__SWIG_2()
at OpenBabel.OBConversion..ctor()
at OpenBabelTesting.Program.Main(String[] args) in C:\Projects\Constellation.HTS\ChemRegistration\OpenBabelTesting\Program.cs:line 10
at System.AppDomain._nExecuteAssembly(Assembly assembly, String[] args)
at System.AppDomain.ExecuteAssembly(String assemblyFile, Evidence assemblySecurity, String[] args)
at Microsoft.VisualStudio.HostingProcess.HostProc.RunUsersAssembly()
at System.Threading.ThreadHelper.ThreadStart_Context(Object state)
at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
at System.Threading.ThreadHelper.ThreadStart()
InnerException: System.TypeInitializationException
Message="The type initializer for 'SWIGExceptionHelper' threw an exception."
Source="OBDotNet"
TypeName="SWIGExceptionHelper"
StackTrace:
at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..ctor()
at OpenBabel.openbabelPINVOKE..cctor()
InnerException: System.DllNotFoundException
Message="Unable to load DLL 'openbabel': The specified module could not be found. (Exception from HRESULT: 0x8007007E)"
Source="OBDotNet"
TypeName=""
StackTrace:
at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper.SWIGRegisterExceptionCallbacks_openbabel(ExceptionDelegate applicationDelegate, ExceptionDelegate arithmeticDelegate, ExceptionDelegate divideByZeroDelegate, ExceptionDelegate indexOutOfRangeDelegate, ExceptionDelegate invalidCastDelegate, ExceptionDelegate invalidOperationDelegate, ExceptionDelegate ioDelegate, ExceptionDelegate nullReferenceDelegate, ExceptionDelegate outOfMemoryDelegate, ExceptionDelegate overflowDelegate, ExceptionDelegate systemExceptionDelegate)
at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..cctor()
InnerException:

I thought it had something to do with openbabel.dll but I could not add it as a reference to my project or the GAC. Any ideas?

Thanks in advance,
Bob

Re: [OpenBabel-scripting] modify coordinates of a molecule

[Noel O'B. <bao...@gm...>]

Hello Xavier,

Pybel does not allow assignment of coordinate values (the next version
will raise an error when you try, instead of failing silently). To set
the coordinates you need to use the SetVector() method of the
underlying OBAtom, e.g.

>>> mol = pybel.readstring("smi", "CCC")
>>> mol.make3D()
>>> mol.atoms[0].coords
(0.9762193757974641, -0.018350366821008612, 0.0057426618097852662)
>>> a = mol.atoms[0].OBAtom
>>> a.SetVector(1,2,3)
>>> mol.atoms[0].coords
(1.0, 2.0, 3.0)
>>>

Perhaps I will add setting coordinates as a feature in a future
version of Pybel?

- Noel

2009/2/18 Xavier Prat-Resina <xav...@gm...>:
> Hi,
>
> I'm trying to change the coordinates of a molecule using
> the coordinates from another file:
>
> gaussbel = pybel.readfile("g03", "myfile.g03").next()
> molbel   = pybel.readfile("mol", "myfile.mol").next()
>
> If I try to change the coordinates directly:
> molbel.atoms[0].coords[0] = gaussbel.atoms[0].coords[0]
> it gives
> TypeError: 'tuple' object does not support item assignment
>
> I can loop over atoms:
>
> for atom in molbel:
>     (assign x,y,z)
>     atom.coords = numpy.array([x,y,z], "float64")
>
> but then, how can I update the molbel molecule with the new atom.coords?
>
> I know I'm missing something very simple.
> Sorry for such naive questions :)
>
> Xavier
>
> --
> Xavier Prat-Resina
> Research Associate
> Journal of Chemical Education and University of Wisconsin
> 209 N. Brooks St. Madison, WI  53715-1116
>
> Tel: 608 8901702 // Fax: 608 2627145
> e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
> http://x.prat.resina.googlepages.com
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] modify coordinates of a molecule

[Xavier Prat-R. <xav...@gm...>]

Hi,

I'm trying to change the coordinates of a molecule using
the coordinates from another file:

gaussbel = pybel.readfile("g03", "myfile.g03").next()
molbel   = pybel.readfile("mol", "myfile.mol").next()

If I try to change the coordinates directly:
molbel.atoms[0].coords[0] = gaussbel.atoms[0].coords[0]
it gives
TypeError: 'tuple' object does not support item assignment

I can loop over atoms:

for atom in molbel:
    (assign x,y,z)
    atom.coords = numpy.array([x,y,z], "float64")

but then, how can I update the molbel molecule with the new atom.coords?

I know I'm missing something very simple.
Sorry for such naive questions :)

Xavier

-- 
Xavier Prat-Resina
Research Associate
Journal of Chemical Education and University of Wisconsin
209 N. Brooks St. Madison, WI  53715-1116

Tel: 608 8901702 // Fax: 608 2627145
e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

Re: [OpenBabel-scripting] SUSE 10.3 problem compiling python bindings

[Noel O'B. <bao...@gm...>]

Sorry - my mistake. This is clearly a different issue. I don't seem to
have any record of the original email (01/07/09).

Good to hear it's working though :-)

Noel

2009/1/8 Noel O'Boyle <bao...@gm...>:
> Am confused. The original issue was resolved at the time (24/10/08).
> It was due to the fact that python didn't remove the build directory
> when you changed versions of GCC.
>
> Noel
>
> 2009/1/8 Nick England <nic...@gm...>:
>> Interestingly I have now got it to compile and work fine, after
>> compiling and using GCC 4.3.2.
>>
>> Were there any important changes from GCC 4.2.1 to 4.3.2 which would
>> affect the python bindings compiling? Seems like a strange error.
>>
>> - Nick England
>>
>> 2009/1/7 Nick England <nic...@gm...>:
>>> My system was recently upgraded to 10.3 from 10.2 since 10.2 was out of support.
>>>
>>> I had to reinstall openbabel, and I had no problems compiling and
>>> running babel itself (both the 2.2.0 release and the SVN version both
>>> work fine.)
>>>
>>> However, when I try to compile the python bindings, I get the attached
>>> error log from
>>>
>>> python setup.up build
>>>
>>> A few google searches seems to show similar problems which were fixed
>>> by altering the source code, but I am assuming it is working for other
>>> people so there must be something wrong with my system?
>>>
>>> Any ideas as to what the problem is?
>>>
>>> gcc version is gcc (GCC) 4.2.1 (SUSE Linux)
>>>
>>> Thanks,
>>>
>>> Nick England
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It is the best place to buy or sell services for
>> just about anything Open Source.
>> http://p.sf.net/sfu/Xq1LFB
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>

Re: [OpenBabel-scripting] SUSE 10.3 problem compiling python bindings

[Noel O'B. <bao...@gm...>]

Am confused. The original issue was resolved at the time (24/10/08).
It was due to the fact that python didn't remove the build directory
when you changed versions of GCC.

Noel

2009/1/8 Nick England <nic...@gm...>:
> Interestingly I have now got it to compile and work fine, after
> compiling and using GCC 4.3.2.
>
> Were there any important changes from GCC 4.2.1 to 4.3.2 which would
> affect the python bindings compiling? Seems like a strange error.
>
> - Nick England
>
> 2009/1/7 Nick England <nic...@gm...>:
>> My system was recently upgraded to 10.3 from 10.2 since 10.2 was out of support.
>>
>> I had to reinstall openbabel, and I had no problems compiling and
>> running babel itself (both the 2.2.0 release and the SVN version both
>> work fine.)
>>
>> However, when I try to compile the python bindings, I get the attached
>> error log from
>>
>> python setup.up build
>>
>> A few google searches seems to show similar problems which were fixed
>> by altering the source code, but I am assuming it is working for other
>> people so there must be something wrong with my system?
>>
>> Any ideas as to what the problem is?
>>
>> gcc version is gcc (GCC) 4.2.1 (SUSE Linux)
>>
>> Thanks,
>>
>> Nick England
>>
>
> ------------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It is the best place to buy or sell services for
> just about anything Open Source.
> http://p.sf.net/sfu/Xq1LFB
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] SUSE 10.3 problem compiling python bindings

[Nick E. <nic...@gm...>]

Interestingly I have now got it to compile and work fine, after
compiling and using GCC 4.3.2.

Were there any important changes from GCC 4.2.1 to 4.3.2 which would
affect the python bindings compiling? Seems like a strange error.

- Nick England

2009/1/7 Nick England <nic...@gm...>:
> My system was recently upgraded to 10.3 from 10.2 since 10.2 was out of support.
>
> I had to reinstall openbabel, and I had no problems compiling and
> running babel itself (both the 2.2.0 release and the SVN version both
> work fine.)
>
> However, when I try to compile the python bindings, I get the attached
> error log from
>
> python setup.up build
>
> A few google searches seems to show similar problems which were fixed
> by altering the source code, but I am assuming it is working for other
> people so there must be something wrong with my system?
>
> Any ideas as to what the problem is?
>
> gcc version is gcc (GCC) 4.2.1 (SUSE Linux)
>
> Thanks,
>
> Nick England
>

[OpenBabel-scripting] SUSE 10.3 problem compiling python bindings

[Nick E. <nic...@gm...>]

My system was recently upgraded to 10.3 from 10.2 since 10.2 was out of support.

I had to reinstall openbabel, and I had no problems compiling and
running babel itself (both the 2.2.0 release and the SVN version both
work fine.)

However, when I try to compile the python bindings, I get the attached
error log from

python setup.up build

A few google searches seems to show similar problems which were fixed
by altering the source code, but I am assuming it is working for other
people so there must be something wrong with my system?

Any ideas as to what the problem is?

gcc version is gcc (GCC) 4.2.1 (SUSE Linux)

Thanks,

Nick England

Re: [OpenBabel-scripting] java bindings installation question

[Noel O'B. <bao...@gm...>]

2008/12/16 Nathan Rice <exn...@gm...>:
>> It shouldn't be necessary to to copy libopenbabel.so anywhere. Don't
>> the instructions in the readme describe how to set LD_LIBRARY_PATH to
>> point to the directory containing libopenbabel.so? Have you tried
>> this?
>
> I did try that, I have two copies of libopenbabel.so, one which was created
> and installed on initial make install of the core package (filesize ~12M),
> and a second one which was in my scripts/java/ directory (filesize ~2M).
> The one that is in my scripts/java directory is the one that has to be in
> the same directory as OBTest.  The LD_LIBRARY_PATH points to the other one.
> Is this incorrect?

The two libopenbabel.so files are different (we should probably rename
the small one). As described in the README, the PATHs to both should
be added to LD_LIBRARY_PATH (in the order shown in the README - this
is important). It shouldn't be necessary to use LD_PRELOAD if these
are set correctly.

If this is done, it might help solve your problems with Eclipse also.
BTW, you are unlikely to get a useful response over at
openbabel-discuss, as very few people will be using the Java bindings,
which were only released in an experimental form in the last OB
release.

- Noel

Re: [OpenBabel-scripting] java bindings installation question

[Noel O'B. <bao...@gm...>]

(please cc to the list - I may need help :-) )

2008/12/16 Nathan Rice <exn...@gm...>:
> Thanks so much for the fast reply Noel.
>
> Everything works for other users if they point their classpath to the
> uncompressed contents of openbabel.jar and copy the compiled libopenbabel.so
> file to the directory that contains the OBTest program.  So if you're busy I
> should be ok now :)

It shouldn't be necessary to to copy libopenbabel.so anywhere. Don't
the instructions in the readme describe how to set LD_LIBRARY_PATH to
point to the directory containing libopenbabel.so? Have you tried
this?

> If the classpath is set to point to either the directory which contains
> openbabel.jar, and the archive itself (as in the directions) or both, a
> classdefnotfound error occurs:
>
> nathan@acelot2:~/test$ ls
> libopenbabel.so  OBTest.java  openbabel.jar
> nathan@acelot2:~/test$ pwd
> /home/nathan/test
> nathan@acelot2:~/test$ echo $CLASSPATH
> /home/nathan/test/openbabel.jar:/home/nathan/test
> nathan@acelot2:~/test$ LD_PRELOAD=$OB_LIBDIR/libopenbabel.so $JAVA/bin/java
> OBTest
> Exception in thread "main" java.lang.NoClassDefFoundError: OBTest
> Caused by: java.lang.ClassNotFoundException: OBTest
>     at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
>     at java.security.AccessController.doPrivileged(Native Method)
>     at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>     at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
>     at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>     at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

If you've sent me the correct commands and output, the problem is that
Java cannot find OBTest.class. You need to compile the OBTest.java
file first.

> If I change the classpath to point to the extracted contents of the jar, it
> works perfectly.  I imagine that is probably an issue on my end, just seemed
> a little strange.  I am using ubuntu (hardy) x86, for reference if that is
> helpful.

I still cannot figure this part out...maybe I've included OBTest.class
by accident in the jar file...?

> Happy Holidays,

> Nathan
>
> On Tue, Dec 16, 2008 at 6:50 AM, Noel O'Boyle <bao...@gm...> wrote:
>>
>> Hello Nathan,
>>
>> If I understand you correctly, you are using the OpenBabel Java
>> bindings available from Cinfony along with OpenBabel 2.2.0 (the next
>> release of OpenBabel will include the Jar file directly). It shouldn't
>> be necessary to extract the jar file. Just add it to your CLASSPATH
>> and it should work.
>>
>> Regarding making it all available to all users on the system, it is
>> just a question of setting the environment variables as described in
>> the README. If it works for you, it should work for other users in the
>> same way. The best way to test is to copy the test program to a new
>> directory, and see whether you can compile and run it there.
>>
>> If it doesn't work for you, please describe exactly what OS you're
>> using, what commands you used, and where it failed.
>>
>> Regards,
>>   Noel
>>
>> 2008/12/16 Noel O'Boyle <bao...@gm...>:
>> > Forwarding to list...
>> >
>> > ---------- Forwarded message ----------
>> > From: Nathan Rice <exn...@gm...>
>> > Date: 2008/12/16
>> > Subject: java bindings installation question
>> > To: bao...@gm...
>> >
>> >
>> > Hello,
>> >
>> > I went through the entire installation process described in the README
>> > file for the installation of the java bindings as a non root user, and
>> > successfully ran the test program  (after extracting the jar file into
>> > the classpath to solve some classdefnotfound errors).  A
>> > libopenbabel.so file was created in the script directory with a
>> > filesize of about 2 megabytes. I would like the bindings to be
>> > available to all users on the system, are there additional
>> > installation steps that I can do so that users only have to call the
>> > library from within java without having to copy/move/etc anything?
>> >
>> > Thank you for any help you can provide,
>> >
>> > Nathan Rice
>> >
>
>

Re: [OpenBabel-scripting] java bindings installation question

[Nathan R. <exn...@gm...>]

I had some other issues which I posted to the openbabel-discussion list, I
hope that wasn't the wrong place to post them - some java bindings stuff on
nabble archives came up there so I went ahead and posted it.

On Tue, Dec 16, 2008 at 1:30 PM, Noel O'Boyle <bao...@gm...> wrote:

> (please cc to the list - I may need help :-) )
>
> 2008/12/16 Nathan Rice <exn...@gm...>:
> > Thanks so much for the fast reply Noel.
> >
> > Everything works for other users if they point their classpath to the
> > uncompressed contents of openbabel.jar and copy the compiled
> libopenbabel.so
> > file to the directory that contains the OBTest program.  So if you're
> busy I
> > should be ok now :)
>
> It shouldn't be necessary to to copy libopenbabel.so anywhere. Don't
> the instructions in the readme describe how to set LD_LIBRARY_PATH to
> point to the directory containing libopenbabel.so? Have you tried
> this?
>

I did try that, I have two copies of libopenbabel.so, one which was created
and installed on initial make install of the core package (filesize ~12M),
and a second one which was in my scripts/java/ directory (filesize ~2M).
The one that is in my scripts/java directory is the one that has to be in
the same directory as OBTest.  The LD_LIBRARY_PATH points to the other one.
Is this incorrect?


> > If the classpath is set to point to either the directory which contains
> > openbabel.jar, and the archive itself (as in the directions) or both, a
> > classdefnotfound error occurs:
> >
> > nathan@acelot2:~/test$ ls
> > libopenbabel.so  OBTest.java  openbabel.jar
> > nathan@acelot2:~/test$ pwd
> > /home/nathan/test
> > nathan@acelot2:~/test$ echo $CLASSPATH
> > /home/nathan/test/openbabel.jar:/home/nathan/test
> > nathan@acelot2:~/test$ LD_PRELOAD=$OB_LIBDIR/libopenbabel.so
> $JAVA/bin/java
> > OBTest
> > Exception in thread "main" java.lang.NoClassDefFoundError: OBTest
> > Caused by: java.lang.ClassNotFoundException: OBTest
> >     at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
> >     at java.security.AccessController.doPrivileged(Native Method)
> >     at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> >     at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> >     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
> >     at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> >     at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
>
> If you've sent me the correct commands and output, the problem is that
> Java cannot find OBTest.class. You need to compile the OBTest.java
> file first.
>
> > If I change the classpath to point to the extracted contents of the jar,
> it
> > works perfectly.  I imagine that is probably an issue on my end, just
> seemed
> > a little strange.  I am using ubuntu (hardy) x86, for reference if that
> is
> > helpful.
>
> I still cannot figure this part out...maybe I've included OBTest.class
> by accident in the jar file...?
>

I went back and checked this, since you are totally right about that error,
and it looks like I probably copied the OBTest.class there accidentally at
some point.  Glad I'm just being a tard on that account.


>
> > Happy Holidays,
>
> > Nathan
> >
> > On Tue, Dec 16, 2008 at 6:50 AM, Noel O'Boyle <bao...@gm...>
> wrote:
> >>
> >> Hello Nathan,
> >>
> >> If I understand you correctly, you are using the OpenBabel Java
> >> bindings available from Cinfony along with OpenBabel 2.2.0 (the next
> >> release of OpenBabel will include the Jar file directly). It shouldn't
> >> be necessary to extract the jar file. Just add it to your CLASSPATH
> >> and it should work.
> >>
> >> Regarding making it all available to all users on the system, it is
> >> just a question of setting the environment variables as described in
> >> the README. If it works for you, it should work for other users in the
> >> same way. The best way to test is to copy the test program to a new
> >> directory, and see whether you can compile and run it there.
> >>
> >> If it doesn't work for you, please describe exactly what OS you're
> >> using, what commands you used, and where it failed.
> >>
> >> Regards,
> >>   Noel
> >>
> >> 2008/12/16 Noel O'Boyle <bao...@gm...>:
> >> > Forwarding to list...
> >> >
> >> > ---------- Forwarded message ----------
> >> > From: Nathan Rice <exn...@gm...>
> >> > Date: 2008/12/16
> >> > Subject: java bindings installation question
> >> > To: bao...@gm...
> >> >
> >> >
> >> > Hello,
> >> >
> >> > I went through the entire installation process described in the README
> >> > file for the installation of the java bindings as a non root user, and
> >> > successfully ran the test program  (after extracting the jar file into
> >> > the classpath to solve some classdefnotfound errors).  A
> >> > libopenbabel.so file was created in the script directory with a
> >> > filesize of about 2 megabytes. I would like the bindings to be
> >> > available to all users on the system, are there additional
> >> > installation steps that I can do so that users only have to call the
> >> > library from within java without having to copy/move/etc anything?
> >> >
> >> > Thank you for any help you can provide,
> >> >
> >> > Nathan Rice
> >> >
> >
> >
>

Re: [OpenBabel-scripting] java bindings installation question

[Noel O'B. <bao...@gm...>]

Hello Nathan,

If I understand you correctly, you are using the OpenBabel Java
bindings available from Cinfony along with OpenBabel 2.2.0 (the next
release of OpenBabel will include the Jar file directly). It shouldn't
be necessary to extract the jar file. Just add it to your CLASSPATH
and it should work.

Regarding making it all available to all users on the system, it is
just a question of setting the environment variables as described in
the README. If it works for you, it should work for other users in the
same way. The best way to test is to copy the test program to a new
directory, and see whether you can compile and run it there.

If it doesn't work for you, please describe exactly what OS you're
using, what commands you used, and where it failed.

Regards,
   Noel

2008/12/16 Noel O'Boyle <bao...@gm...>:
> Forwarding to list...
>
> ---------- Forwarded message ----------
> From: Nathan Rice <exn...@gm...>
> Date: 2008/12/16
> Subject: java bindings installation question
> To: bao...@gm...
>
>
> Hello,
>
> I went through the entire installation process described in the README
> file for the installation of the java bindings as a non root user, and
> successfully ran the test program  (after extracting the jar file into
> the classpath to solve some classdefnotfound errors).  A
> libopenbabel.so file was created in the script directory with a
> filesize of about 2 megabytes. I would like the bindings to be
> available to all users on the system, are there additional
> installation steps that I can do so that users only have to call the
> library from within java without having to copy/move/etc anything?
>
> Thank you for any help you can provide,
>
> Nathan Rice
>

[OpenBabel-scripting] Fwd: java bindings installation question

[Noel O'B. <bao...@gm...>]

Forwarding to list...

---------- Forwarded message ----------
From: Nathan Rice <exn...@gm...>
Date: 2008/12/16
Subject: java bindings installation question
To: bao...@gm...


Hello,

I went through the entire installation process described in the README
file for the installation of the java bindings as a non root user, and
successfully ran the test program  (after extracting the jar file into
the classpath to solve some classdefnotfound errors).  A
libopenbabel.so file was created in the script directory with a
filesize of about 2 megabytes. I would like the bindings to be
available to all users on the system, are there additional
installation steps that I can do so that users only have to call the
library from within java without having to copy/move/etc anything?

Thank you for any help you can provide,

Nathan Rice

Re: [OpenBabel-scripting] Bus error using OBMol.Separate

[Noel O'B. <bao...@gm...>]

Chris made the point this bug has already been fixed in r2700. All you
need to do to fix it yourself is to remove the word "return" at line
237 (or so) in obiter.cpp as shown here:
http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/src/obiter.cpp?r1=2627&r2=2700&pathrev=2700

Just rerun "make" and "make install" (no need to redo the configure),
and the Python bindings should work straightaway (no need to
recompile).

Noel

2008/12/9 Noel O'Boyle <bao...@gm...>:
> Hello Fredrik,
>
> I must admit that OBMol.Separate() usually causes a segfault for me
> too, but I've never gotten around to reporting the bug. I've just
> tested it a little bit. It seems that separating a methane is fine,
> but separating ethane causes a segault.
>
>>>> import pybel
>>>> pybel.readstring("smi", "C").OBMol.Separate()
> (<openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *' at 0x12887
> 78> >,)
>>>> pybel.readstring("smi", "CC").OBMol.Separate()
> # It's a segger
>
> I'll file a bug.
>
> Noel
>
>
> 2008/12/9 Noel O'Boyle <bao...@gm...>:
>> ---------- Forwarded message ----------
>> From:  <fre...@gm...>
>> Date: 2008/12/9
>> Subject: Bus error using OBMol.Separate
>> To: Cinfony <ci...@go...>
>>
>> Hi!
>>
>> I'm trying to use pybel from cinfony in order to find the different R-
>> groups on a general scaffold. I have managed to delete the scaffold,
>> leaving the R-groups as disconnected fragments in the molecule.
>> However, when I tried to separate the fragments I ran into a bus
>> error. The error appears every time I try to do .Separate() on a OBMol
>> such as in the following code:
>>
>> from cinfony import pybel
>>
>> mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
>> print "Initial molecule: ", mol.write("smi")
>> mol.OBMol.StripSalts(2)
>> print "After StripSalts(2): ", mol.write("smi")
>> mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
>> print "Back again: ", mol.write("smi")
>> temp = mol.OBMol.Separate()
>> for tempMol in temp:
>>       print "Fragment: ", tempMol.write("smi")
>>
>> Do you know what can be the problem, or should I rather post the
>> question with OpenBabel?
>>
>> I'm running cinfony on an Intel Mac with 10.5.5 and Python2.5 from
>> fink and OpenBabel 2.2.0
>>
>> Kind regards,
>> Fredrik Wallner
>>
>> --~--~---------~--~----~------------~-------~--~----~
>> You received this message because you are subscribed to the Google
>> Groups "Cinfony" group.
>> To post to this group, send email to ci...@go...
>> To unsubscribe from this group, send email to
>> cin...@go...
>> For more options, visit this group at
>> http://groups.google.com/group/cinfony?hl=en
>> -~----------~----~----~----~------~----~------~--~---
>>
>

Re: [OpenBabel-scripting] Bus error using OBMol.Separate

[Noel O'B. <bao...@gm...>]

Hello Fredrik,

I must admit that OBMol.Separate() usually causes a segfault for me
too, but I've never gotten around to reporting the bug. I've just
tested it a little bit. It seems that separating a methane is fine,
but separating ethane causes a segault.

>>> import pybel
>>> pybel.readstring("smi", "C").OBMol.Separate()
(<openbabel.OBMol; proxy of <Swig Object of type 'OpenBabel::OBMol *' at 0x12887
78> >,)
>>> pybel.readstring("smi", "CC").OBMol.Separate()
# It's a segger

I'll file a bug.

Noel


2008/12/9 Noel O'Boyle <bao...@gm...>:
> ---------- Forwarded message ----------
> From:  <fre...@gm...>
> Date: 2008/12/9
> Subject: Bus error using OBMol.Separate
> To: Cinfony <ci...@go...>
>
> Hi!
>
> I'm trying to use pybel from cinfony in order to find the different R-
> groups on a general scaffold. I have managed to delete the scaffold,
> leaving the R-groups as disconnected fragments in the molecule.
> However, when I tried to separate the fragments I ran into a bus
> error. The error appears every time I try to do .Separate() on a OBMol
> such as in the following code:
>
> from cinfony import pybel
>
> mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
> print "Initial molecule: ", mol.write("smi")
> mol.OBMol.StripSalts(2)
> print "After StripSalts(2): ", mol.write("smi")
> mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
> print "Back again: ", mol.write("smi")
> temp = mol.OBMol.Separate()
> for tempMol in temp:
>       print "Fragment: ", tempMol.write("smi")
>
> Do you know what can be the problem, or should I rather post the
> question with OpenBabel?
>
> I'm running cinfony on an Intel Mac with 10.5.5 and Python2.5 from
> fink and OpenBabel 2.2.0
>
> Kind regards,
> Fredrik Wallner
>
> --~--~---------~--~----~------------~-------~--~----~
> You received this message because you are subscribed to the Google
> Groups "Cinfony" group.
> To post to this group, send email to ci...@go...
> To unsubscribe from this group, send email to
> cin...@go...
> For more options, visit this group at
> http://groups.google.com/group/cinfony?hl=en
> -~----------~----~----~----~------~----~------~--~---
>

[OpenBabel-scripting] Fwd: Bus error using OBMol.Separate

[Noel O'B. <bao...@gm...>]

---------- Forwarded message ----------
From:  <fre...@gm...>
Date: 2008/12/9
Subject: Bus error using OBMol.Separate
To: Cinfony <ci...@go...>

Hi!

I'm trying to use pybel from cinfony in order to find the different R-
groups on a general scaffold. I have managed to delete the scaffold,
leaving the R-groups as disconnected fragments in the molecule.
However, when I tried to separate the fragments I ran into a bus
error. The error appears every time I try to do .Separate() on a OBMol
such as in the following code:

from cinfony import pybel

mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
print "Initial molecule: ", mol.write("smi")
mol.OBMol.StripSalts(2)
print "After StripSalts(2): ", mol.write("smi")
mol = pybel.readstring("smi", "[NH3+]c1ccccc1.[Cl-]")
print "Back again: ", mol.write("smi")
temp = mol.OBMol.Separate()
for tempMol in temp:
       print "Fragment: ", tempMol.write("smi")

Do you know what can be the problem, or should I rather post the
question with OpenBabel?

I'm running cinfony on an Intel Mac with 10.5.5 and Python2.5 from
fink and OpenBabel 2.2.0

Kind regards,
Fredrik Wallner

--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google
Groups "Cinfony" group.
To post to this group, send email to ci...@go...
To unsubscribe from this group, send email to
cin...@go...
For more options, visit this group at
http://groups.google.com/group/cinfony?hl=en
-~----------~----~----~----~------~----~------~--~---

Re: [OpenBabel-scripting] Adding methods to perl bindings

[Noel O'B. <bao...@gm...>]

Hello David,

The handling of descriptors changed between 2.1.0 and 2.2.0. It was
decided to implement them as plugins so we didn't need to add a new
class for every new descriptor. So the current API (at
http://openbabel.org/api/2.2.0/classes.shtml) doesn't have an OBLogP
class.

Here's how you use them (just tested in OB2.2.0):

my $obdesc = Chemistry::OpenBabel::OBDescriptor::FindType("LogP");
my $logp = $obdesc->Predict($obMol);
print $logp."\n";

By the way, you are absolutely correct in how to add classes to SWIG.
In this case, this isn't the problem.

Regards,
    Noel

2008/12/8 David Rose <tom...@gm...>:
> Hi:
>   18 months ago or so I posted a question about using OBLogP from perl.  I
> turned out that support for the method had not been added to the perl
> bindings; Geoff was good enough to cook up a version of Chemistry::OpenBabel
> that supported the method, and I was all set.
>   Now I'm installing the latest version of OB on a new machine, and I've got
> the same problem.  Because Geoff was kind enough to fix it for me before, I
> don't know how to fix it for myself this time, so I'm back; sorry about
> that.
>    My understanding is that I need to make a change to openbabel-perl.i,
> then configure openbabel using --enable-maintainer-mode, then build
> openbabel and then build the perl bindings.  What I don't know is what
> changes I need to make to openbabel-perl.i.  It appears that OBLogP is in
> groupcontrib.h, so I tried adding
> the following lines to openbabel-perl.i:
> #include <openbabel/groupcontrib.h>
> %include <openbabel/groupcontrib.h>
> in places where similar include statements were located.  Went through the
> build steps without any errors but  still no OBLogP.  If it is not too
> involved, can someone give me a quick tutorial on adding methods to the
> bindings?
> Thanks,
> David Rose
> ------------------------------------------------------------------------------
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>

[OpenBabel-scripting] Adding methods to perl bindings

[David R. <tom...@gm...>]

Hi:
  18 months ago or so I posted a question about using OBLogP from perl.  I
turned out that support for the method had not been added to the perl
bindings; Geoff was good enough to cook up a version of Chemistry::OpenBabel
that supported the method, and I was all set.

  Now I'm installing the latest version of OB on a new machine, and I've got
the same problem.  Because Geoff was kind enough to fix it for me before, I
don't know how to fix it for myself this time, so I'm back; sorry about
that.

   My understanding is that I need to make a change to openbabel-perl.i,
then configure openbabel using --enable-maintainer-mode, then build
openbabel and then build the perl bindings.  What I don't know is what
changes I need to make to openbabel-perl.i.  It appears that OBLogP is in
groupcontrib.h, so I tried adding
the following lines to openbabel-perl.i:

#include <openbabel/groupcontrib.h>

%include <openbabel/groupcontrib.h>

in places where similar include statements were located.  Went through the
build steps without any errors but  still no OBLogP.  If it is not too
involved, can someone give me a quick tutorial on adding methods to the
bindings?

Thanks,
David Rose

Re: [OpenBabel-scripting] [openbabel-scripting] OBdotnet

[Brian B. <bri...@am...>]

Hi Matt,
     It works! The key was dropping the whole folder contents into the debug
folder as you said. Here is the working code in case there is some other VB
soul out there:

Imports OpenBabel

Public Class Form1
    Private Sub Button1_Click(ByVal sender As System.Object, ByVal e As
System.EventArgs) Handles Button1.Click
        Dim strFolder As String = "c:\Structures\"
        Dim OBConv As New OBConversion()
        Dim OBMol As New OBMol()

        OBConv.SetInAndOutFormats("sdf", "smi")

        OBConv.ReadFile(OBMol, strFolder & "Structure1.sdf")
        OBConv.WriteFile(OBMol, strFolder & "Structure1.smi")

    End Sub
End Class

Just replace the Structure1.sdf with your own sdf file.

Enjoy!

Brian




Brian Bordeau wrote:
> 
> Hi Matt,
>     I've referenced the OBdotnet.dll in my project and based on the errors
> am wondering if I missed referencing a library or set up the OBConv
> incorrectly. Could you check the following app (in VB.net 2008) and see if
> there is anything obvious:
> 
> Imports OpenBabel
> 
> Public Class Form1
>     Private Sub Button1_Click(ByVal sender As System.Object, ByVal e As
> System.EventArgs) Handles Button1.Click
>         Dim strFolder As String = "c:\Structures\"
>         Dim OBConv As New OBConversion()
>         Dim OBBase As New OBBase()
> 
>         OBConv.SetInAndOutFormats("sdf", "smi")
> 
>         OBConv.ReadFile(OBBase, strFolder & "*.sdf")
>         OBConv.WriteFile(OBBase, strFolder & "*.smi")
> 
>     End Sub
> End Class
> 
> I'm getting the error(s) :
> 
> System.TypeInitializationException was unhandled
>   Message="The type initializer for 'OpenBabel.openbabelPINVOKE' threw an
> exception."
>   Source="OBDotNet"
>   TypeName="OpenBabel.openbabelPINVOKE"
> 
> and inner exceptions:
> 
>   InnerException: System.TypeInitializationException
>        Message="The type initializer for 'SWIGExceptionHelper' threw an
> exception."
>        Source="OBDotNet"
>        TypeName="SWIGExceptionHelper"
> 
> and
> 
>        InnerException: System.DllNotFoundException
>             Message="Unable to load DLL 'openbabel': The specified module
> could not be found. (Exception from HRESULT: 0x8007007E)"
>             Source="OBDotNet"
>             TypeName=""
>             StackTrace:
>                  at
> OpenBabel.openbabelPINVOKE.SWIGExceptionHelper.SWIGRegisterExceptionCallbacks_openbabel(ExceptionDelegate
> applicationDelegate, ExceptionDelegate arithmeticDelegate,
> ExceptionDelegate divideByZeroDelegate, ExceptionDelegate
> indexOutOfRangeDelegate, ExceptionDelegate invalidCastDelegate,
> ExceptionDelegate invalidOperationDelegate, ExceptionDelegate ioDelegate,
> ExceptionDelegate nullReferenceDelegate, ExceptionDelegate
> outOfMemoryDelegate, ExceptionDelegate overflowDelegate, ExceptionDelegate
> systemExceptionDelegate)    at
> OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..cctor()
>             InnerException: 
> 
> Thanks
> 
> Brian
> 
> 
> 
> 
> 
> 
> 
> Matt Sprague wrote:
>> 
>> Hi Brian,
>> 
>> In regards to your question about OBDotNet it is useable from any
>> language
>> that compiles for the CLR. This includes C#, VB, F#, S# (small talk.net)
>> etc. Because all of these languages compile to a common byte code and use
>> the FCL (framework class library) the assemblies are mostly
>> interchangeable
>> and the choice of language is really just a matter of personal
>> preference.
>> VB.Net is a core MS language so OBDotNet should work just fine. Worst
>> case,
>> if something wasn't supported it just won't be exposed when you reference
>> an
>> assembly but it won't prevent the rest of the library from functioning.
>> 
>> If you have any further questions or need any help just post to the
>> mailing
>> list. Noel knows  more about OpenBabel and I handle the more specific
>> CLR/FCL related stuff.
>> 
>> -Matt Sprague
>> 
>> 
>> On Thu, Nov 13, 2008 at 12:57 AM, Noel O'Boyle <bao...@gm...>
>> wrote:
>> 
>>> 2008/11/13 Bordeau, Brian <Bri...@am...>:
>>> > Hi Noel,
>>> >
>>> >             I am relatively new to using open source libraries,
>>> message
>>> > boards and the like so I don't know if/how people post messages or
>>> > questions.
>>> Generally, we cc everything to ope...@li... so
>>> that we have a record. I've forwarded your original message. Welcome
>>> to open source. :-)
>>>
>>> > I am a relatively proficient VB.net programmer and would like to
>>> > use the OBdotnet.dll library but am not sure if it has been designed
>>> for
>>> > this purpose – is this library solely for IronPython or could it be
>>> used
>>> in
>>> > a .net program.
>>> It's actually designed for .NET. I'm just more interested in
>>> IronPython than the other .NET languages. The main OBdotnet developer
>>> is interested in C# (Matt Sprague).
>>>
>>> We welcome feedback on this code, so let us know how it goes.
>>>
>>> Regards,
>>>    Noel
>>>
>>> -------------------------------------------------------------------------
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>> 
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>> 
>> 
> 
> 

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Re: [OpenBabel-scripting] [openbabel-scripting] OBdotnet

[Matt S. <mes...@gm...>]

As an addendum:

After the first problem is corrected... This code will probably fail

       Dim OBBase As New OBBase()

       OBConv.SetInAndOutFormats("sdf", "smi")

>
>        OBConv.ReadFile(OBBase, strFolder & "*.sdf")
>        OBConv.WriteFile(OBBase, strFolder & "*.smi")


Pass the method an OBMol not an OBBase. OBMol extends OBBase but if you
declare the object as an OBBase the code will probably fail because
OpenBabel won't be able to cast it down to an OBMol when it goes to process
the file.

-Matt

Re: [OpenBabel-scripting] [openbabel-scripting] OBdotnet

[Matt S. <mes...@gm...>]

Because OBDotNet was built with SWIG it uses an intermediate managed C++ dll
to access OpenBabel. Thats what openbabel.dll is. The program needs to be
able to see the full contents of the OBDotNet distribution. Follow the
directions in the IronPython instructions with regards to setting
environment variables. Remember that VS (I assume thats what your using) by
default will copy a referenced assembly to the release/debug directories but
won't know to bring any dependencies with it.

I'm working on creating an installer for the package but it won't be ready
for a while yet.

-Matt

On Thu, Nov 13, 2008 at 11:33 AM, Brian Bordeau <
bri...@am...> wrote:

>
> Hi Matt,
>    I've referenced the OBdotnet.dll in my project and based on the errors
> am wondering if I missed referencing a library or set up the OBConv
> incorrectly. Could you check the following app (in VB.net 2008) and see if
> there is anything obvious:
>
> Imports OpenBabel
>
> Public Class Form1
>    Private Sub Button1_Click(ByVal sender As System.Object, ByVal e As
> System.EventArgs) Handles Button1.Click
>        Dim strFolder As String = "c:\Structures\"
>        Dim OBConv As New OBConversion()
>        Dim OBBase As New OBBase()
>
>        OBConv.SetInAndOutFormats("sdf", "smi")
>
>        OBConv.ReadFile(OBBase, strFolder & "*.sdf")
>        OBConv.WriteFile(OBBase, strFolder & "*.smi")
>
>    End Sub
> End Class
>
> I'm getting the error(s) :
>
> System.TypeInitializationException was unhandled
>  Message="The type initializer for 'OpenBabel.openbabelPINVOKE' threw an
> exception."
>  Source="OBDotNet"
>  TypeName="OpenBabel.openbabelPINVOKE"
>
> and inner exceptions:
>
>  InnerException: System.TypeInitializationException
>       Message="The type initializer for 'SWIGExceptionHelper' threw an
> exception."
>       Source="OBDotNet"
>       TypeName="SWIGExceptionHelper"
>
> and
>
>       InnerException: System.DllNotFoundException
>            Message="Unable to load DLL 'openbabel': The specified module
> could not be found. (Exception from HRESULT: 0x8007007E)"
>            Source="OBDotNet"
>            TypeName=""
>            StackTrace:
>                 at
>
> OpenBabel.openbabelPINVOKE.SWIGExceptionHelper.SWIGRegisterExceptionCallbacks_openbabel(ExceptionDelegate
> applicationDelegate, ExceptionDelegate arithmeticDelegate,
> ExceptionDelegate
> divideByZeroDelegate, ExceptionDelegate indexOutOfRangeDelegate,
> ExceptionDelegate invalidCastDelegate, ExceptionDelegate
> invalidOperationDelegate, ExceptionDelegate ioDelegate, ExceptionDelegate
> nullReferenceDelegate, ExceptionDelegate outOfMemoryDelegate,
> ExceptionDelegate overflowDelegate, ExceptionDelegate
> systemExceptionDelegate)    at
> OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..cctor()
>            InnerException:
>
> Thanks
>
> Brian
>
>
>
>
>
>
>
> Matt Sprague wrote:
> >
> > Hi Brian,
> >
> > In regards to your question about OBDotNet it is useable from any
> language
> > that compiles for the CLR. This includes C#, VB, F#, S# (small talk.net)
> > etc. Because all of these languages compile to a common byte code and use
> > the FCL (framework class library) the assemblies are mostly
> > interchangeable
> > and the choice of language is really just a matter of personal
> preference.
> > VB.Net is a core MS language so OBDotNet should work just fine. Worst
> > case,
> > if something wasn't supported it just won't be exposed when you reference
> > an
> > assembly but it won't prevent the rest of the library from functioning.
> >
> > If you have any further questions or need any help just post to the
> > mailing
> > list. Noel knows  more about OpenBabel and I handle the more specific
> > CLR/FCL related stuff.
> >
> > -Matt Sprague
> >
> >
> > On Thu, Nov 13, 2008 at 12:57 AM, Noel O'Boyle <bao...@gm...>
> > wrote:
> >
> >> 2008/11/13 Bordeau, Brian <Bri...@am...>:
> >> > Hi Noel,
> >> >
> >> >             I am relatively new to using open source libraries,
> message
> >> > boards and the like so I don't know if/how people post messages or
> >> > questions.
> >> Generally, we cc everything to ope...@li... so
> >> that we have a record. I've forwarded your original message. Welcome
> >> to open source. :-)
> >>
> >> > I am a relatively proficient VB.net programmer and would like to
> >> > use the OBdotnet.dll library but am not sure if it has been designed
> >> for
> >> > this purpose – is this library solely for IronPython or could it be
> >> used
> >> in
> >> > a .net program.
> >> It's actually designed for .NET. I'm just more interested in
> >> IronPython than the other .NET languages. The main OBdotnet developer
> >> is interested in C# (Matt Sprague).
> >>
> >> We welcome feedback on this code, so let us know how it goes.
> >>
> >> Regards,
> >>    Noel
> >>
> >>
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>
> --
> View this message in context:
> http://www.nabble.com/Re%3A-OBdotnet-tp20476218p20486773.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
>
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