Thread: [OpenBabel-scripting] Fwd: OBdotnet

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openbabel-scripting

[OpenBabel-scripting] Fwd: OBdotnet

From: Noel O'B. <bao...@gm...> - 2008-11-13 07:51:34

---------- Forwarded message ----------
From: Bordeau, Brian <Bri...@am...>
Date: 2008/11/13
Subject: OBdotnet
To: bao...@gm...


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. 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. I'd be happy to post
this to an appropriate board but don't exactly know where.



Thanks



Brian



Brian Bordeau

Research Scientist III,  In Vitro Biology

AMRI

Bothell Research Center

18804 North Creek Parkway

Bothell, WA 98011

email:bri...@am...

Phone:1-425-424-7293

Fax: 1-425-424-7299

Re: [OpenBabel-scripting] OBdotnet

From: Noel O'B. <bao...@gm...> - 2008-11-13 07:57:18

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

Re: [OpenBabel-scripting] OBdotnet

From: Matt S. <mes...@gm...> - 2008-11-13 09:00:22

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
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

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

From: Brian B. <bri...@am...> - 2008-11-13 18:33:52

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
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the
> world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 

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

From: Brian B. <bri...@am...> - 2008-11-13 21:38:12

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
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great
>>> prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>> world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>
>> 
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> 
>> 
> 
> 

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

From: Matt S. <mes...@gm...> - 2008-11-13 18:44:57

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
> >>
> >>
> -------------------------------------------------------------------------
> >> This SF.Net email is sponsored by the Moblin Your Move Developer's
> >> challenge
> >> Build the coolest Linux based applications with Moblin SDK & win great
> >> prizes
> >> Grand prize is a trip for two to an Open Source event anywhere in the
> >> world
> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> >> _______________________________________________
> >> OpenBabel-scripting mailing list
> >> Ope...@li...
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> >
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> > challenge
> > Build the coolest Linux based applications with Moblin SDK & win great
> > prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> > world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
>
> --
> 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.
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

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

From: Matt S. <mes...@gm...> - 2008-11-13 18:52:56

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