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

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

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
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
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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.

Re: [OpenBabel-scripting] OBdotnet

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

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] OBdotnet

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

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

[OpenBabel-scripting] Fwd: OBdotnet

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

---------- 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] Problem

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

The deeper cause is that the OpenBabel library cannot find the various
file formats. Maybe I should improve the error message. :)

I recommend that you 'reboot' by uninstalling OpenBabel and Pybel, and
then reinstalling according to the instructions on our website. If you
still have a problem, please describe your operating system, and how
you installed everything. Did you remember to run "make install"?

Regards,
Noel

2008/10/31 Kamran Haider <ha...@ys...>:
> Dear openbabel scripting community
> I have a problem in importing PyBel. The 'import pybel' statement gives
> the following output. I have tried to look through pybel.py and spot the
> problem and its obviously about the _formatstodict which is trying to
> unpack members of a list that do not contain more than 1 elements . The
> problem seems to have some deeper cause.
> I would be grateful, if you could help me out.
> Thanks
>
>  >>> import pybel
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/y/people/haider/python_add_modules/lib/python/pybel.py", line
> 25, in <module>
>    informats = _formatstodict(_obconv.GetSupportedInputFormat())
>  File "/y/people/haider/python_add_modules/lib/python/pybel.py", line
> 21, in _formatstodict
>    broken = [(x,y.strip()) for x,y in broken]
> ValueError: need more than 1 value to unpack
>
> --
> ***********************************************************
> Kamran Haider
> York Structural Biology Laboratory
> University of York
> Heslington
> York, UK
> YO10 5YW
> Email: ha...@ys... mk...@yo...
> Mobile: +44(0)7902974801 Lab: +44 1904 328259
> Fax: +44 1904 328266
> URL: http://www.ysbl.york.ac.uk/people/haider.htm
> ***********************************************************
>
>
> -------------------------------------------------------------------------
> 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
>

[OpenBabel-scripting] Problem

[Kamran H. <ha...@ys...>]

Dear openbabel scripting community
I have a problem in importing PyBel. The 'import pybel' statement gives 
the following output. I have tried to look through pybel.py and spot the 
problem and its obviously about the _formatstodict which is trying to 
unpack members of a list that do not contain more than 1 elements . The 
problem seems to have some deeper cause.
I would be grateful, if you could help me out.
Thanks

 >>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/y/people/haider/python_add_modules/lib/python/pybel.py", line 
25, in <module>
    informats = _formatstodict(_obconv.GetSupportedInputFormat())
  File "/y/people/haider/python_add_modules/lib/python/pybel.py", line 
21, in _formatstodict
    broken = [(x,y.strip()) for x,y in broken]
ValueError: need more than 1 value to unpack

-- 
***********************************************************
Kamran Haider
York Structural Biology Laboratory
University of York
Heslington
York, UK
YO10 5YW
Email: ha...@ys... mk...@yo...
Mobile: +44(0)7902974801 Lab: +44 1904 328259
Fax: +44 1904 328266
URL: http://www.ysbl.york.ac.uk/people/haider.htm
***********************************************************

Re: [OpenBabel-scripting] OBConversion Options

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

2008/10/19 Matt Sprague <mes...@gm...>:
> I checked the conversion options in OBDotNet and the input and output
> options seem to work. The GENOPTIONS don't cause any errors in
> OBDotNet but neither do they effect the output. It might be useful to
> work on getting the typemaps for the scripting languages to handle
> std::map<T,T> so we can check and see what options the wrapper object
> has set.

IsOption seems to be working, so you can loop over a-zA-Z and check
the values. As far as I can see, the option are being set correctly -
it's just that OB never uses them.

I've just tested an OUTOPTION, and it seems to be working as you say.
So it looks like the problem is limited to GENOPTIONS. I find it
difficult to figure out how the conversion framework operates, so I
can't see where DoTransformations is being called if it is being
called...

> -Matt
>
> -------------------------------------------------------------------------
> 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
>

[OpenBabel-scripting] OBConversion Options

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

I checked the conversion options in OBDotNet and the input and output
options seem to work. The GENOPTIONS don't cause any errors in
OBDotNet but neither do they effect the output. It might be useful to
work on getting the typemaps for the scripting languages to handle
std::map<T,T> so we can check and see what options the wrapper object
has set.

-Matt

Re: [OpenBabel-scripting] cast needed for OBChiralData in Python bindings

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

Yes. Sorry about this. I'll add the casts for all types of data to all
of the bindings.

2008/10/15 Beda Kosata <Bed...@vs...>:
> Hello,
>
> I would like to use python bindings to opanbabel to access
> stereochemical information stored in OBChiralData.
> Unfortunately what I get from the atom by using GetData() is an
> OBGenericData type object, which should be cast to OBChiralData in order
> to work properly.
> Would it be possible to add a conversion function to the bindings,
> similarly to the toPairData() and toUnitCell() functions?
>
> Best regards
>
>        Beda
>
> --
> Bedrich Kosata
> Laboratory of Informatics and Chemistry
> ICT Prague
> Czech Republic
>
> -------------------------------------------------------------------------
> 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
>
>

[OpenBabel-scripting] cast needed for OBChiralData in Python bindings

[Beda K. <Bed...@vs...>]

Hello,

I would like to use python bindings to opanbabel to access
stereochemical information stored in OBChiralData.
Unfortunately what I get from the atom by using GetData() is an
OBGenericData type object, which should be cast to OBChiralData in order
to work properly.
Would it be possible to add a conversion function to the bindings,
similarly to the toPairData() and toUnitCell() functions?

Best regards

	Beda

-- 
Bedrich Kosata
Laboratory of Informatics and Chemistry
ICT Prague
Czech Republic

Re: [OpenBabel-scripting] How to use option when converting a file..

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

The enum part is fine. e.g. openbabel.OBConversion.GENOPTIONS is 1,
etc. Even if you use this, you get a segfault.

2008/10/14 Chris Morley <c.m...@ga...>:
> Jérôme Hert wrote:
>> Dear Colleaugues,
>>
>> I was trying to use an option when converting a file into a different
>> format.
>>
>> I use Perl so I write something like
>> use Chemistry::OpenBabel;
>> my $obMol = new Chemistry::OpenBabel::OBMol;
>> my $obConversion = new Chemistry::OpenBabel::OBConversion;
>> $obConversion->SetInAndOutFormats( "mol2", "pdb" );
>> $obConversion->ReadFile( $obMol, "infile.mol2");
>> $obConversion->WriteFile( $obMol, "outfile.pdb" );
>>
>> That works fine.
>>
>> Now I am trying to add something like:
>> $obConversion->AddOption("d");
>> before reading thr file in, the program doesn't complain but nothing
>> happens (i.e., the hydrogens are still present in the output file).
>>
>> Anybody has any idea how these options are named? Any has any clue about
>> all those GetOptions, SetOption, GetOptions etc of that class in Perl?
>>
> In C++ it would be necessary to use:
>
> obConversion->AddOption("d", OBConversion::GENOPTIONS);
>
> where the second parameter is an enum. I don't know how this is
> translated with the scripting interfaces.
>
> There are three types of option INOPTIONS, OUTOPTIONS and GENOPTIONS.
> On the babel command-line the INOPTIONS, OUTOPTIONS have a prefix,
> e.g. -as and -xn respectively.
> The default for this function is OUTOPTIONS, but -d needs GENOPTIONS.
> Multi-character options are all GENOPTIONS.
>
> It's a bit confusing for the scripting interface user, and perhaps we
> need something like AddGenOption("d")
>
> You could also use a direct function call of DeleteHydrogens().
>
> Chris
>
> -------------------------------------------------------------------------
> 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
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>

Re: [OpenBabel-scripting] fpt file format exception

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

I get a segfault in Python too.

2008/10/14 Matt Sprague <mes...@gm...>:
> It has been brought to my attention that OBDotNet throws an exception
> when trying to use WriteFile or WriteString with the fpt format.
>
> I've traced it to this line of the OBConversion wrapper...
>
> bool ret = openbabelPINVOKE.OBConversion_WriteFile(swigCPtr,
> OBBase.getCPtr(pOb), filePath);
>
> This is the error detail.
>
> AppName: chemsharp_test.vshost.exe       AppVer: 9.0.21022.8     ModName: msvcr80.dll
> ModVer: 8.0.50727.1433   Offset: 00008aa0
>
> Is this a OBDotNet problem or does it occur in the bindings for other
> languages? Any thoughts on a cause/solution?
>
> -Matt
>

Re: [OpenBabel-scripting] How to use option when converting a file..

[Chris M. <c.m...@ga...>]

Jérôme Hert wrote:
> Dear Colleaugues,
> 
> I was trying to use an option when converting a file into a different 
> format.
> 
> I use Perl so I write something like
> use Chemistry::OpenBabel;
> my $obMol = new Chemistry::OpenBabel::OBMol;
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInAndOutFormats( "mol2", "pdb" ); 
> $obConversion->ReadFile( $obMol, "infile.mol2");
> $obConversion->WriteFile( $obMol, "outfile.pdb" );
> 
> That works fine.
> 
> Now I am trying to add something like:
> $obConversion->AddOption("d");
> before reading thr file in, the program doesn't complain but nothing 
> happens (i.e., the hydrogens are still present in the output file).
> 
> Anybody has any idea how these options are named? Any has any clue about 
> all those GetOptions, SetOption, GetOptions etc of that class in Perl?
> 
In C++ it would be necessary to use:

obConversion->AddOption("d", OBConversion::GENOPTIONS);

where the second parameter is an enum. I don't know how this is 
translated with the scripting interfaces.

There are three types of option INOPTIONS, OUTOPTIONS and GENOPTIONS. 
On the babel command-line the INOPTIONS, OUTOPTIONS have a prefix, 
e.g. -as and -xn respectively.
The default for this function is OUTOPTIONS, but -d needs GENOPTIONS.
Multi-character options are all GENOPTIONS.

It's a bit confusing for the scripting interface user, and perhaps we 
need something like AddGenOption("d")

You could also use a direct function call of DeleteHydrogens().

Chris

Re: [OpenBabel-scripting] How to use option when converting a file..

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

Just tested from Python and doesn't seem to work either. In fact, a
nice way of generating a segfault is to call
obconversion.GetOptions().

This sounds like a serious problem, so I wouldn't be hopeful there is
a workaround. I'll file a bug...

Noel

2008/10/13 Jérôme Hert <j...@hm...>:
> Dear Colleaugues,
>
> I was trying to use an option when converting a file into a different
> format.
>
> I use Perl so I write something like
> use Chemistry::OpenBabel;
> my $obMol = new Chemistry::OpenBabel::OBMol;
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInAndOutFormats( "mol2", "pdb" );
> $obConversion->ReadFile( $obMol, "infile.mol2");
> $obConversion->WriteFile( $obMol, "outfile.pdb" );
>
> That works fine.
>
> Now I am trying to add something like:
> $obConversion->AddOption("d");
> before reading thr file in, the program doesn't complain but nothing
> happens (i.e., the hydrogens are still present in the output file).
>
> Anybody has any idea how these options are named? Any has any clue about
> all those GetOptions, SetOption, GetOptions etc of that class in Perl?
>
> Help will be very much appreciated.
> Thanks a lot,
> Jerome.
>
> -------------------------------------------------------------------------
> 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
>

[OpenBabel-scripting] fpt file format exception

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

It has been brought to my attention that OBDotNet throws an exception
when trying to use WriteFile or WriteString with the fpt format.

I've traced it to this line of the OBConversion wrapper...

bool ret = openbabelPINVOKE.OBConversion_WriteFile(swigCPtr,
OBBase.getCPtr(pOb), filePath);

This is the error detail.

AppName: chemsharp_test.vshost.exe	 AppVer: 9.0.21022.8	 ModName: msvcr80.dll
ModVer: 8.0.50727.1433	 Offset: 00008aa0

Is this a OBDotNet problem or does it occur in the bindings for other
languages? Any thoughts on a cause/solution?

-Matt

[OpenBabel-scripting] How to use option when converting a file..

[Jérôme H. <j...@hm...>]

Dear Colleaugues,

I was trying to use an option when converting a file into a different 
format.

I use Perl so I write something like
use Chemistry::OpenBabel;
my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInAndOutFormats( "mol2", "pdb" ); 
$obConversion->ReadFile( $obMol, "infile.mol2");
$obConversion->WriteFile( $obMol, "outfile.pdb" );

That works fine.

Now I am trying to add something like:
$obConversion->AddOption("d");
before reading thr file in, the program doesn't complain but nothing 
happens (i.e., the hydrogens are still present in the output file).

Anybody has any idea how these options are named? Any has any clue about 
all those GetOptions, SetOption, GetOptions etc of that class in Perl?

Help will be very much appreciated.
Thanks a lot,
Jerome.

Re: [OpenBabel-scripting] Rotable bonds

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

Apparently, the atom IDs returned by TorsionIter are off by one (you
need to add to each of them to get the correct atom ID - I'll file a
bug report I think about this). Hence the segfault when you tried to
access a non-existent atom (or non existent torsion...).

Noel

2008/10/13 Thomas Greve Kristensen <tg...@da...>:
> Hi,
>
> thanks for the help, but I still not sure how to do this. My problem is that
> I can extract the atom ids from TorsionIter, and wtih those I can extract
> the atoms, which I need for getting and setting torsions, but the enclosed
> script results in a segmentation fault.
>
> Is this due to a broken TorsionIter or is it me who are misunderstanding
> something?
>
> Thanks for all your help,
>
> Thomas
>
>
>
>
> On Oct 11, 2008, at 5:15 PM, Noel O'Boyle wrote:
>
>> OBMolTorsionIter may not be working correctly. Apart from that, see
>> OBMol::SetTorsion and OBMol::GetTorsion in the C++ documentation
>> (openbabel.org/api)
>>
>> 2008/10/11 Thomas Greve Kristensen <tg...@da...>:
>>>
>>> Hi all,
>>>
>>> I'm trying to rotate parts of a molecule around a rotable bond, but I
>>> can't seem to figure out how to do this from python.
>>> My experiments try to rotate the bonds of a ligand to see how the energy
>>> landscape changes. My goal is to experiment with energy minimization
>>> algorithms.
>>>
>>> I appreciate all the help I can get...
>>>
>>> Thomas G. Kristensen
>>> (phd student, Aarhus University, Denmark)
>>>
>>> p.s: This is how far I've gotten so far:
>>>
>>> #!/usr/bin/env python
>>> """
>>> A (hopefully) small test that will reviel how easy
>>> it is to calculate the energy of a molecule using
>>> the open babel python swig bindings.
>>> """
>>> import pybel
>>> import openbabel
>>>
>>> forcefield = openbabel.OBForceField.FindForceField("MMFF94")
>>>
>>> if __name__ == "__main__":
>>>  for mol in pybel.readfile("mol2", "ligands.mol2"):
>>>    obmol = mol.OBMol
>>>    forcefield.Setup(obmol)
>>>    print forcefield.Energy()
>>>
>>>    for bond in openbabel.OBMolBondIter(obmol):
>>>      print bond.IsRotor() # I cant ask this object to rotate :(
>>>
>>>    for torsion in openbabel.OBMolTorsionIter(obmol):
>>>      print torsion # Is not an object, can not be manipulated :(
>>>
>>> -------------------------------------------------------------------------
>>> 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] Rotable bonds

[Thomas G. K. <tg...@da...>]

Hi,

thanks for the help, but I still not sure how to do this. My problem  
is that I can extract the atom ids from TorsionIter, and wtih those I  
can extract the atoms, which I need for getting and setting torsions,  
but the enclosed script results in a segmentation fault.

Is this due to a broken TorsionIter or is it me who are  
misunderstanding something?

Thanks for all your help,

Thomas

Re: [OpenBabel-scripting] Rotable bonds

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

OBMolTorsionIter may not be working correctly. Apart from that, see
OBMol::SetTorsion and OBMol::GetTorsion in the C++ documentation
(openbabel.org/api)

2008/10/11 Thomas Greve Kristensen <tg...@da...>:
> Hi all,
>
> I'm trying to rotate parts of a molecule around a rotable bond, but I
> can't seem to figure out how to do this from python.
> My experiments try to rotate the bonds of a ligand to see how the energy
> landscape changes. My goal is to experiment with energy minimization
> algorithms.
>
> I appreciate all the help I can get...
>
> Thomas G. Kristensen
> (phd student, Aarhus University, Denmark)
>
> p.s: This is how far I've gotten so far:
>
> #!/usr/bin/env python
> """
> A (hopefully) small test that will reviel how easy
> it is to calculate the energy of a molecule using
> the open babel python swig bindings.
> """
> import pybel
> import openbabel
>
> forcefield = openbabel.OBForceField.FindForceField("MMFF94")
>
> if __name__ == "__main__":
>    for mol in pybel.readfile("mol2", "ligands.mol2"):
>      obmol = mol.OBMol
>      forcefield.Setup(obmol)
>      print forcefield.Energy()
>
>      for bond in openbabel.OBMolBondIter(obmol):
>        print bond.IsRotor() # I cant ask this object to rotate :(
>
>      for torsion in openbabel.OBMolTorsionIter(obmol):
>        print torsion # Is not an object, can not be manipulated :(
>
> -------------------------------------------------------------------------
> 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
>

[OpenBabel-scripting] Perl iterators now in SVN

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

I've just learnt Perl and checked in some SWIG code for generating
Perl classes to allow the C++ iterators to be used natively from Perl
as follows:

my $iter = new Chemistry::OpenBabel::OBMolAtomIter($obMol);
while (my $atom = $iter->()) {
   print $atom->GetIdx()."\n";
}

Is this reasonably Perlish? If you want to try this out, you'll either
have to wait for the next release, or compile the SWIG bindings
yourself on the OB22X branch.

Noel

[OpenBabel-scripting] Rotable bonds

[Thomas G. K. <tg...@da...>]

Hi all,

I'm trying to rotate parts of a molecule around a rotable bond, but I
can't seem to figure out how to do this from python.
My experiments try to rotate the bonds of a ligand to see how the energy
landscape changes. My goal is to experiment with energy minimization
algorithms.

I appreciate all the help I can get...

Thomas G. Kristensen
(phd student, Aarhus University, Denmark)

p.s: This is how far I've gotten so far:

#!/usr/bin/env python
"""
A (hopefully) small test that will reviel how easy
it is to calculate the energy of a molecule using
the open babel python swig bindings.
"""
import pybel
import openbabel

forcefield = openbabel.OBForceField.FindForceField("MMFF94")

if __name__ == "__main__":
    for mol in pybel.readfile("mol2", "ligands.mol2"):
      obmol = mol.OBMol
      forcefield.Setup(obmol)
      print forcefield.Energy()

      for bond in openbabel.OBMolBondIter(obmol):
        print bond.IsRotor() # I cant ask this object to rotate :(

      for torsion in openbabel.OBMolTorsionIter(obmol):
        print torsion # Is not an object, can not be manipulated :(

Re: [OpenBabel-scripting] Pybel - localopt() error?!

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

Tim has solved this problem. The main problem was that pybel wasn't
checking whether the force field was able to initialise properly. To
workaround in pybel.py, you will need to replace the line:

ff.Setup(self.OBMol)

with

success = ff.Setup(self.OBMol)
if not success:
    return

Noel

2008/7/27 Noel O'Boyle <bao...@gm...>:
>> Hi Noel,
>>
>> as far as i know are you one of the main developer behind the great
>> pybel bindungs for openbabel. I'm unable to find an irc channel or
>> something like this, so i'm trying to cantact you directly. Hope that is
>> ok.
>
> Google "Pybel". :-) 4th line:
> "If you have any problems or want to ask a question, please send an
> email to the openbabel-scripting mailing list."
>
>> I'm playing around with the new functions draw, localopt, addh etc. And
>> i get a strange error if i try to generate 3D structures from inchis.
>> Attached you can find a inchi.txt with several inchis from chemid-plus.
>> The script inchi23dmolfile.py tries to read each inchi and generate 3D
>> structures. With one inchi i get a segmentation fault, with an other i
>> get a small backtrace (see below). If i try these procedure in ipython i
>> can't reproduce it. But with the script i get every time the same error.
>> Do you have any clue what is causing by error? Any hint to debug it
>> further, or how i can absorb these error, to proceed with the script (my
>> initial script have a few hundred inchis)?
>
> The problem isn't reading the inchis but generating the 3D structures.
> There's some weird memory stuff going on. There's no short term
> solution I'm afraid. I'll file a bug and one of the other developers
> will look into it.

>> I would be happy to provide you with more informations if you like.
>>
>> Thank you very much,
>> Bjoern
>>
>> P.S. Is their any irc channel, or mailing list for pybel?
>>
>> Segmentation fault
>> InChI=1/C10H18O6/c1-9(11)15-7-5-13-3-4-14-6-8-16-10(2)12/h3-8H2,1-2H3
>>
>>
>> InChI=1/2Cr.2Na.7O/q;;2*
>> +1;;;;;;2*-1/rCr2O7.2Na/c3-1(4,5)9-2(6,7)8;;/q-2;2*+1
>> -------------- backtrace ------------------------
>> *** glibc detected *** python: corrupted double-linked list:
>> 0x00000000010f3420 ***
>> ======= Backtrace: =========
>> /lib/libc.so.6[0x7f2f822bc28c]
>> /lib/libc.so.6(cfree+0x8c)[0x7f2f822bfc1c]
>> python[0x435ed7]
>> python[0x434944]
>> python(PyEval_EvalFrameEx+0x85c)[0x4837fc]
>> python(PyEval_EvalCodeEx+0x776)[0x48a376]
>> python(PyEval_EvalCode+0x32)[0x48a492]
>> python(PyRun_FileExFlags+0x10e)[0x4abdce]
>> python(PyRun_SimpleFileExFlags+0x1a9)[0x4ac069]
>> python(Py_Main+0x8fd)[0x4145ad]
>> /lib/libc.so.6(__libc_start_main+0xf4)[0x7f2f822661c4]
>> python[0x413b29]
>> ======= Memory map: ========
>> 00400000-00522000 r-xp 00000000 08:02
>> 574300                             /usr/bin/python2.5
>> 00721000-00753000 rw-p 00121000 08:02
>> 574300                             /usr/bin/python2.5
>> 00753000-011c7000 rw-p 00753000 00:00 0
>> [heap]
>> 401d3000-401d4000 ---p 401d3000 00:00 0
>> 401d4000-409d4000 rw-p 401d4000 00:00 0
>> 7f2f6c000000-7f2f6c021000 rw-p 7f2f6c000000 00:00 0
>> 7f2f6c021000-7f2f70000000 ---p 7f2f6c021000 00:00 0
>> 7f2f700b3000-7f2f700b8000 r-xp 00000000 08:02
>> 781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
>> 7f2f700b8000-7f2f702b8000 ---p 00005000 08:02
>> 781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
>> 7f2f702b8000-7f2f702b9000 rw-p 00005000 08:02
>> 781861                     /usr/lib/openbabel/2.2/2.2.0/zindoformat.so
>> 7f2f702b9000-7f2f702c4000 r-xp 00000000 08:02
>> 781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
>> 7f2f702c4000-7f2f704c4000 ---p 0000b000 08:02
>> 781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
>> 7f2f704c4000-7f2f704c5000 rw-p 0000b000 08:02
>> 781720                     /usr/lib/openbabel/2.2/2.2.0/fchkformat.so
>> 7f2f704c5000-7f2f704cf000 r-xp 00000000 08:02
>> 781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
>> 7f2f704cf000-7f2f706ce000 ---p 0000a000 08:02
>> 781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
>> 7f2f706ce000-7f2f706cf000 rw-p 00009000 08:02
>> 781604                     /usr/lib/openbabel/2.2/2.2.0/fastsearchformat.so
>> 7f2f706cf000-7f2f706d7000 r-xp 00000000 08:02
>> 781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
>> 7f2f706d7000-7f2f708d6000 ---p 00008000 08:02
>> 781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
>> 7f2f708d6000-7f2f708d7000 rw-p 00007000 08:02
>> 781676                     /usr/lib/openbabel/2.2/2.2.0/cacaoformat.so
>> 7f2f708d7000-7f2f708dd000 r-xp 00000000 08:02
>> 781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
>> 7f2f708dd000-7f2f70add000 ---p 00006000 08:02
>> 781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
>> 7f2f70add000-7f2f70ade000 rw-p 00006000 08:02
>> 781856                     /usr/lib/openbabel/2.2/2.2.0/mpqcformat.so
>> 7f2f70ade000-7f2f70ae7000 r-xp 00000000 08:02
>> 781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
>> 7f2f70ae7000-7f2f70ce6000 ---p 00009000 08:02
>> 781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
>> 7f2f70ce6000-7f2f70ce7000 rw-p 00008000 08:02
>> 781606                     /usr/lib/openbabel/2.2/2.2.0/thermoformat.so
>> 7f2f70ce7000-7f2f70cf5000 r-xp 00000000 08:02
>> 781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
>> 7f2f70cf5000-7f2f70ef5000 ---p 0000e000 08:02
>> 781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
>> 7f2f70ef5000-7f2f70ef6000 rw-p 0000e000 08:02
>> 781879                     /usr/lib/openbabel/2.2/2.2.0/pdbformat.so
>> 7f2f70ef6000-7f2f70efd000 r-xp 00000000 08:02
>> 781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
>> 7f2f70efd000-7f2f710fd000 ---p 00007000 08:02
>> 781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
>> 7f2f710fd000-7f2f710fe000 rw-p 00007000 08:02
>> 781867                     /usr/lib/openbabel/2.2/2.2.0/reportformat.so
>> 7f2f710fe000-7f2f71104000 r-xp 00000000 08:02
>> 780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
>> 7f2f71104000-7f2f71303000 ---p 00006000 08:02
>> 780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
>> 7f2f71303000-7f2f71304000 rw-p 00005000 08:02
>> 780096                     /usr/lib/openbabel/2.2/2.2.0/unichemformat.so
>> 7f2f71304000-7f2f71309000 r-xp 00000000 08:02
>> 781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
>> 7f2f71309000-7f2f71509000 ---p 00005000 08:02
>> 781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
>> 7f2f71509000-7f2f7150a000 rw-p 00005000 08:02
>> 781868                     /usr/lib/openbabel/2.2/2.2.0/fhformat.so
>> 7f2f7150a000-7f2f71607000 r-xp 00000000 08:02
>> 781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
>> 7f2f71607000-7f2f71806000 ---p 000fd000 08:02
>> 781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
>> 7f2f71806000-7f2f7181b000 rw-p 000fc000 08:02
>> 781612                     /usr/lib/openbabel/2.2/2.2.0/inchiformat.so
>> 7f2f7181b000-7f2f71820000 r-xp 00000000 08:02
>> 781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
>> 7f2f71820000-7f2f71a20000 ---p 00005000 08:02
>> 781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
>> 7f2f71a20000-7f2f71a21000 rw-p 00005000 08:02
>> 781885                     /usr/lib/openbabel/2.2/2.2.0/molreportformat.so
>> 7f2f71a21000-7f2f71a26000 r-xp 00000000 08:02
>> 781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
>> 7f2f71a26000-7f2f71c26000 ---p 00005000 08:02
>> 781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
>> 7f2f71c26000-7f2f71c27000 rw-p 00005000 08:02
>> 781857                     /usr/lib/openbabel/2.2/2.2.0/CSRformat.so
>> 7f2f71c27000-7f2f71c30000 r-xp 00000000 08:02
>> 781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
>> 7f2f71c30000-7f2f71e2f000 ---p 00009000 08:02
>> 781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
>> 7f2f71e2f000-7f2f71e30000 rw-p 00008000 08:02
>> 781866                     /usr/lib/openbabel/2.2/2.2.0/crkformat.so
>> 7f2f71e30000-7f2f71e37000 r-xp 00000000 08:02
>> 781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
>> 7f2f71e37000-7f2f72037000 ---p 00007000 08:02
>> 781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
>> 7f2f72037000-7f2f72038000 rw-p 00007000 08:02
>> 781860                     /usr/lib/openbabel/2.2/2.2.0/chem3dformat.so
>> 7f2f72038000-7f2f7203e000 r-xp 00000000 08:02
>> 780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
>> 7f2f7203e000-7f2f7223e000 ---p 00006000 08:02
>> 780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
>> 7f2f7223e000-7f2f7223f000 rw-p 00006000 08:02
>> 780115                     /usr/lib/openbabel/2.2/2.2.0/ghemicalformat.so
>> 7f2f7223f000-7f2f72245000 r-xp 00000000 08:02
>> 781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
>> 7f2f72245000-7f2f72444000 ---p 00006000 08:02
>> 781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
>> 7f2f72444000-7f2f72445000 rw-p 00005000 08:02
>> 781882                     /usr/lib/openbabel/2.2/2.2.0/fastaformat.so
>> 7f2f72445000-7f2f7244a000 r-xp 00000000 08:02
>> 781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
>> 7f2f7244a000-7f2f7264a000 ---p 00005000 08:02
>> 781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
>> 7f2f7264a000-7f2f7264b000 rw-p 00005000 08:02
>> 781869                     /usr/lib/openbabel/2.2/2.2.0/cssrformat.so
>> 7f2f7264b000-7f2f72651000 r-xp 00000000 08:02
>> 780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
>> 7f2f72651000-7f2f72850000 ---p 00006000 08:02
>> 780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
>> 7f2f72850000-7f2f72851000 rw-p 00005000 08:02
>> 780107                     /usr/lib/openbabel/2.2/2.2.0/hinformat.so
>> 7f2f72851000-7f2f72857000 r-xp 00000000 08:02
>> 781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
>> 7f2f72857000-7f2f72a56000 ---p 00006000 08:02
>> 781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
>> 7f2f72a56000-7f2f72a57000 rw-p 00005000 08:02
>> 781881                     /usr/lib/openbabel/2.2/2.2.0/carformat.so
>> 7f2f72a57000-7f2f72a5d000 r-xp 00000000 08:02
>> 781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
>> 7f2f72a5d000-7f2f72c5c000 ---p 00006000 08:02
>> 781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
>> 7f2f72c5c000-7f2f72c5d000 rw-p 00005000 08:02
>> 781608                     /usr/lib/openbabel/2.2/2.2.0/cacheformat.so
>> 7f2f72c5d000-7f2f72c66000 r-xp 00000000 08:02
>> 781865                     /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
>> 7f2f72c66000-7f2f72e65000 ---p 00009000 08:02
>> 781865                     /usr/lib/openbabel/2.2/2.2.0/opendxformat.so
>> 7f2f72e65000-7f2f72e66000 rw-p 00008000 08:02
>> 781865                     /usr/lib/openbabel/2.2Aborted
>>
>> --
>> ==========================================
>> Björn Grüning
>> D-14612 Falkensee, Germany
>> Tel. +49-3322-212968, Fax +49-3322-4287528
>> email: bj...@gr...
>> jid:   ba...@gr...
>>
>

[OpenBabel-scripting] Two issues with Csharp bindings

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

Hello Matt,

I've been implementing Pybel in IronPython on top of the CSharp
bindings as a test case. There's two issues I've come across:

(1) I'd like to rename openbabel.dll to openbabel-csharp.dll or so.
The reason is that I'm thinking it might be good to unify all of the
Windows releases into one (Python, CSharp, Java, GUI? etc.) , and the
java swig bindings also make an openbabel.dll (which I want to rename
to openbabel-java.dll).

(2) Regarding the API, I have a problem accessing unitcell data (e.g.
for http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/scripts/python/examples/hashizume.cif?revision=2042).
OBUnitCell is a subclass of OBGenericData but with extra methods.
Unfortunately, those methods don't 'appear' when inspecting the
OBGenericData object in IronPython. Is this the same from C#? In C++,
it's possible to cast the superclass to an instance of the subclass,
but this doesn't work in Python. In fact, in the CPython bindings, I
needed to add a convenience C++ function in the SWIG interface file
which performs the cast. Although in the CPython bindings I added this
as a global method, I guess you would argue for it being a method of
the OBGenericData object. Either way, how does this sound?

Noel

[OpenBabel-scripting] Using iterators from Perl (Was: A few questions about scripting OB with Perl)

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

I'm sorry - I'm not very familiar with Perl. However it should be
possible to call the inc() method of the $ai object. To see whether
the iteration is finished, you should test the value of the good()
method.

If there are any Perl users out there who are familiar with writing an
iterator class, it would really help here. We could add that code to
the Perl bindings like I have done for the Python bindings.

Noel

2008/9/23 IN SUK JOUNG <i....@gm...>:
> I don't know how to iterate using OBResidueAtomIter.
>
> I tried
> $ai = Chemistry::OpenBabel::OBResidueAtomIter->new( $res );
>
> I could use $ai as OBAtom object and I could get information from the first
> atom of the residue like
> $x = $ai->GetX;
>
> It was successful, but I don't know how I move to the next atom.
>
> --
> Best,
> In-Suk Joung
>
> -------------------------------------------------------------------------
> 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] A few questions about scripting OB with Perl

[IN S. J. <i....@gm...>]

I don't know how to iterate using OBResidueAtomIter.

I tried
$ai = Chemistry::OpenBabel::OBResidueAtomIter->new( $res );

I could use $ai as OBAtom object and I could get information from the first
atom of the residue like
$x = $ai->GetX;

It was successful, but I don't know how I move to the next atom.

-- 
Best,
In-Suk Joung