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Re: [OpenBabel-scripting] Problems with Swigtypes, FastSearch etc.

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

On 8 March 2010 22:48, Mikko Kasanen <kas...@ho...> wrote:
> No i havent tryed anything else, getting the FastSearch methods would be
> importants since building own algoriths from scratch could be disastrous for
> the project and the usability of the program. Everytime user does a
> similarity search, the comparison has to be done with 500+ k molecyles. What
> functions u have in mind?

The functions were described in my original email. They use fastsearch.

> Even getting the results in a text file would be awesome.
>
>> Date: Mon, 8 Mar 2010 22:39:17 +0000
>> Subject: Re: [OpenBabel-scripting] Problems with Swigtypes, FastSearch
>> etc.
>> From: bao...@gm...
>> To: kas...@ho...
>> CC: ope...@li...
>>
>> On 8 March 2010 22:26, Mikko Kasanen <kas...@ho...> wrote:
>> > Like in previous post our uni project had a problem with Similarity
>> > searching.
>> > We started our project with C#, but had to lose that since last reply
>> > here
>> > was that the Findsimilar etc does not work in C#.
>>
>> Actually, my last reply stated that it was possible...but using
>> different functions instead. Did you try that?
>>
>> > The problem is that we dont have any coding examples that could help us.
>> > We
>> > switched the language to Java now.
>> >
>> > Here is how our program is supposed to work.
>> >
>> > 1. I have generated a .fs file out of a huge chembl database.
>> > In the program code i use FastSearch.ReadIndexFile("location"); to
>> > identify
>> > the fs. file.
>> >
>> > 2. The user of our project feeds the program with his mol file, .mol or
>> > .smi
>> > etc.
>> > The program reads the file into a OBMol object so that i can use it in
>> > next
>> > step.
>> >
>> > 3. Here i would like to do a Similarity search with the users file, the
>> > idea
>> > is to seek from the Chembl db for similar objects.
>> > What i have understood from Open Babel API, is that FindSimilar method
>> > needs
>> > (Input [the users OBMol object], Output [SWIGtype multimap], search
>> > criteria
>> > like 0.7 tanimoto coeffincy).
>> >
>> > Could you guys help us with code examples since we have NO knowledge of
>> > C++
>> > and NO knowledge of how to use it in Java etc.
>> >
>> > How do i create a multimap in Java? If type SWIGTYPE_..._... multimap;
>> > it
>> > gives error about initialization.
>> > Then how do i use that multimap even if i get it to work?, how can i
>> > take
>> > objects / objects info from there and print it to user?
>> >
>> > This is pretty serious problem for us since we have less than 2 months
>> > to
>> > projects finish and we have written alot of documentation, but the
>> > programming is giving us a bad headache.
>> > (Other project groups have way way more easier projects)
>> >
>> > ________________________________
>> > Uudessa IE8 selaimessa on uudet pikatoiminnot. Lataa.
>> >
>> > ------------------------------------------------------------------------------
>> > Download Intel® Parallel Studio Eval
>> > Try the new software tools for yourself. Speed compiling, find bugs
>> > proactively, and fine-tune applications for parallel performance.
>> > See why Intel Parallel Studio got high marks during beta.
>> > http://p.sf.net/sfu/intel-sw-dev
>> > _______________________________________________
>> > OpenBabel-scripting mailing list
>> > Ope...@li...
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >
>> >
>
> ________________________________
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Re: [OpenBabel-scripting] Problems with Swigtypes, FastSearch etc.

[Mikko K. <kas...@ho...>]

I just realized that i could run a cmd line from Java and get the results from there, gotta try that tomorrow.
Anyways thank you for quick replys.
 		 	   		  
_________________________________________________________________
Uudessa IE8 selaimessa on uudet pikatoiminnot.
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Re: [OpenBabel-scripting] Problems with Swigtypes, FastSearch etc.

[Mikko K. <kas...@ho...>]

No i havent tryed anything else, getting the FastSearch methods would be importants since building own algoriths from scratch could be disastrous for the project and the usability of the program. Everytime user does a similarity search, the comparison has to be done with 500+ k molecyles. What functions u have in mind?

Even getting the results in a text file would be awesome.

> Date: Mon, 8 Mar 2010 22:39:17 +0000
> Subject: Re: [OpenBabel-scripting] Problems with Swigtypes, FastSearch etc.
> From: bao...@gm...
> To: kas...@ho...
> CC: ope...@li...
> 
> On 8 March 2010 22:26, Mikko Kasanen <kas...@ho...> wrote:
> > Like in previous post our uni project had a problem with Similarity
> > searching.
> > We started our project with C#, but had to lose that since last reply here
> > was that the Findsimilar etc does not work in C#.
> 
> Actually, my last reply stated that it was possible...but using
> different functions instead. Did you try that?
> 
> > The problem is that we dont have any coding examples that could help us. We
> > switched the language to Java now.
> >
> > Here is how our program is supposed to work.
> >
> > 1. I have generated a .fs file out of a huge chembl database.
> > In the program code i use FastSearch.ReadIndexFile("location"); to identify
> > the fs. file.
> >
> > 2. The user of our project feeds the program with his mol file, .mol or .smi
> > etc.
> > The program reads the file into a OBMol object so that i can use it in next
> > step.
> >
> > 3. Here i would like to do a Similarity search with the users file, the idea
> > is to seek from the Chembl db for similar objects.
> > What i have understood from Open Babel API, is that FindSimilar method needs
> > (Input [the users OBMol object], Output [SWIGtype multimap], search criteria
> > like 0.7 tanimoto coeffincy).
> >
> > Could you guys help us with code examples since we have NO knowledge of C++
> > and NO knowledge of how to use it in Java etc.
> >
> > How do i create a multimap in Java? If type SWIGTYPE_..._... multimap; it
> > gives error about initialization.
> > Then how do i use that multimap even if i get it to work?, how can i take
> > objects / objects info from there and print it to user?
> >
> > This is pretty serious problem for us since we have less than 2 months to
> > projects finish and we have written alot of documentation, but the
> > programming is giving us a bad headache.
> > (Other project groups have way way more easier projects)
> >
> > ________________________________
> > Uudessa IE8 selaimessa on uudet pikatoiminnot. Lataa.
> > ------------------------------------------------------------------------------
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed compiling, find bugs
> > proactively, and fine-tune applications for parallel performance.
> > See why Intel Parallel Studio got high marks during beta.
> > http://p.sf.net/sfu/intel-sw-dev
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
 		 	   		  
_________________________________________________________________
Uudessa IE8 selaimessa on uudet pikatoiminnot.
http://www.microsoft.com/finland/windows/products/winfamily/ie/beta/default.mspx

Re: [OpenBabel-scripting] Problems with Swigtypes, FastSearch etc.

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

On 8 March 2010 22:26, Mikko Kasanen <kas...@ho...> wrote:
> Like in previous post our uni project had a problem with Similarity
> searching.
> We started our project with C#, but had to lose that since last reply here
> was that the Findsimilar etc does not work in C#.

Actually, my last reply stated that it was possible...but using
different functions instead. Did you try that?

> The problem is that we dont have any coding examples that could help us. We
> switched the language to Java now.
>
> Here is how our program is supposed to work.
>
> 1. I have generated a .fs file out of a huge chembl database.
> In the program code i use FastSearch.ReadIndexFile("location"); to identify
> the fs. file.
>
> 2. The user of our project feeds the program with his mol file, .mol or .smi
> etc.
> The program reads the file into a OBMol object so that i can use it in next
> step.
>
> 3. Here i would like to do a Similarity search with the users file, the idea
> is to seek from the Chembl db for similar objects.
> What i have understood from Open Babel API, is that FindSimilar method needs
> (Input [the users OBMol object], Output [SWIGtype multimap], search criteria
> like 0.7 tanimoto coeffincy).
>
> Could you guys help us with code examples since we have NO knowledge of C++
> and NO knowledge of how to use it in Java etc.
>
> How do i create a multimap in Java? If type SWIGTYPE_..._... multimap; it
> gives error about initialization.
> Then how do i use that multimap even if i get it to work?, how can i take
> objects / objects info from there and print it to user?
>
> This is pretty serious problem for us since we have less than 2 months to
> projects finish and we have written alot of documentation, but the
> programming is giving us a bad headache.
> (Other project groups have way way more easier projects)
>
> ________________________________
> Uudessa IE8 selaimessa on uudet pikatoiminnot. Lataa.
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] Problems with Swigtypes, FastSearch etc.

[Mikko K. <kas...@ho...>]

Like in previous post our uni project had a problem with Similarity searching.
We started our project with C#, but had to lose that since last reply here was that the Findsimilar etc does not work in C#.
The problem is that we dont have any coding examples that could help us. We switched the language to Java now.

Here is how our program is supposed to work.

1. I have generated a .fs file out of a huge chembl database.
In the program code i use FastSearch.ReadIndexFile("location"); to identify the fs. file.

2. The user of our project feeds the program with his mol file, .mol or .smi etc.
The program reads the file into a OBMol object so that i can use it in next step.

3. Here i would like to do a Similarity search with the users file, the idea is to seek from the Chembl db for similar objects.
What i have understood from Open Babel API, is that FindSimilar method needs (Input [the users OBMol object], Output [SWIGtype multimap], search criteria like 0.7 tanimoto coeffincy).

Could you guys help us with code examples since we have NO knowledge of C++ and NO knowledge of how to use it in Java etc.

How do i create a multimap in Java? If type SWIGTYPE_..._... multimap; it gives error about initialization.
Then how do i use that multimap even if i get it to work?, how can i take objects / objects info from there and print it to user?

This is pretty serious problem for us since we have less than 2 months to projects finish and we have written alot of documentation, but the programming is giving us a bad headache.
(Other project groups have way way more easier projects)
 		 	   		  
_________________________________________________________________
Windows puhelimella saat enemmän vastinetta rahoillesi.
http://www.windowsmobile.fi

Re: [OpenBabel-scripting] Hi! Our uni project has a small problem with OBdotNet.

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

I don't think it will work using the FastSearch class, but it should
work fine using the FastSearch format.

See http://old.nabble.com/Re%3A-Using-fastsearch-from-Python-p17430663.html
for instructions on use from Python.

- Noel

On 2 March 2010 16:14, Mikko Kasanen <kas...@ho...> wrote:
>
>
> Greetings from Finland!
>
> We are currently developing a small program in University of Eastern Finland
> (www.uef.fi) at Kuopio campus.
> In the program we are using OBdotNet from Open Babel and as a molecylar
> database we use the Chembl database.
> We are currently having some problems trying to write the code in C# using
> Visual Studio, since we cannot get Similarity searches working.
> The problem is that we try to use FindSimilar methods but all the Swig types
> etc give us problems since we cannot get it to work.
>
>
> I am trying to ask that is it even possible at this moment to get it work,
> and if so, could u help with a small sample code.
>
> Thx in advance, Mikko Kasanen.
>
> ________________________________
> Uusi Spaces ja 25 Gt ilmaista SkyDrive tallennustilaa. Lataa Live paketti.
> ________________________________
> Tutustu videoiden avulla Windows Live tuotteisiin. Opi mestariksi.
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] Hi! Our uni project has a small problem with OBdotNet.

[Mikko K. <kas...@ho...>]

Greetings from Finland!

 

We are currently developing a small program in University of Eastern Finland (www.uef.fi) at Kuopio campus.

In the program we are using OBdotNet from Open Babel and as a molecylar database we use the Chembl database.

We are currently having some problems trying to write the code in C# using Visual Studio, since we cannot get Similarity searches working.

The problem is that we try to use FindSimilar methods but all the Swig types etc give us problems since we cannot get it to work.


 

I am trying to ask that is it even possible at this moment to get it work, and if so, could u help with a small sample code.

 

Thx in advance, Mikko Kasanen.
 		 	   		  
Uusi Spaces ja 25 Gt ilmaista SkyDrive tallennustilaa. Lataa Live paketti. 		 	   		  
_________________________________________________________________
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http://www.microsoft.fi/live

Re: [OpenBabel-scripting] Problem reading large PDB file (Was: need your help !!!)

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

Hello,

This is a known bug with OpenBabel (see bug report at
http://sourceforge.net/tracker/?func=detail&aid=2841031&group_id=40728&atid=428740).
I'm afraid there's no way around it at the moment.

- Noel

On 18 February 2010 18:44, benomrane brahim <ben...@ya...> wrote:
> Hi,
> i need to integrate OpenBabel into my application which created with JAVA so
> for that i Used your API OpenBabel.jar
> the result is perfectly when i use small file BUT when i use big file  for
> example if i convert 114D.pdb (size 44Ko) into input mopac my program block
> and Win Dialog error Start (lock in jointed file)
> my class is
> package viewer;
> import org.openbabel.*;
> public class OpenBabelConverter {
>
>   public OpenBabelConverter()
>  {
>    System.loadLibrary("openbabel_java");
>  }
>   public void startconvert(String typein,
>                            String filein,
>                            String typeout,
>                            String fileout
>                            ) {
>       OBConversion conv = new OBConversion();
>
>       OBMol mol = new OBMol();
>
>        conv.SetInFormat(typein);
>        conv.ReadFile(mol,filein);
>
>        conv.SetOutFormat(typeout);
>        conv.WriteFile(mol,fileout);
>        conv.CloseOutFile();
>   }
> }
> Please i need your Help Thank's
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] OBConformer question

[Marat T. <mi...@ma...>]

Greetings,

As is known, obconformer utility generates a number of conformers,
and, after MM optimization, prints XYZ coords of the most stable one.
The question is, how to modify obconformer behaviour to make it
print coords not one but N most stable conformer XYZs?


-- 
Sincerely yours,,
 Marat                          mailto:mi...@ma...

Re: [OpenBabel-scripting] Building Python Bindings from SVN

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

Fixed in r3513. As Geoff says, more work to be done but at least it's
compiling again now - thanks for reporting.

- Noel

On 4 February 2010 15:28, Geoffrey Hutchison <ge...@ge...> wrote:
>> the Python instructions reference a "Step A2" which doesn't exist when installing from source.  In particular, it doesn't look like the trunk uses "configure" anymore.
>
> No, the problem with trunk is that CMake does things "a little different" from configure. In particular, it thinks it can build the Python bindings itself, when it's probably better to generate the SWIG code, and then let Python build everything.
>
> I should have some time to address this today -- it's been on my TODO list for a while.
>
> Thanks for the reminder,
> -Geoff
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
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>

Re: [OpenBabel-scripting] Building Python Bindings from SVN

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

> the Python instructions reference a "Step A2" which doesn't exist when installing from source.  In particular, it doesn't look like the trunk uses "configure" anymore.

No, the problem with trunk is that CMake does things "a little different" from configure. In particular, it thinks it can build the Python bindings itself, when it's probably better to generate the SWIG code, and then let Python build everything.

I should have some time to address this today -- it's been on my TODO list for a while.

Thanks for the reminder,
-Geoff

[OpenBabel-scripting] Building Python Bindings from SVN

[A. H. <ab...@cs...>]

Hi OpenBabelers,

I'm trying to build Python bindings against the OpenBabel trunk.  I'd like
to follow the instructions for SVN building (
http://openbabel.org/wiki/Install_%28source_code%29) and the Python binding
building instructions (http://openbabel.org/wiki/Install_Python_bindings)
but the Python instructions reference a "Step A2" which doesn't exist when
installing from source.  In particular, it doesn't look like the trunk uses
"configure" anymore.

Instead, I set the CMake options listed at the end of this email and
received the following error.  It looks like everything except the Python
bindings is working.  Any suggestions for how to get the Python built?

Cheers,
Abe


The Python-related CMake options:
  // Enable Python bindings
  ENABLE_PYTHON:BOOL=ON
  // Path to a program.
  PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.5
  // Path to a file.
  PYTHON_INCLUDE_PATH:PATH=/usr/include/python2.5
  // Path to a library.
  PYTHON_LIBRARY:FILEPATH=/usr/lib64/python2.5/config/libpython2.5.so
  // No help, variable specified on the command line.
  SWIG_DIR:PATH=/home/myself/swig-1.3.40/build/share/swig/1.3.40
  // No help, variable specified on the command line.
  SWIG_EXECUTABLE:FILEPATH=/home/myself/swig-1.3.40/build/bin/swig


The error:
[myself@yoyodyne openbabel-svn]$ make
[ 34%] Built target openbabel
[ 52%] Built target inchi
...etc...
[ 99%] Built target obrotate
[ 99%] Building CXX object
scripts/CMakeFiles/_openbabel.dir/openbabel-pythonC++_wrap.cxx.o
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx: In function
‘PyObject* _wrap_OBBuilder_IsSpiroAtom(PyObject*, PyObject*)’:
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27731:
error: ‘OBStereo’ has not been declared
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27731:
error: expected `;' before ‘arg1’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘OBStereo’ has not been declared
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘temp’ was not declared in this scope
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected type-specifier before ‘OBStereo’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected `>' before ‘OBStereo’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected `(' before ‘OBStereo’
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘OBStereo’ has not been declared
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected primary-expression before ‘>’ token
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: expected `)' before ‘;’ token
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27737:
error: ‘arg1’ was not declared in this scope
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27738:
error: type ‘<type error>’ argument given to ‘delete’, expected pointer
/home/myself/openbabel-svn/scripts/openbabel-pythonC++_wrap.cxx:27743:
error: ‘arg1’ was not declared in this scope
make[2]: ***
[scripts/CMakeFiles/_openbabel.dir/openbabel-pythonC++_wrap.cxx.o] Error 1
make[1]: *** [scripts/CMakeFiles/_openbabel.dir/all] Error 2
make: *** [all] Error 2

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

Re: [OpenBabel-scripting] [C#] How to retrive OBGridData?

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

Hi Alex,

As you found, there was a bug in Downcast. I've fixed it and made a
zip of a new release at
http://www.redbrick.dcu.ie/~noel/tmp/Release.zip

Can you test this, and let me know if it works for you. If so, I'll
make a new OBDotNet release.

- Noel

On 29 January 2010 08:25, Demiurg HG <dem...@gm...> wrote:
> Hello,
>
> I`m trying to retrive charge density (OBGridData) from Gaussuan Cube using
> OBDotNet (latest version).
>
> My code looks like this:
>
> elem_table    =    new OBElementTable();
> conv          =    new OBConversion();
> mol           =    new OBMol();
>
> if (!conv.SetInFormat("CUBE")) { throw new Exception("cann`t set input
> format");}
> if (!conv.ReadFile(mol, "test3.cube")) { throw new Exception("cann`t open
> \"test3.cube\" file"); }
>
> mol.FindRingAtomsAndBonds();
> mol.Center();
>
> VectorpData    data_set = mol.GetAllData(openbabelcsharp.GridData);
>
> for (int i=0; i<data_set.Count; i++) {
>     OBGenericData data = data_set[i];
>     OBGridData    grid = data.Downcast<OBGridData>();  // <-- exception
> }
>
> An unhandled exception of type 'System.InvalidCastException' occurred in
> OBDotNet.dll
> Additional information: No explicit downcast is defined for GridData.
>
> Thanks before hand.
> Alex.
>
> ------------------------------------------------------------------------------
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> business
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>
>

[OpenBabel-scripting] [C#] How to retrive OBGridData?

[Demiurg HG <dem...@gm...>]

Hello,

I`m trying to retrive charge density (OBGridData) from Gaussuan Cube using
OBDotNet (latest version).

My code looks like this:

elem_table    =    new OBElementTable();

conv          =    new OBConversion();
mol           =    new OBMol();

if (!conv.SetInFormat("CUBE")) { throw new Exception("cann`t set input
format");}
if (!conv.ReadFile(mol, "test3.cube")) { throw new Exception("cann`t open
\"test3.cube\" file"); }

mol.FindRingAtomsAndBonds();
mol.Center();


VectorpData    data_set = mol.GetAllData(openbabelcsharp.GridData);

for (int i=0; i<data_set.Count; i++) {
    OBGenericData data = data_set[i];
    OBGridData    grid = data.Downcast<OBGridData>();  // <-- exception
}

An unhandled exception of type 'System.InvalidCastException' occurred in
OBDotNet.dll
Additional information: No explicit downcast is defined for GridData.

Thanks before hand.
Alex.

Re: [OpenBabel-scripting] [Openbabel-Scripting] Reading charge density from Gaussian Cube (C#)

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

Hello Alex,

As far I understand, the code as written should work. It could be that
we don't wrap the GridData object correctly.

- Noel

On 25 January 2010 08:40, Demiurg HG <dem...@gm...> wrote:
> Hello Noel,
>
> I've reviewed this article
> http://openbabel.org/wiki/OBDotNet#Handling_OBGenericData
> As I understand I have to use .Downcast<> method. Unfortunetly it does not
> help :(
>
> Now my code looks like this:
>
> elem_table    =    new OBElementTable();
> conv          =    new OBConversion();
> mol           =    new OBMol();
>
> if (!conv.SetInFormat("CUBE")) { throw new Exception("cann`t set input
> format");}
> if (!conv.ReadFile(mol, "test3.cube")) { throw new Exception("cann`t open
> \"test.cube\" file"); }
>
> mol.FindRingAtomsAndBonds();
> mol.Center();
>
> VectorpData    data_set = mol.GetAllData(openbabelcsharp.GridData);
>
> for (int i=0; i<data_set.Count; i++) {
>     OBGenericData data = data_set[i];
>     OBGridData    grid = data.Downcast<OBGridData>();  // <-- exception
> }
>
> An unhandled exception of type 'System.InvalidCastException' occurred in
> OBDotNet.dll
> Additional information: No explicit downcast is defined for GridData.
>
> Thanks before hand.
> Alex.
>
> 2010/1/22 Noel O'Boyle <bao...@gm...>
>>
>> Hello Alex,
>>
>> See the OBDotNet documentation for information on casting OB data
>> types. BTW, questions about development with OB are better sent to the
>> openbabel-scripting list.
>>
>> Hope this helps....
>>
>> - Noel
>>
>> 2010/1/22 Demiurg HG <dem...@gm...>:
>> > Hello,
>> >
>> > I`m trying to retrive charge density (OBGridData) from Gaussuan Cube
>> > using
>> > OBDotNet (latest version).
>> > My code looks like this:
>> >
>> > conv    =    new OBConversion();
>> > mol     =    new OBMol();
>> >
>> > if (!conv.SetInFormat("CUBE")) {
>> >     throw new Exception("cann`t set input format");
>> > }
>> >
>> > if (!conv.ReadFile(mol, "test3.cube")) {
>> >     throw new Exception("cann`t open \"test3.cube\" file");
>> > }
>> >
>> > VectorpData    data_set = mol.GetAllData(openbabelcsharp.GridData);
>> >
>> > for (int i=0; i<data_set.Count; i++) {
>> >     OBGenericData data = data_set[i];
>> >     Debug.WriteLine("Data #" + i + " : " + data.GetAttribute() + ",
>> > type="+data.GetDataType() + data.ToString());
>> >
>> >     OBGridData    grid = (OBGridData)data; // <-- InvalidCastException
>> > }
>> >
>> > Molecule is loaded successfully.
>> > data.GetDataType() returns 24 (openbabelcsharp.GridData)
>> > An exception on type casting is occurs.
>> >
>> > What is a right way get OBGridData?
>> >
>> > Thanks before hand.
>> > Alex.
>> >
>
>

Re: [OpenBabel-scripting] pybel error

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

You should probably try to reinstall OpenBabel and its Python
bindings. The instructions are on our install page:
http://openbabel.org/wiki/Get_Open_Babel

- Noel

2010/1/22 Cianchetta, Giovanni <GCi...@le...>:
> Hi everybody,
> until yesterday pybel was working fine but today it refuses to work
> when I try to open any file I get this message
>
>    for mol in pybel.readfile(filetype,sys.argv[1]):
>  File "/usr/local/lib/python2.5/site-packages/pybel.py", line 66, in readfile
>    raise ValueError,"%s is not a recognised OpenBabel format" % format
> ValueError: sdf is not a recognised OpenBabel format
>
> this morning I updated scipy and installed ipython but I don't know if these can have anything to do with it. do you know what is going on here?
>
> another question: I was trying to download the python extensions to re-install them but I found only the exe files on sourceforge and I am working under linux Centos. do you know where I can find the right file
>
> thanks a lot
>
> Giovanni
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>

[OpenBabel-scripting] pybel error

[Cianchetta, G. <GCi...@Le...>]

Hi everybody,
until yesterday pybel was working fine but today it refuses to work
when I try to open any file I get this message

    for mol in pybel.readfile(filetype,sys.argv[1]):
  File "/usr/local/lib/python2.5/site-packages/pybel.py", line 66, in readfile
    raise ValueError,"%s is not a recognised OpenBabel format" % format
ValueError: sdf is not a recognised OpenBabel format

this morning I updated scipy and installed ipython but I don't know if these can have anything to do with it. do you know what is going on here?

another question: I was trying to download the python extensions to re-install them but I found only the exe files on sourceforge and I am working under linux Centos. do you know where I can find the right file

thanks a lot

Giovanni

[OpenBabel-scripting] Error installing Perl bindings

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

Hi:

  I am trying to install Open Babel 2.2.3 and the perl bindings on a machine
running Mac OS Server 10.6.  Open Babel installation itself goes fine, but
when I try to install the perl bindings and run 'make' I get this error:

i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
powerpc-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
lipo: can't figure out the architecture type of: /var/tmp//cc4ZVpKH.out
make: *** [blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle] Error 1

 Any ideas?

thanks,
David Rose

Re: [OpenBabel-scripting] OBDotNet v0.3

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

2009/12/29 Matt Sprague <mes...@gm...>:
> I'm finished with v0.3 of the .Net bindings. Before I upload the changes I
> have a couple of questions. I may have asked some of these before, but it's
> been awhile.
>
> 1) In the new bindings I've implemented a system to preserve inheritance
> chains when returning classing from unmanaged code (type factory with cached
> delegates for dynamically constructed methods FTW!). This means that we no
> longer need the ugly Cast methods on OBGeneric data. Should I remove them or
> mark them as deprecated to give end users some warning and remove them in
> the next version?

I'd prefer to mark as deprecated.

> 2) A couple support classes like the aforementioned type factory are
> currently implemented in stand alone source files. Where should I put them
> to avoid screwing up the non-VS build? If necessary I can make them internal
> to the imclass, but I'd prefer not to as it would make the interface file
> much longer.

If you just stick them in scripts/cpp or so, it would be fine.

> 3) I've found it advantageous to split up the swig instructions into
> multiple interface files as follows.
>     -openbabel-csharp.i -> interface file processed through swig in
> \scripts\
>     - obswig_ignores.i -> master list of ignored classes/methods
>     - obswig_macros.i -> useful macros for things like wrapping overloaded
> operators
>     - ob_enums.i -> definitions of enums that force swig to generate enums
> for groups of global constants defined in header
>                              files (much easier for end users to understand
> than having dozens of constatns in a module class)
>     - multimap.i -> multimap wrapper for fast search (not currently a part
> of swig C# or java)
>     - stl_streams.i -> minimal stream class definitions for java and C#
>
>    Currently I've got the supporting interface files in  \scripts\swigcommon
> so that they can be used by both the java and C#                interface
> files. Is that acceptable? If so, I know that the make files will need to be
> updated. Can someone who is more familiar          with  the build process
> handle that after check in?

I'll sort it out.

> 4) Functions defined in header files with unnamed parameters really cause
> problems when applying typemaps. For example,            SomeFunc(int*),
> SomeOther(int*) can't have to different typemaps for the parameters. Can we
> go through and name all the              currently unnamed parameters? The
> only workaround for swig is to ignore the method and extend the class
> definition with an            identical method with named parameters. That
> gets pretty ugly.

Are you happy to identify and correct these or do you need a hand?

> Let me know what you think about this stuff and I'll start checking in the
> new code.
>
> -Matt
>

Re: [OpenBabel-scripting] OBDotNet v0.3

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

The cpp files are not parsed by swig so nothing needs to be done there.
Also, unused parameters in the headers could remain unnamed if since we can
probably no customization of typemaps would really be necessary.

-Matt

On Tue, Dec 29, 2009 at 4:47 AM, Chris Morley <c.m...@ga...> wrote:

> Matt Sprague wrote:
>
> > 4) Functions defined in header files with unnamed parameters really
> > cause problems when applying typemaps. For example,
> > SomeFunc(int*), SomeOther(int*) can't have to different typemaps for the
> > parameters. Can we go through and name all the              currently
> > unnamed parameters? The only workaround for swig is to ignore the method
> > and extend the class definition with an            identical method with
> > named parameters. That gets pretty ugly.
>
> There seems to be a style of header file which uses parameter names
> only in the documentation above the declaration. I don't like this and
> so would be happy to require all parameters to have informative names.
> (I presume that it is still ok to have missing parameter names in
> function definitions in cpp files, which serve to highlight when a
> parameter is not used in the implementation.)
>
> Chris
>
>
>
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Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

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

We could do that. I'm leery of doing so because it would seem to require
also bundling in the windows version of the posix threading library
(pgthreads.dll) and because I still don't know what the problem is. It might
just be something about the setup on my machine. Noel seemed to indicate
that he didn't see the problem with the python bindings. If you think that's
the best short term solution, I'll check in my build of libxml2.dll when I
check in the updated files for OBDotNet v0.3.

-Matt


On Tue, Dec 29, 2009 at 3:40 AM, Chris Morley <c.m...@ga...> wrote:

> Matt Sprague wrote:
> > Nope, that didn't help. The program is crashing inside of the the call
> > to xmlFreeTextReader. You can view the source here:
> >
> http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup
> > <
> http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup
> >
> > <
> http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup
> >
> > Whatever is happening occurs between the beginning of the function (line
> > 2177)
> > and the call to xmlFreeParserInputBuffer(input) (line 2245). I thought I
> > was closing in on the problem, but the version of libxml2 I built with
> > MinGW works just fine. So now I'm really puzzled.
>
> Sorry to be slow to respond to this. If you have built a libxml2 DLL
> (and lib) that works for you, we could use that instead of the current
> one, which was just downloaded from somewhere. Or have I misunderstood?
>
> Chris
>
>
> ------------------------------------------------------------------------------
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>

Re: [OpenBabel-scripting] OBDotNet v0.3

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

> There seems to be a style of header file which uses parameter names
> only in the documentation above the declaration. I don't like this and
> so would be happy to require all parameters to have informative names.

Actually, oxygen should complain about this when generating documentation. So yes, I think we should require all parameters to have names.

> (I presume that it is still ok to have missing parameter names in 
> function definitions in cpp files, which serve to highlight when a 
> parameter is not used in the implementation.)

In fact, GCC will generate warnings about unused parameters if you leave them in.

-Geoff

Re: [OpenBabel-scripting] OBDotNet v0.3

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

Matt Sprague wrote:

> 4) Functions defined in header files with unnamed parameters really 
> cause problems when applying typemaps. For example,            
> SomeFunc(int*), SomeOther(int*) can't have to different typemaps for the 
> parameters. Can we go through and name all the              currently 
> unnamed parameters? The only workaround for swig is to ignore the method 
> and extend the class definition with an            identical method with 
> named parameters. That gets pretty ugly.

There seems to be a style of header file which uses parameter names
only in the documentation above the declaration. I don't like this and
so would be happy to require all parameters to have informative names.
(I presume that it is still ok to have missing parameter names in 
function definitions in cpp files, which serve to highlight when a 
parameter is not used in the implementation.)

Chris

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

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

Matt Sprague wrote:
> Nope, that didn't help. The program is crashing inside of the the call 
> to xmlFreeTextReader. You can view the source here:
> http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup 
> <http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup>
> <http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup>
> Whatever is happening occurs between the beginning of the function (line 
> 2177)
> and the call to xmlFreeParserInputBuffer(input) (line 2245). I thought I 
> was closing in on the problem, but the version of libxml2 I built with 
> MinGW works just fine. So now I'm really puzzled. 

Sorry to be slow to respond to this. If you have built a libxml2 DLL 
(and lib) that works for you, we could use that instead of the current 
one, which was just downloaded from somewhere. Or have I misunderstood?

Chris

[OpenBabel-scripting] OBDotNet v0.3

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

I'm finished with v0.3 of the .Net bindings. Before I upload the changes I
have a couple of questions. I may have asked some of these before, but it's
been awhile.

1) In the new bindings I've implemented a system to preserve inheritance
chains when returning classing from unmanaged code (type factory with cached
delegates for dynamically constructed methods FTW!). This means that we no
longer need the ugly Cast methods on OBGeneric data. Should I remove them or
mark them as deprecated to give end users some warning and remove them in
the next version?

2) A couple support classes like the aforementioned type factory are
currently implemented in stand alone source files. Where should I put them
to avoid screwing up the non-VS build? If necessary I can make them internal
to the imclass, but I'd prefer not to as it would make the interface file
much longer.

3) I've found it advantageous to split up the swig instructions into
multiple interface files as follows.
    -openbabel-csharp.i -> interface file processed through swig in
\scripts\
    - obswig_ignores.i -> master list of ignored classes/methods
    - obswig_macros.i -> useful macros for things like wrapping overloaded
operators
    - ob_enums.i -> definitions of enums that force swig to generate enums
for groups of global constants defined in header
                             files (much easier for end users to understand
than having dozens of constatns in a module class)
    - multimap.i -> multimap wrapper for fast search (not currently a part
of swig C# or java)
    - stl_streams.i -> minimal stream class definitions for java and C#

   Currently I've got the supporting interface files in  \scripts\swigcommon
so that they can be used by both the java and C#                interface
files. Is that acceptable? If so, I know that the make files will need to be
updated. Can someone who is more familiar          with  the build process
handle that after check in?

4) Functions defined in header files with unnamed parameters really cause
problems when applying typemaps. For example,            SomeFunc(int*),
SomeOther(int*) can't have to different typemaps for the parameters. Can we
go through and name all the              currently unnamed parameters? The
only workaround for swig is to ignore the method and extend the class
definition with an            identical method with named parameters. That
gets pretty ugly.

Let me know what you think about this stuff and I'll start checking in the
new code.

-Matt