openbabel-scripting — This list is deprecated. Please use openbabel-discuss instead.

[OpenBabel-scripting] dl module error

[Ahmet B. <ah...@pi...>]

Hi All,

I have followed the instructions to install Python wrapper for OpenBabel on
Linux.  I have had an error or a warning on every line as I was running the
provided setup.py code.
Also after the build and install finished I could not import openbabel
module due "ImportError: No module named dl".
The errors on build and installation is as follows:
openbabel_python.cpp:46242: error: `OpenBabel' has not been declared
openbabel_python.cpp:46242: error: `OUTOPTIONS' was not declared in this
scope

If you can figure out that I am missing something, can you please let me
know?
I use
Python 2.4.3
[GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2

Thanks in advance.
Ahmet

-- 
Ahmet Bakan
Department of Computational Biology
University of Pittsburgh School of Medicine
3501 Fifth Avenue
Suite 3064 BST3
Pittsburgh, PA  15213-3301

Re: [OpenBabel-scripting] pyopenbabel

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

It's included in the development version of openbabel. You can get it from
here...

http://svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/scripts/python/

I'm sorry to say that I haven't had any time to work on this for several
months, so it may not work perfectly at this stage.

Regards,
  Noel

On 04/10/06, S Joshua Swamidass <swa...@gm...> wrote:
>
> Hey All,
>
> >From where can we download pyopenbabel?  (not openbabel).
>
> Josh
>
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[OpenBabel-scripting] pyopenbabel

[S J. S. <swa...@gm...>]

Hey All,

>From where can we download pyopenbabel?  (not openbabel).

Josh

Re: [OpenBabel-scripting] Graph Kernels

[Noel O'B. <noe...@ma...>]

I think you are getting your wires crossed. The Python interface to
OpenBabel is simply called the openbabel module. The pyopenbabel module
is a wrapper around this, which although described on the web site (see
Geoff's links below) is not included with the current version of
OpenBabel.

So, I think your question is: how do I use the DFS in OpenBabel?
Unfortunately, the answer appears to be the same, as shown in this quote
from Geoff's earlier email:

> There are both DFS and BFS iterators in the 2.1 development code,  
> which incidentally is the only version with PyOpenBabel.

So, DFS is not currently in OpenBabel. However, this does not stop you
from writing one yourself if you are familiar with recursion. Otherwise,
I'm afraid that you will have to wait until OpenBabel 2.1 is released,
or else install the development version.

Regards,
  Noel

On Tue, 2006-08-29 at 21:04 -0400, Geoffrey Hutchison wrote:
> On Aug 29, 2006, at 12:31 PM, priyashree saxena wrote:
> 
> > Could you please tell me how exactly I could use DFS thats there in  
> > pyopenbabel. Or it would be great if you could direct me to the  
> > part of documentation which shows the syntax or the parameters that  
> > should be passed to DFS. Also could you also direct me to the  
> > documentation of pyopenbabel so that I know the functionalities I  
> > can make use in my code.
> 
> Well, I didn't write pyopenbabel and the only documentation that I  
> know is:
> http://openbabel.sourceforge.net/wiki/Python#The_pyopenbabel_module
> http://openbabel.sourceforge.net/pyopenbabel.html
> 
> I don't know how recent this is, so I don't know if it includes DFS  
> support. The openbabel python interface should.
> 
> Cheers,
> -Geoff
> 
> -------------------------------------------------------------------------
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Re: [OpenBabel-scripting] Graph Kernels

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

On Aug 29, 2006, at 12:31 PM, priyashree saxena wrote:

> Could you please tell me how exactly I could use DFS thats there in  
> pyopenbabel. Or it would be great if you could direct me to the  
> part of documentation which shows the syntax or the parameters that  
> should be passed to DFS. Also could you also direct me to the  
> documentation of pyopenbabel so that I know the functionalities I  
> can make use in my code.

Well, I didn't write pyopenbabel and the only documentation that I  
know is:
http://openbabel.sourceforge.net/wiki/Python#The_pyopenbabel_module
http://openbabel.sourceforge.net/pyopenbabel.html

I don't know how recent this is, so I don't know if it includes DFS  
support. The openbabel python interface should.

Cheers,
-Geoff

Re: [OpenBabel-scripting] [openbabel-scripting] Open Babel Warnings

[Geoffrey H. <gr...@co...>]

On Aug 18, 2006, at 2:04 PM, A. Sebastian wrote:

> Finally I tried adding the following perl lines:
>
> 	my $obMessageHandler=new Chemistry::OpenBabel::OBMessageHandler;
> 	$obMessageHandler->StopLogging();
>
> ...
> could be the problem that the class OBMessageHandler is not  
> implemented in
> Perl?

No, that's correct -- it's not included in the wrapper. I'll make  
sure to fix that now for the 2.1 beta snapshots.

Cheers,
-Geoff

Re: [OpenBabel-scripting] [openbabel-scripting] Open Babel Warnings

[A. S. <oli...@ya...>]

Chris Morley wrote:
> 
> A. Sebastian wrote:
>> I use OpenBabel Perl Module to parse mol files to a database and by the
>> way I
>> use the following code to obtain smiles format:
>> 	my $obMol=new Chemistry::OpenBabel::OBMol;
>> 	my $obConversion=new Chemistry::OpenBabel::OBConversion;
>> 	$obConversion->SetInAndOutFormats("mol","smi");
>> 	$obConversion->ReadString($obMol,$mol_file);
>> 	my $outSmiles=$obConversion->WriteString($obMol);
>> 
>> All works OK, but I obtain sometimes warning messages on screen that make
>> slower the process, I'd like to avoid this messages but I don't know how
>> to
>> do that.
>> 
>> An example of the warning messages:
>> *** Open Babel Warning  in WriteMolecule
>>   1-[(4-Acetyl-phenylcarbamoyl)-methyl]-pyridinium Proton(s)
>> added/removed
>> 
>> With the InChi format I have success avoiding this messages with this
>> code:
>> 	my $obMol=new Chemistry::OpenBabel::OBMol;
>> 	my $obConversion=new Chemistry::OpenBabel::OBConversion;
>> 	$obConversion->SetInAndOutFormats("mol","inchi");
>> 	$obConversion->ReadString($obMol,$mol_file);
>> 	$obConversion->SetOptions("w",1);
>> 	my $outInchi=$obConversion->WriteString($obMol);
>> 
>> I want to know if exists a similar solution for smiles, because the
>> former
>> doen't work ($obConversion->SetOptions("w",1);)
>> 
> 
> You can control the severity of OpenBabel error messages that are 
> displayed in C++ code using:
> 
> obErrorLog.SetOutputLevel(0);
> 
> 0 supresses all the messages; 5 allows everything.
> 
> OpenBabel::obErrorLog is a global variable; the number is an enum of 
> type obMessageLevel. I don't know how well this works in the Perl 
> version, but if it doesn't we should do something about it.
> 
> obErrorLog.StopLogging();
> is an alternative to supress everything.
> 
> (In the command-line version use the option ---errorlevel n )
> 
> Chris
> 
> -------------------------------------------------------------------------
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> 
> 

Finally I tried adding the following perl lines:

	my $obMessageHandler=new Chemistry::OpenBabel::OBMessageHandler;
	$obMessageHandler->StopLogging();

And I obtained the following error:

Can't locate Chemistry/OpenBabel/OBMessageHandler.pm in @INC (@INC contains:
/etc/perl /usr/local/lib/perl/5.8.7 /usr/local/share/perl/5.8.7
/usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8
/usr/local/lib/site_perl .)

Perhaps there is something wrong in the former two lines of my code, or
could be the problem that the class OBMessageHandler is not implemented in
Perl?

Alvaro
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Re: [OpenBabel-scripting] Open Babel Warnings

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

A. Sebastian wrote:
> I use OpenBabel Perl Module to parse mol files to a database and by the way I
> use the following code to obtain smiles format:
> 	my $obMol=new Chemistry::OpenBabel::OBMol;
> 	my $obConversion=new Chemistry::OpenBabel::OBConversion;
> 	$obConversion->SetInAndOutFormats("mol","smi");
> 	$obConversion->ReadString($obMol,$mol_file);
> 	my $outSmiles=$obConversion->WriteString($obMol);
> 
> All works OK, but I obtain sometimes warning messages on screen that make
> slower the process, I'd like to avoid this messages but I don't know how to
> do that.
> 
> An example of the warning messages:
> *** Open Babel Warning  in WriteMolecule
>   1-[(4-Acetyl-phenylcarbamoyl)-methyl]-pyridinium Proton(s) added/removed
> 
> With the InChi format I have success avoiding this messages with this code:
> 	my $obMol=new Chemistry::OpenBabel::OBMol;
> 	my $obConversion=new Chemistry::OpenBabel::OBConversion;
> 	$obConversion->SetInAndOutFormats("mol","inchi");
> 	$obConversion->ReadString($obMol,$mol_file);
> 	$obConversion->SetOptions("w",1);
> 	my $outInchi=$obConversion->WriteString($obMol);
> 
> I want to know if exists a similar solution for smiles, because the former
> doen't work ($obConversion->SetOptions("w",1);)
> 

You can control the severity of OpenBabel error messages that are 
displayed in C++ code using:

obErrorLog.SetOutputLevel(0);

0 supresses all the messages; 5 allows everything.

OpenBabel::obErrorLog is a global variable; the number is an enum of 
type obMessageLevel. I don't know how well this works in the Perl 
version, but if it doesn't we should do something about it.

obErrorLog.StopLogging();
is an alternative to supress everything.

(In the command-line version use the option ---errorlevel n )

Chris

[OpenBabel-scripting] Open Babel Warnings

[A. S. <oli...@ya...>]

I use OpenBabel Perl Module to parse mol files to a database and by the way I
use the following code to obtain smiles format:
	my $obMol=new Chemistry::OpenBabel::OBMol;
	my $obConversion=new Chemistry::OpenBabel::OBConversion;
	$obConversion->SetInAndOutFormats("mol","smi");
	$obConversion->ReadString($obMol,$mol_file);
	my $outSmiles=$obConversion->WriteString($obMol);

All works OK, but I obtain sometimes warning messages on screen that make
slower the process, I'd like to avoid this messages but I don't know how to
do that.

An example of the warning messages:
*** Open Babel Warning  in WriteMolecule
  1-[(4-Acetyl-phenylcarbamoyl)-methyl]-pyridinium Proton(s) added/removed

With the InChi format I have success avoiding this messages with this code:
	my $obMol=new Chemistry::OpenBabel::OBMol;
	my $obConversion=new Chemistry::OpenBabel::OBConversion;
	$obConversion->SetInAndOutFormats("mol","inchi");
	$obConversion->ReadString($obMol,$mol_file);
	$obConversion->SetOptions("w",1);
	my $outInchi=$obConversion->WriteString($obMol);

I want to know if exists a similar solution for smiles, because the former
doen't work ($obConversion->SetOptions("w",1);)

Thanks.
-- 
View this message in context: http://www.nabble.com/Open-Babel-Warnings-tf2080646.html#a5731811
Sent from the openbabel-scripting forum at Nabble.com.

Re: [OpenBabel-scripting] Graph Kernels

[Noel O'B. <no...@ca...>]

The install procedure is as follows. Please let me know if this is
confusing, if you have any problems, or if you do not have root access.

(1) You should download OpenBabel 2.0.2 for Linux by clicking on
"Download" under the picture of the fish on
http://openbabel.sourceforge.net/wiki/Main_Page and choose
openbabel-2.0.2.tar.gz. You should save this into a folder called
'openbabel' somewhere on your computer.

(2) Open a command window, change directory into 'openbabel', and
decompress the downloaded file with following command:

tar zxvf openbabel-2.0.2.tar.gz

This will create a folder called 'openbabel-2.0.2'.

(3) You now need to configure and compile openbabel. To do this, change
directory into 'openbabel-2.0.2'. Run the following commands, one after
the other

./configure | tee configure.out
make | tee make.out

If there are any errors at this point, send an email to the
openbabel-discuss mailing list (ope...@li...)
and attach the files 'configure.out' and 'make.out'.

(4) If you have root permissions, you should install openbabel globally.
As root, run the following command:

make install

(5) You now need to compile the python extension. Change directory to
'openbabel-2.0.2/scripts/python' and run:

python setup.py build

(6) To install the python interface globally, as root type:

python setup.py install

(7) It's all done. Test out the 'openbabel' module by trying some of the
Python code at:
http://openbabel.sourceforge.net/wiki/Python#The_openbabel_module

Hope this helps,
   Noel



On Tue, 2006-08-08 at 10:57 -0400, Geoffrey Hutchison wrote:
> > Openbabel is more of a molecule parsing program then a graph kernel
> > program.
> 
> Not!
> 
> >> Regarding DFS specifically, I believe it is present but I am not sure
> >> where. I'm sure that Geoff can comment on this.
> 
> There are both DFS and BFS iterators in the 2.1 development code,  
> which incidentally is the only version with PyOpenBabel.
> 
> >> Regarding installation, we should have an install page on the web  
> >> site.
> >> At the moment we don't have one, but I will write one as soon as
> >> possible. What operating system do you use? If you are using  
> >> Windows, I
> >> am afraid you will not be able to use Python to access OpenBabel, you
> >> can only use C++.
> 
> Well, that's not quite correct. In principle, you can use Windows to  
> access Python -- however, since there aren't many currently active  
> developers on Open Babel who use Windows, it's currently not  
> available. There's absolutely nothing technically holding back the  
> Python interface through SWIG -- I just don't have time to figure out  
> what needs to be linked.
> 
> I'm not particularly versed on "tanimoto" vs. "hybrid". There is  
> already support for Tanimoto based on various fingerprint methods:
> http://openbabel.sourceforge.net/wiki/Tutorial:Fingerprints
> 
> These should already be available via the Python SWIG interface -- I  
> don't know if that's true of PyOpenBabel or not.
> 
> Cheers,
> -Geoff
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting

Re: [OpenBabel-scripting] Graph Kernels

[joerg.wegner <joe...@we...>]

Hi all,

> > Openbabel is more of a molecule parsing program then a graph kernel
> > program.
Well I would define that differently.
1. OpenBabel is a chemical expert system and has everything in place to
transform stupid element graphs into chemical meaningful molecules.
2. A graph kernel is just a specific similarity measure working on graphs
which has specific mathematical properties.
In fact there is no strict separation, because just a direct graph
transformation without chemical information is for sure the last thing we
want!

> >> Regarding DFS specifically, I believe it is present but I am not sure
> >> where. I'm sure that Geoff can comment on this.
> There are both DFS and BFS iterators in the 2.1 development code,
> which incidentally is the only version with PyOpenBabel.
A DFS is really primitive to implement, the only thing you nee is a queue,
for e.g. using STL. Beside of that there might be more efficient solutions
using graph algorithm libraries or machine learning algorithms. 
One thing is for sure ... nothing comes for free ... there is no free lunch
... also not for mining.

> I'm not particularly versed on "tanimoto" vs. "hybrid". There is
> already support for Tanimoto based on various fingerprint methods:
> http://openbabel.sourceforge.net/wiki/Tutorial:Fingerprints
Tanimoto similarity *ARRGH* usually most people think if they use "tanimoto
similarity" all their problems will be solved, you can use it for curing any
illness and save the world. To be very clear here, Tanimoto is just a metric
like tons of other metrics. The similarity getting with it depends on the
coding used, for tanimoto e.g. a vector coding based on any kind of features
like complexity, substructures, etc. or on maximum common substructures
(MCS). Yes, there is a tanimoto metric for MCS, check out one of the
Willet/Gillet publications.

If you are interested in publishing I heavily recommend comparing against
existing kernels and graph mining methods. Since most algorithms in this
area a freely available anyway this should not be a problem. Well this will
also be the tough part, since you are really comparing algorithms. This is a
big advantage to a huge number of QSAR papers where it is often not really
clear what is compared ... the chemical expert system or the transformation
rule followed by mining? Please ensure that your comparison is fair. You can
not compare black-box algorithms with OpenBabel/JOELib since it is not clear
if mining differences might come from the chemical expert system or from the
following mining step, so any error up to ten percent is just in range of
the standard deviation (just a rough guess of my experience).

Exactly this is the reason why you should contribute any code to OpenBabel,
also the algorithms you test against. Anyway, you have to dig into the code
somehow, since you need the "raw" access to chemical graphs, only there you
can create new, innovate, better and faster algorithms. If you will just use
the usual stuff you will get what all the others have already ... the
precious Tanimoto similarity.

Joerg

Re: [OpenBabel-scripting] Graph Kernels

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

> Openbabel is more of a molecule parsing program then a graph kernel
> program.

Not!

>> Regarding DFS specifically, I believe it is present but I am not sure
>> where. I'm sure that Geoff can comment on this.

There are both DFS and BFS iterators in the 2.1 development code,  
which incidentally is the only version with PyOpenBabel.

>> Regarding installation, we should have an install page on the web  
>> site.
>> At the moment we don't have one, but I will write one as soon as
>> possible. What operating system do you use? If you are using  
>> Windows, I
>> am afraid you will not be able to use Python to access OpenBabel, you
>> can only use C++.

Well, that's not quite correct. In principle, you can use Windows to  
access Python -- however, since there aren't many currently active  
developers on Open Babel who use Windows, it's currently not  
available. There's absolutely nothing technically holding back the  
Python interface through SWIG -- I just don't have time to figure out  
what needs to be linked.

I'm not particularly versed on "tanimoto" vs. "hybrid". There is  
already support for Tanimoto based on various fingerprint methods:
http://openbabel.sourceforge.net/wiki/Tutorial:Fingerprints

These should already be available via the Python SWIG interface -- I  
don't know if that's true of PyOpenBabel or not.

Cheers,
-Geoff

Re: [OpenBabel-scripting] Graph Kernels

[S J. S. <swa...@gm...>]

Priyashree,

Openbabel is more of a molecule parsing program then a graph kernel
program. Your best bet might be to use it just for SDF parsing, then
write the DFS code (pretty simple) yourself, and the tanimoto/minmax
yourself too.

S Joshua Swamidass

On 8/8/06, Noel O'Boyle <no...@ca...> wrote:
> Hello Priyashree,
>
> I am copying this email to the openbabel-scripting mailing list so that
> other developers can help with this question.
>
> On Mon, 2006-08-07 at 15:08 -0700, pri...@ya... wrote:
> > I need to use pyopenbabel to obtain the outcome (i.e. similarity
> > measures) of tanimoto kernel, Minmax and Hybrid kernel on a SDF file
> > which contains a large number of molecules. Are these kernels already
> > implemented in this software or do I need to code them. Also in order
> > to implement the above kernels I will need to perform DFS on the
> > molecules, is this functionality provided in pyopenbabel. Also it
> > would be great if you could guide me to the installation process as i
> > am new to pyopenbabel.
> First of all, I am fairly sure that these methods are not present in
> OpenBabel. However, I know that Joerg Wegner has done a lot of work with
> graph kernels, and these features may be available in JOELIB2 (a Java
> cheminformatics library similar to OpenBabel). I have copied him into
> this reply.
>
> If you decide to code these yourself, either in C++ or Python, we would
> encourage you to donate your code to OpenBabel so that it will be
> available to others. We can discuss this further if you are interested.
>
> Regarding DFS specifically, I believe it is present but I am not sure
> where. I'm sure that Geoff can comment on this.
>
> Regarding installation, we should have an install page on the web site.
> At the moment we don't have one, but I will write one as soon as
> possible. What operating system do you use? If you are using Windows, I
> am afraid you will not be able to use Python to access OpenBabel, you
> can only use C++.
>
> Best regards,
>   Noel
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Graph Kernels

[Noel O'B. <no...@ca...>]

Hello Priyashree,

I am copying this email to the openbabel-scripting mailing list so that
other developers can help with this question.

On Mon, 2006-08-07 at 15:08 -0700, pri...@ya... wrote:
> I need to use pyopenbabel to obtain the outcome (i.e. similarity
> measures) of tanimoto kernel, Minmax and Hybrid kernel on a SDF file
> which contains a large number of molecules. Are these kernels already
> implemented in this software or do I need to code them. Also in order
> to implement the above kernels I will need to perform DFS on the
> molecules, is this functionality provided in pyopenbabel. Also it
> would be great if you could guide me to the installation process as i
> am new to pyopenbabel.
First of all, I am fairly sure that these methods are not present in
OpenBabel. However, I know that Joerg Wegner has done a lot of work with
graph kernels, and these features may be available in JOELIB2 (a Java
cheminformatics library similar to OpenBabel). I have copied him into
this reply.

If you decide to code these yourself, either in C++ or Python, we would
encourage you to donate your code to OpenBabel so that it will be
available to others. We can discuss this further if you are interested.

Regarding DFS specifically, I believe it is present but I am not sure
where. I'm sure that Geoff can comment on this.

Regarding installation, we should have an install page on the web site.
At the moment we don't have one, but I will write one as soon as
possible. What operating system do you use? If you are using Windows, I
am afraid you will not be able to use Python to access OpenBabel, you
can only use C++.

Best regards,
  Noel

[OpenBabel-scripting] ANNOUNCE: Open Babel 2.0.2 Released

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

The Open Babel project is extremely proud to announce the release of  
Open Babel 2.0.2, the latest stable version of the free chemistry  
file translation program and chemistry software library.

This release represents a bug-fix release and should be a stable  
upgrade, strongly recommended for all users of Open Babel. Highlights  
include a large number of SMILES and SMARTS bug fixes, several  
crashes fixed, and countless bug fixes.


What's new? See the full release notes at:
  http://openbabel.sourceforge.net/wiki/Open_Babel_2.0.2

To download, see:
  http://sourceforge.net/project/showfiles.php? 
group_id=40728&package_id=32894&release_id=434410

For more information, see the project website and new wiki at:
  http://openbabel.sourceforge.net/

Many thanks to all the contributors to Open Babel including those of  
you who submitted feedback, bug reports, and code contributions.

Cheers,
-Geoff

Re: [OpenBabel-scripting] a question about openbabel python bindings

[Dr N. O'B. <no...@ca...>]

On Jul 22 2006, Rajarshi Guha wrote:

>I'm using the code I got on your website:
>
>obconversion = OBConversion()
>obconversion.SetInFormat("sdf")
>obmol = OBMol()
>
>notatend = obconversion.ReadFile(obmol,"test.sdf")
>while notatend:
>    print obmol.GetMolWt()
>    print obmol.NumAtoms()
>    obmol = OBMol()
>    notatend = obconversion.Read(obmol)
>
>So this is for iterating over the molecules in a single file. I would
>like to do this for multiple files. My question is do I need to make a
>new obmol object (using the first 3 lines) for each input file. Or can I
>just reuse obconversiona and obmol for each new input file?

I don't know the answer to this without checking. It would be reasonable to 
expect that it is possible. Note that you definitely need to create a new 
obmol every time or else it reads in the new atoms into the previous obmol 
(without first wiping it clean - it is more memory efficient to wipe it 
clean though if you do not need to keep the molecule).

You need to test something like the following:

obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()

for filename in ["file1.sdf", "file2.sdf"]:
    notatend = obconversion.ReadFile(obmol, filename)
    while notatend:
        print obmol.GetMolWt()
        print obmol.NumAtoms()
        obmol = OBMol()
        notatend = obconversion.Read(obmol)

Regards,
  Noel

Re: [OpenBabel-scripting] OpenBabel::OBTypeTable

[S J. S. <swa...@gm...>]

Hello All,

I found a fix for this problem in the babel wrapper. Add this line
right before the %import "data.h" line in the openbabel.i file.

%apply std::string &OUTPUT { std::string &to };

The only problem is that this fix exposes a bug in the swig wrapper
code, causing a leak. This leak is a documented bug set to be fixed in
the near future. I think it is worth adding this line right now anyway
because this fucntion is rarely called from python and the bug should
be fixed in the near future. Also, without this line, the Translage
methods output is completely unaccessable from python.

ALSO, it should be possible using the swig exception handler to make
all functions using bool to throw python exceptions. Please let me
know if this is worth the effort.

Thanks!

Josh


On 6/30/06, S Joshua Swamidass <swa...@gm...> wrote:
> The problem is that 'dest' is not accessible from the swig wrapped
> code. You have to specify it as an output typmap for that to work.
>
> ttab.Translate(dest, "C3")
>
> Doesn't work because in pythong strings are immutable. So the function
> signature should be changed in the wrapper to be somethign like:
>
> dest=ttab.Translate("C3")
>
> Once again, this can be done by a typemap in swig (i think).
>
> Josh
>
> On 6/30/06, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Jun 30, 2006, at 2:45 PM, S Joshua Swamidass wrote:
> >
> > > So here is an interactive session which displays the unusability of
> > > OBTypeTable: I think the problem lyes in the Translate method.
> >
> > That might not be a bad idea, but the current code works just fine.
> > If you're looking for examples, you should take a look at the various
> > file format translators, e.g., src/format/tinkerformat.cpp.
> >
> > In general, the current code doesn't use exceptions. Historically, it
> > hasn't always been well supported by
> >
> > >>>> ttab.Translate('1','1')
> > > ==============================
> > > *** Open Babel Warning  in Translate
> > >   Cannot perform atom type translation: table cannot find requested
> > > types.
> > > False
> >
> > Yes, but "1" isn't a valid INT atom type. (Check data/types.txt if
> > you're curious) I'm also not sure what Python thinks about returning
> > something into the constant string '1'.
> >
> > How about:
> > ttab.Translate(dest, "C3")
> >
> > I bet that works. Check dest for the output.
> >
> > -Geoff
> >
> > Using Tomcat but need to do more? Need to support web services, security?
> > Get stuff done quickly with pre-integrated technology to make your job easier
> > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>

[OpenBabel-scripting] Problems with 2.0.1 wrappers

[S J. S. <swa...@gm...>]

Hello again :),

I have the 2.0.0 wrappers up and running using the patch we worked out
when it was first relaeased.

for 2.0.1 on a Linux machine using python2.4 I don't have problems
compiling. But I get this error trying to import the library:

Python 2.4.2 (#1, Jan  4 2006, 00:45:40)
[GCC 3.2.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/dock/linux/lib/python2.4/site-packages/openbabel.py",
line 638, in ?
    VZero = cvar.VZero
AttributeError: 'swigvarlink' object has no attribute 'VZero'
>>>

Any help?

Josh

Re: [OpenBabel-scripting] OpenBabel::OBTypeTable

[S J. S. <swa...@gm...>]

The problem is that 'dest' is not accessible from the swig wrapped
code. You have to specify it as an output typmap for that to work.

ttab.Translate(dest, "C3")

Doesn't work because in pythong strings are immutable. So the function
signature should be changed in the wrapper to be somethign like:

dest=ttab.Translate("C3")

Once again, this can be done by a typemap in swig (i think).

Josh

On 6/30/06, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Jun 30, 2006, at 2:45 PM, S Joshua Swamidass wrote:
>
> > So here is an interactive session which displays the unusability of
> > OBTypeTable: I think the problem lyes in the Translate method.
>
> That might not be a bad idea, but the current code works just fine.
> If you're looking for examples, you should take a look at the various
> file format translators, e.g., src/format/tinkerformat.cpp.
>
> In general, the current code doesn't use exceptions. Historically, it
> hasn't always been well supported by
>
> >>>> ttab.Translate('1','1')
> > ==============================
> > *** Open Babel Warning  in Translate
> >   Cannot perform atom type translation: table cannot find requested
> > types.
> > False
>
> Yes, but "1" isn't a valid INT atom type. (Check data/types.txt if
> you're curious) I'm also not sure what Python thinks about returning
> something into the constant string '1'.
>
> How about:
> ttab.Translate(dest, "C3")
>
> I bet that works. Check dest for the output.
>
> -Geoff
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] OpenBabel::OBTypeTable

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

On Jun 30, 2006, at 2:45 PM, S Joshua Swamidass wrote:

> So here is an interactive session which displays the unusability of
> OBTypeTable: I think the problem lyes in the Translate method.

That might not be a bad idea, but the current code works just fine.  
If you're looking for examples, you should take a look at the various  
file format translators, e.g., src/format/tinkerformat.cpp.

In general, the current code doesn't use exceptions. Historically, it  
hasn't always been well supported by

>>>> ttab.Translate('1','1')
> ==============================
> *** Open Babel Warning  in Translate
>   Cannot perform atom type translation: table cannot find requested  
> types.
> False

Yes, but "1" isn't a valid INT atom type. (Check data/types.txt if  
you're curious) I'm also not sure what Python thinks about returning  
something into the constant string '1'.

How about:
ttab.Translate(dest, "C3")

I bet that works. Check dest for the output.

-Geoff

Re: [OpenBabel-scripting] OpenBabel::OBTypeTable

[S J. S. <swa...@gm...>]

On second thought, maybe not modified to take a single string OR int
(as required) for input and output a stirng OR int (as required).

Right now, I think it is output its value by reference through the
second arg. This arg isn't being output. A single working example
whoudl be very useful.

Josh

On 6/30/06, S Joshua Swamidass <swa...@gm...> wrote:
> Geoff,
>
> So here is an interactive session which displays the unusability of
> OBTypeTable: I think the problem lyes in the Translate method. It
> should be rerwapped ot take a single int as input and return a string
> or throw an exception.
>
> Josh
>
> ===========================
>
> >>> import openbabel
> >>> ttab=openbabel.OBTypeTable()
> >>> ttab.SetToType("SYB")
> True
> >>> ttab.SetFromType("INT")
> True
>
> >>> ttab.Translate(1)
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/home/dock/linux/lib/python2.4/site-packages/openbabel.py",
> line 188, in Translate
>    def Translate(*args): return _openbabel.OBTypeTable_Translate(*args)
> NotImplementedError: No matching function for overloaded 'OBTypeTable_Translate'
>
> >>> ttab.Translate(1,1)
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/home/dock/linux/lib/python2.4/site-packages/openbabel.py",
> line 188, in Translate
>    def Translate(*args): return _openbabel.OBTypeTable_Translate(*args)
> NotImplementedError: No matching function for overloaded 'OBTypeTable_Translate'
>
> >>> ttab.Translate('1','1')
> ==============================
> *** Open Babel Warning  in Translate
>  Cannot perform atom type translation: table cannot find requested types.
> False
>
> On 6/30/06, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Jun 29, 2006, at 6:50 PM, S Joshua Swamidass wrote:
> >
> > > How are we to use OpenBabel::OBTypeTable in python?
> > >
> > > It seems as if the wrapper is broken.
> >
> > As I don't use Python much myself, I think you'll have to be a bit
> > more specific. What did you try to do that didn't work? What version
> > of the wrapper (and Open Babel) are you using?
> >
> > Thanks,
> > -Geoff
> >
>

Re: [OpenBabel-scripting] OpenBabel::OBTypeTable

[S J. S. <swa...@gm...>]

Geoff,

So here is an interactive session which displays the unusability of
OBTypeTable: I think the problem lyes in the Translate method. It
should be rerwapped ot take a single int as input and return a string
or throw an exception.

Josh

===========================

>>> import openbabel
>>> ttab=openbabel.OBTypeTable()
>>> ttab.SetToType("SYB")
True
>>> ttab.SetFromType("INT")
True

>>> ttab.Translate(1)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/dock/linux/lib/python2.4/site-packages/openbabel.py",
line 188, in Translate
    def Translate(*args): return _openbabel.OBTypeTable_Translate(*args)
NotImplementedError: No matching function for overloaded 'OBTypeTable_Translate'

>>> ttab.Translate(1,1)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/dock/linux/lib/python2.4/site-packages/openbabel.py",
line 188, in Translate
    def Translate(*args): return _openbabel.OBTypeTable_Translate(*args)
NotImplementedError: No matching function for overloaded 'OBTypeTable_Translate'

>>> ttab.Translate('1','1')
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
False

On 6/30/06, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Jun 29, 2006, at 6:50 PM, S Joshua Swamidass wrote:
>
> > How are we to use OpenBabel::OBTypeTable in python?
> >
> > It seems as if the wrapper is broken.
>
> As I don't use Python much myself, I think you'll have to be a bit
> more specific. What did you try to do that didn't work? What version
> of the wrapper (and Open Babel) are you using?
>
> Thanks,
> -Geoff
>

Re: [OpenBabel-scripting] OpenBabel::OBTypeTable

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

On Jun 29, 2006, at 6:50 PM, S Joshua Swamidass wrote:

> How are we to use OpenBabel::OBTypeTable in python?
>
> It seems as if the wrapper is broken.

As I don't use Python much myself, I think you'll have to be a bit  
more specific. What did you try to do that didn't work? What version  
of the wrapper (and Open Babel) are you using?

Thanks,
-Geoff

[OpenBabel-scripting] OpenBabel::OBTypeTable

[S J. S. <swa...@gm...>]

Hello,

How are we to use OpenBabel::OBTypeTable in python?

It seems as if the wrapper is broken.

Josh

Re: [OpenBabel-scripting] [openbabel-scripting] Where can I get the perl wrapper for open babel?

[Geoffrey H. <gr...@co...>]

Hi Patricia,

Well, the Perl (and Python) wrappers are currently distributed with  
the Open Babel source code, version 2.0 or later, e.g.:
http://sourceforge.net/project/showfiles.php? 
group_id=40728&package_id=32894&release_id=410464

When you download the source code, it's under scripts/perl/ -- see  
the README file for more.

At some point (probably with version 2.1), the scripting wrappers  
will also be available for installation from standard repositories  
like CPAN for Perl. But right now, the installation scripts don't  
have enough tests for living outside the source directories.

Hope that helps!

Cheers,
-Geoff