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[OpenBabel-scripting] pybel script seqfaults

[Eiso AB <e....@ch...>]

hi

if I import pybel , my python session
seqfaults on exit. I can do stuff with pybel before exit
as normal. without importing pybel exit is also normal



[]$ python2.3
Python 2.3.4 (#1, Oct  9 2006, 18:22:22)
[GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import pybel
 >>> [Crtl-D]
Segmentation fault


the same happens for python2.4

[]$ python2.4
Python 2.4.2 (#8, Jan 25 2006, 19:03:28)
[GCC 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import pybel
 >>> [Crtl-D]
Segmentation fault



can anyone give me a clue how I can prevent or find the
cause of this behaviour.

thanks in advance,

Eiso AB

Re: [OpenBabel-scripting] [Open Babel] Open Babel in Python

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

On 26/08/07, Felix Plasser <fel...@gm...> wrote:
> hi,
> the problem was that the file iconf.dll is not contained in the openbabel
> for python distribution.
Oh, oh - sorry about that. I should have tested this better.

> what I did is changing the BABELDATA_DIR to the
> folder where  the regular openbabel was already installed. then I could a=
lso
> erase all the .dll files and the openbabel_data folder and it still works
> and I like it.
>
> it may be a good idea if one could just download the python packages and
> would not have to download everything else again.

Sure - this is what we want to do. I will try to reproduce this
problem and fix it.

> Felix
>
> -----Urspr=FCngliche Nachricht-----
> Von: Noel O'Boyle [mailto:bao...@gm...]
> Gesendet: Samstag, 25. August 2007 19:40
> An: Felix Plasser
> Cc: ope...@li...
> Betreff: Re: [Open Babel] Open Babel in Python
>
> (I've moved this thread to openbabel-scripting instead)
>
> On 24/08/07, Felix Plasser <fel...@gm...> wrote:
> > I installed the Open Babel for Python 2.5
> > (openbabel-python-1.2.1.py2.5.exe) on my Windows XP
> > Professional machine.
> >
> > My problem is that there is an error when I try "import openbabel":
> >
> > the module _openbabel is not found. when I check the folder, there real=
ly
> is
> > no _openbabel file there. the only file like it is _openbabel.pyd (whic=
h
> is
> > not a Python file).
>
> On my computer, in C:\Program Files\Python2.5\Lib\site-packages I have:
> OpenBabelDLL.dll, _openbabel.pyd, and openbabel.py.
>
> The most common problem is a mix up between different versions of the
> installed python. Can you make sure that: (a) you have Python2.5
> installed, (b) that you have installed the Python 2.5 version of OB
> (which you seem to have done), and (c) that you are running this
> particular version when you are typing "import openbabel". You may
> find it helpful to use "python -v" when starting python, and
> doublecheck all the paths.
>
> It really should work first time, so let us know if there is still a
> problem.
>
> Noel
> >
> >
> > -------
> >
> > Felix Plasser
> >
> > fel...@gm...
> >
> > www.chemical-quantum-images.blogspot.com
> >
> >
> > -----------------------------------------------------------------------=
--
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> > _______________________________________________
> > OpenBabel-discuss mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
> >
>
>

Re: [OpenBabel-scripting] [Open Babel] Open Babel in Python

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

(I've moved this thread to openbabel-scripting instead)

On 24/08/07, Felix Plasser <fel...@gm...> wrote:
> I installed the Open Babel for Python 2.5
> (openbabel-python-1.2.1.py2.5.exe) on my Windows XP
> Professional machine.
>
> My problem is that there is an error when I try "import openbabel":
>
> the module _openbabel is not found. when I check the folder, there really is
> no _openbabel file there. the only file like it is _openbabel.pyd (which is
> not a Python file).

On my computer, in C:\Program Files\Python2.5\Lib\site-packages I have:
OpenBabelDLL.dll, _openbabel.pyd, and openbabel.py.

The most common problem is a mix up between different versions of the
installed python. Can you make sure that: (a) you have Python2.5
installed, (b) that you have installed the Python 2.5 version of OB
(which you seem to have done), and (c) that you are running this
particular version when you are typing "import openbabel". You may
find it helpful to use "python -v" when starting python, and
doublecheck all the paths.

It really should work first time, so let us know if there is still a problem.

Noel
>
>
> -------
>
> Felix Plasser
>
> fel...@gm...
>
> www.chemical-quantum-images.blogspot.com
>
>
> -------------------------------------------------------------------------
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> Still grepping through log files to find problems?  Stop.
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> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

[OpenBabel-scripting] fragmentation

[<an...@av...>]

Dear members and subscribers,


I am interested in cleaving a host of chemical compound structures to the
smallest fragment possible.I would like to have script for doing the same.

Regards
Anand

[OpenBabel-scripting] Chemistry::OpenBabel and glibc

[Dieden R. <Rei...@uc...>]

Hello,

Hadn't too many problems with installation but when I try out the exampe
script I get :
  perl /usr/local/src/openbabel-2.1.1/scripts/perl/examples/example.pl
*** glibc detected *** free(): invalid pointer: 0x09b9d1d4 ***
Aborted

Any hint ?

Cheers,

Reiner

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Re: [OpenBabel-scripting] Failed Tests during perl binding installation

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

Sorry - I've no idea, and our resident perl expert is away at the moment.

But...
(1) Did you run "make install" first?
(2) Is babel working correctly? (i.e. does babel -H list all of the formats)
(3) If so...maybe $obConversion wasn't created correctly...

Change:
$obConversion->SetInAndOutFormats("smi", "mdl");
to
$myperlvariable = $obConversion->SetInAndOutFormats("smi", "mdl");

and then test that the value of $myperlvariable is TRUE.

Regards,
   Noel



On 08/08/07, David Rose <tom...@gm...> wrote:
> Hi:
>
>   I've just installed openbabel-2.1.1 from source without incident (though
> make and configure outputs are attached), and when I then create the perl
> makefile and run make, I also experience no errors).  However, when I run
> 'make test', the conversion test fails:
>
>
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/atom.............ok
> t/bond.............ok
> t/conversion.......FAILED tests 5-6, 8
>
>         Failed 3/9 tests, 66.67% okay
> t/data.............ok
> t/format...........ok
>
> t/internalcoord....ok
> t/mol..............ok
> t/residue..........ok
>
> Failed Test    Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/conversion.t                9    3  33.33%  5-6 8
> Failed 1/8 test scripts, 87.50% okay. 3/35 subtests failed, 91.43% okay.
> make: *** [test_dynamic] Error 2
> Doing a little debugging of the conversion test script, it looks like the
> line:
>
>
>   $obConversion->ReadString($obMol,"C1=CC=CS1");
>
>
> is failing silently as it creates an empty $obMol object, with no atoms.
> Also, the line:
>
> $obConversion->WriteFile($obMol, "test.mdl");
>
>  appears to be failing silently as no file is created.
>
> Any ideas about what might be going on? I am installing on an Apple XServe
> (G5) running Mac OS X Server 10.4.10.
>
>
> thanks,
> David
>
> -------------------------------------------------------------------------
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>
>

Re: [OpenBabel-scripting] Problems installing

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

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cHRpbmcKPgo+Cg==

[OpenBabel-scripting] Problems installing

[Jurgens de B. <deb...@gm...>]

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Cg==

Re: [OpenBabel-scripting] WriteMapList using Perl

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

Here are three different ways to access this data from Python,
hopefully one of which can be modified to work from Perl. If these
don't work, I'm sure that Geoff will be able to help once he gets back
from a well-deserved break:

>>> c = smarts.obsmarts.GetUMapList()
>>> dir(c)
['__class__', '__del__', '__delattr__', '__delitem__', '__delslice__', '__dict__
', '__doc__', '__getattr__', '__getattribute__', '__getitem__', '__getslice__',
'__hash__', '__init__', '__iter__', '__len__', '__module__', '__new__', '__nonze
ro__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__setitem__',
'__setslice__', '__str__', '__swig_destroy__', '__swig_getmethods__', '__swig_se
tmethods__', '__weakref__', 'append', 'assign', 'back', 'begin', 'capacity', 'cl
ear', 'empty', 'end', 'erase', 'front', 'get_allocator', 'insert', 'iterator', '
pop', 'pop_back', 'push_back', 'rbegin', 'rend', 'reserve', 'resize', 'size', 's
wap', 'this']
>>> c
<openbabel.vvInt; proxy of <Swig Object of type 'std::vector<std::vector<int,std
::allocator<int > >,std::allocator<std::vector<int,std::allocator<int > > > > *'
 at 0x125bc18> >

****** Method 1 (by index) *******

>>> c[0]
(1, 2)
>>> c[1]
(4, 5)
>>> c[2]
(6, 7)
>>> c.size()
3

****** Method 2 (by std::vector iterator) *******

>>> c.begin()
<openbabel.PySwigIterator; proxy of <Swig Object of type 'swig::PySwigIterator *
' at 0x125d938> >
>>> d = c.begin()
>>> d.next()
(1, 2)
>>> d.next()
(4, 5)
>>> d.next()
(6, 7)

****** Method 3 (by Python iterator) *******
>>> for x in c:
...     print x
...
(1, 2)
(4, 5)
(6, 7)

Noel

On 02/08/07, Kieron Taylor <kr...@so...> wrote:
> Duangrudee Tanramluk wrote:
> > Thanks a lot Noel. My problem is not about matching, but about how to retreive
> > the data from the maplist. I have tried treating it as an array but it
> > doesn't seem to be either a simple array or a 2D array.
> >
> > Duangrudee
> >
> >>>>
> >>>>  my $obsmartpattern = new
> >>>> Chemistry::OpenBabel::OBSmartsPattern;
> >>>>
> >>>>  $obsmartpattern->Init('n1c2ccccc2ccc1');
> >>>>
> >>>>  $obsmartpattern->Match($obMol);
> >>>>
> >>>>
> >>>> I guess the next step should be:
> >>>>
> >>>>  my $maplist = $obsmartpattern->GetUMapList();
>
> If I had to guess, I would say $maplist might be a pointer rather than
> an array in its own right. My suggestions for you to try:
>
> 1) Check the boolean result of $obsmartpattern->Match($obMol);
>
> If it's not matching anything, then there may not be a list to return.
>
> 2) Try dereferencing $maplist in some way.
>
> The documentation says the method returns:
> std::vector< std::vector< int > >
>
> In Perl you might have to interpret this as:
> $maplist->[$index1]->[$index2]
>
> Alternatively you can try forcing treatment as an array eg.
> @{$maplist}[$index1].......
>
> In any case, when fighting with APIs, I find it very helpful to use a
> live debugger to look at the memory structures. ddd or ptkdb can do this
> for you.
>
> Once you've worked out what you're dealing with, you can write neater
> code to catch the data structure you're receiving from Babel. Without an
> appropriate object, you will struggle to use the iterator class used in
> the sample code.
>
> 3) Find the secret or generic class for iterators that will give you
> something to drop the output of $obsmartpattern->BeginMList() into. I've
> not had much luck looking for it so far. It may not exist, since the c++
> sample code already seems to understand what an iterator is.
>
>
> Good luck,
>
> Kieron
>
>
>
> -------------------------------------------------------------------------
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> Still grepping through log files to find problems?  Stop.
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>

Re: [OpenBabel-scripting] WriteMapList using Perl

[Kieron T. <kr...@so...>]

Duangrudee Tanramluk wrote:
> Thanks a lot Noel. My problem is not about matching, but about how to retreive 
> the data from the maplist. I have tried treating it as an array but it 
> doesn't seem to be either a simple array or a 2D array. 
> 
> Duangrudee
> 
>>>>
>>>>  my $obsmartpattern = new
>>>> Chemistry::OpenBabel::OBSmartsPattern;
>>>>
>>>>  $obsmartpattern->Init('n1c2ccccc2ccc1');
>>>>
>>>>  $obsmartpattern->Match($obMol);
>>>>
>>>>
>>>> I guess the next step should be:
>>>>
>>>>  my $maplist = $obsmartpattern->GetUMapList();

If I had to guess, I would say $maplist might be a pointer rather than 
an array in its own right. My suggestions for you to try:

1) Check the boolean result of $obsmartpattern->Match($obMol);

If it's not matching anything, then there may not be a list to return.

2) Try dereferencing $maplist in some way.

The documentation says the method returns:
std::vector< std::vector< int > >

In Perl you might have to interpret this as:
$maplist->[$index1]->[$index2]

Alternatively you can try forcing treatment as an array eg. 
@{$maplist}[$index1].......

In any case, when fighting with APIs, I find it very helpful to use a 
live debugger to look at the memory structures. ddd or ptkdb can do this 
for you.

Once you've worked out what you're dealing with, you can write neater 
code to catch the data structure you're receiving from Babel. Without an 
appropriate object, you will struggle to use the iterator class used in 
the sample code.

3) Find the secret or generic class for iterators that will give you 
something to drop the output of $obsmartpattern->BeginMList() into. I've 
not had much luck looking for it so far. It may not exist, since the c++ 
sample code already seems to understand what an iterator is.


Good luck,

Kieron

Re: [OpenBabel-scripting] WriteMapList using Perl

[Duangrudee T. <dt...@ca...>]

Thanks a lot Noel. My problem is not about matching, but about how to retreive 
the data from the maplist. I have tried treating it as an array but it 
doesn't seem to be either a simple array or a 2D array. 

Duangrudee



On Wednesday 01 August 2007 16:43, you wrote:
> Why not try an easier example to begin with?
>
> In the Python docs, the example I use is the SMILES string for
> triethylamine "CCN(CC)CC", in which I search for ethyl groups (Smarts
> pattern "[#6][#6]"), and the result is three matches, one for each
> ethyl:
>     [(1, 2), (4, 5), (6, 7)]
>
> (Note that OpenBabel indexes atoms from 1)
>
> Noel
>
> On 01/08/07, Noel O'Boyle <bao...@gm...> wrote:
> > On 01/08/07, Duangrudee Tanramluk <DT...@ca...> wrote:
> > First of all, I'm delighted to see someone (else!) using Open Babel in
> > Cambridge.
> >
> > > I am trying to print out a list of atom index and a mol2 file
> > > containing the substructure which matches the SMARTS query.
> > >
> > >
> > >
> > > Below is what I have written so far:
> > >
> > >
> > >
> > >  my $file_to_read = "test.pdb";
> > >
> > >  my $obMol = new Chemistry::OpenBabel::OBMol;
> > >
> > >  my $obConverter = new Chemistry::OpenBabel::OBConversion;
> > >
> > >  $obConverter->SetInAndOutFormats("pdb","mol2");
> > >
> > >  $obConverter->ReadFile($obMol,$file_to_read);
> > >
> > >
> > >
> > >  my $obsmartpattern = new
> > > Chemistry::OpenBabel::OBSmartsPattern;
> > >
> > >  $obsmartpattern->Init('n1c2ccccc2ccc1');
> > >
> > >  $obsmartpattern->Match($obMol);
> > >
> > >
> > >
> > > I guess the next step should be:
> > >
> > >
> > >
> > >  my $maplist = $obsmartpattern->GetUMapList();
> > >
> > >
> > >
> > > However, I have no success in iterating through the maplist to print
> > > out which atoms match the SMARTS by using Perl. Any suggestion of how
> > > to print out the atoms would be greatly appreciated.
> >
> > Well, you're doing everything correctly and it should work. $maplist
> > should be a list of a list of integers. In Perl, I think you should be
> > using @maplist and not $maplist. But I'm not a Perl programmer. Maybe
> > someone else can comment.
> >
> > Noel

Re: [OpenBabel-scripting] FastSearchIndexer from python

[Pascoe, S \(Stephen\) <S.P...@rl...>]

=20
Many thanks for these valuable links.

I worked out that my real problem was a lack of understanding of how to
use fingerprints.  I cam across this excellent introduction:

http://www.daylight.com/dayhtml/doc/theory/theory.finger.html

Which made everything clear.  I think for my application it is overkill
to use an embedded OpenBabel in the database (although It's good to know
implementations are being developed).  I can just fold the fingerprints
down to a reasonable number of bytes, store them raw and use bit logic
in my SQL queries to select molecules that might contain a substructure.

Cheers,
Stephen.

---
Stephen Pascoe  +44 (0)1235 445980
British Atmospheric Data Centre
Rutherford Appleton Laboratory

-----Original Message-----
From: Noel O'Boyle [mailto:bao...@gm...]=20
Sent: 01 August 2007 14:09
To: Pascoe, S (Stephen)
Subject: Re: [OpenBabel-scripting] FastSearchIndexer from python

Here is some more discussion on the OpenBabel lists:
http://www.nabble.com/Mychem-t3656537.html

On 01/08/07, Noel O'Boyle <bao...@gm...> wrote:
> Well, first of all, check out the solutions that people have already
used. See:
> http://depth-first.com/articles/2007/04/13/roll-your-own-chemical-data
> base-with-free-components and especially the comments by Rajarshi.
>
> There's Mychem at:
> http://mychem.sourceforge.net/
> I suggest you contact Jerome Pansanel for more info if interested.
>
> Also, http://www.unm.edu/~tharun/smdb.html
>
> If you want to do it yourself, you will need to add some sort of field

> for holding bits (or lots of fields with binary values) and set the=20
> field based on myfp.bits. Hopefully, the other options provide simpler

> solutions for substructure searching. You may be able to do clever=20
> things like sort the bits by which help subdivide the space as quickly

> as possible if you want to max out on speed.
>
> Noel
>
> On 01/08/07, Pascoe, S (Stephen) <S.P...@rl...> wrote:
> > I have a MySQL database containing SMILES strings and want to do=20
> > substructure search on them.  I decided that the best way to do this

> > would be to build a FastSearch index file that mirrors the=20
> > information in the database.
> >
> > Of course I could dump the SMILES string to a file and use the babel

> > command line program but I was hoping that it would be possible to=20
> > do completely within the python bindings.
> >
> > I read that FastSearch uses fingerprints but I have no idea how=20
> > these are used.  Maybe there is a way to store fingerprints in MySQL

> > for use in substructure searching?
> >
> > Many Thanks,
> > Stephen.
> >
> >
> > ---
> > Stephen Pascoe  +44 (0)1235 445980
> > British Atmospheric Data Centre
> > Rutherford Appleton Laboratory
> >
> > -----Original Message-----
> > From: Noel O'Boyle [mailto:bao...@gm...]
> > Sent: 01 August 2007 13:30
> > To: Pascoe, S (Stephen)
> > Cc: ope...@li...
> > Subject: Re: [OpenBabel-scripting] FastSearchIndexer from python
> >
> > Python doesn't do streams, at least not in the C++ sense. So the=20
> > current FastSearchIndexer is a no go. However, perhaps you could=20
> > describe the exact problem and I can try to help you up with a=20
> > general solution from Python.
> >
> > Noel
> >
> > On 01/08/07, Pascoe, S (Stephen) <S.P...@rl...> wrote:
> > > I am trying to build a FastSearch index file from Python.  There=20
> > > appears to be a openbabel.FastSearchIndexer class but I have so=20
> > > far failed to instantiate it.  The class requires an ostream=20
> > > object, which
> >
> > > I recognise from C++ but don't know how to create in python.  E.g.
> > >
> > > >>> fs =3D openbabel.FastSearchIndexer('test.smi', fh, 'FP2', 0)
> > > Traceback (most recent call last):
> > >   File "<stdin>", line 1, in <module>
> > >   File=20
> > > "/opt/python-2.5.1/lib/python2.5/site-packages/openbabel.py",
> > > line 2115, in __init__
> > >
> > > _openbabel.FastSearchIndexer_swiginit(self,_openbabel.new_FastSear
> > > chIn
> > > de
> > > xer(*args))
> > > NotImplementedError: Wrong number of arguments for overloaded=20
> > > function
> >
> > > 'new_FastSearchIndexer'.
> > >   Possible C/C++ prototypes are:
> > >     OpenBabel::FastSearchIndexer(std::string &,std::ostream=20
> > > *,std::string &,int)
> > >     OpenBabel::FastSearchIndexer(std::string &,std::ostream=20
> > > *,std::string &)
> > >     OpenBabel::FastSearchIndexer(OpenBabel::FptIndex=20
> > > *,std::ostream *)
> > >
> > > Where fh is a python file object.  Can anyone help?
> > >
> > > Thanks,
> > > Stephen.
> > >
> > > ---
> > > Stephen Pascoe  +44 (0)1235 445980 British Atmospheric Data Centre

> > > Rutherford Appleton Laboratory
> > >
> > > ------------------------------------------------------------------
> > > ----
> > > --- This SF.net email is sponsored by: Splunk Inc.
> > > Still grepping through log files to find problems?  Stop.
> > > Now Search log events and configuration files using AJAX and a
> > browser.
> > > Download your FREE copy of Splunk now >>  http://get.splunk.com/=20
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
> >
>

Re: [OpenBabel-scripting] WriteMapList using Perl

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

Why not try an easier example to begin with?

In the Python docs, the example I use is the SMILES string for
triethylamine "CCN(CC)CC", in which I search for ethyl groups (Smarts
pattern "[#6][#6]"), and the result is three matches, one for each
ethyl:
    [(1, 2), (4, 5), (6, 7)]

(Note that OpenBabel indexes atoms from 1)

Noel

On 01/08/07, Noel O'Boyle <bao...@gm...> wrote:
> On 01/08/07, Duangrudee Tanramluk <DT...@ca...> wrote:
> First of all, I'm delighted to see someone (else!) using Open Babel in
> Cambridge.
>
> > I am trying to print out a list of atom index and a mol2 file containing the
> > substructure which matches the SMARTS query.
> >
> >
> >
> > Below is what I have written so far:
> >
> >
> >
> >  my $file_to_read = "test.pdb";
> >
> >  my $obMol = new Chemistry::OpenBabel::OBMol;
> >
> >  my $obConverter = new Chemistry::OpenBabel::OBConversion;
> >
> >  $obConverter->SetInAndOutFormats("pdb","mol2");
> >
> >  $obConverter->ReadFile($obMol,$file_to_read);
> >
> >
> >
> >  my $obsmartpattern = new
> > Chemistry::OpenBabel::OBSmartsPattern;
> >
> >  $obsmartpattern->Init('n1c2ccccc2ccc1');
> >
> >  $obsmartpattern->Match($obMol);
> >
> >
> >
> > I guess the next step should be:
> >
> >
> >
> >  my $maplist = $obsmartpattern->GetUMapList();
> >
> >
> >
> > However, I have no success in iterating through the maplist to print out
> > which atoms match the SMARTS by using Perl. Any suggestion of how to print
> > out the atoms would be greatly appreciated.
> >
> Well, you're doing everything correctly and it should work. $maplist
> should be a list of a list of integers. In Perl, I think you should be
> using @maplist and not $maplist. But I'm not a Perl programmer. Maybe
> someone else can comment.
>
> Noel
>

Re: [OpenBabel-scripting] WriteMapList using Perl

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

On 01/08/07, Duangrudee Tanramluk <DT...@ca...> wrote:
First of all, I'm delighted to see someone (else!) using Open Babel in
Cambridge.

> I am trying to print out a list of atom index and a mol2 file containing the
> substructure which matches the SMARTS query.
>
>
>
> Below is what I have written so far:
>
>
>
>  my $file_to_read = "test.pdb";
>
>  my $obMol = new Chemistry::OpenBabel::OBMol;
>
>  my $obConverter = new Chemistry::OpenBabel::OBConversion;
>
>  $obConverter->SetInAndOutFormats("pdb","mol2");
>
>  $obConverter->ReadFile($obMol,$file_to_read);
>
>
>
>  my $obsmartpattern = new
> Chemistry::OpenBabel::OBSmartsPattern;
>
>  $obsmartpattern->Init('n1c2ccccc2ccc1');
>
>  $obsmartpattern->Match($obMol);
>
>
>
> I guess the next step should be:
>
>
>
>  my $maplist = $obsmartpattern->GetUMapList();
>
>
>
> However, I have no success in iterating through the maplist to print out
> which atoms match the SMARTS by using Perl. Any suggestion of how to print
> out the atoms would be greatly appreciated.
>
Well, you're doing everything correctly and it should work. $maplist
should be a list of a list of integers. In Perl, I think you should be
using @maplist and not $maplist. But I'm not a Perl programmer. Maybe
someone else can comment.

Noel

Re: [OpenBabel-scripting] FastSearchIndexer from python

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

Well, first of all, check out the solutions that people have already used. See:
http://depth-first.com/articles/2007/04/13/roll-your-own-chemical-database-with-free-components
and especially the comments by Rajarshi.

There's Mychem at:
http://mychem.sourceforge.net/
I suggest you contact Jerome Pansanel for more info if interested.

Also, http://www.unm.edu/~tharun/smdb.html

If you want to do it yourself, you will need to add some sort of field
for holding bits (or lots of fields with binary values) and set the
field based on myfp.bits. Hopefully, the other options provide simpler
solutions for substructure searching. You may be able to do clever
things like sort the bits by which help subdivide the space as quickly
as possible if you want to max out on speed.

Noel

On 01/08/07, Pascoe, S (Stephen) <S.P...@rl...> wrote:
> I have a MySQL database containing SMILES strings and want to do
> substructure search on them.  I decided that the best way to do this
> would be to build a FastSearch index file that mirrors the information
> in the database.
>
> Of course I could dump the SMILES string to a file and use the babel
> command line program but I was hoping that it would be possible to do
> completely within the python bindings.
>
> I read that FastSearch uses fingerprints but I have no idea how these
> are used.  Maybe there is a way to store fingerprints in MySQL for use
> in substructure searching?
>
> Many Thanks,
> Stephen.
>
>
> ---
> Stephen Pascoe  +44 (0)1235 445980
> British Atmospheric Data Centre
> Rutherford Appleton Laboratory
>
> -----Original Message-----
> From: Noel O'Boyle [mailto:bao...@gm...]
> Sent: 01 August 2007 13:30
> To: Pascoe, S (Stephen)
> Cc: ope...@li...
> Subject: Re: [OpenBabel-scripting] FastSearchIndexer from python
>
> Python doesn't do streams, at least not in the C++ sense. So the current
> FastSearchIndexer is a no go. However, perhaps you could describe the
> exact problem and I can try to help you up with a general solution from
> Python.
>
> Noel
>
> On 01/08/07, Pascoe, S (Stephen) <S.P...@rl...> wrote:
> > I am trying to build a FastSearch index file from Python.  There
> > appears to be a openbabel.FastSearchIndexer class but I have so far
> > failed to instantiate it.  The class requires an ostream object, which
>
> > I recognise from C++ but don't know how to create in python.  E.g.
> >
> > >>> fs = openbabel.FastSearchIndexer('test.smi', fh, 'FP2', 0)
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in <module>
> >   File "/opt/python-2.5.1/lib/python2.5/site-packages/openbabel.py",
> > line 2115, in __init__
> >
> > _openbabel.FastSearchIndexer_swiginit(self,_openbabel.new_FastSearchIn
> > de
> > xer(*args))
> > NotImplementedError: Wrong number of arguments for overloaded function
>
> > 'new_FastSearchIndexer'.
> >   Possible C/C++ prototypes are:
> >     OpenBabel::FastSearchIndexer(std::string &,std::ostream
> > *,std::string &,int)
> >     OpenBabel::FastSearchIndexer(std::string &,std::ostream
> > *,std::string &)
> >     OpenBabel::FastSearchIndexer(OpenBabel::FptIndex *,std::ostream *)
> >
> > Where fh is a python file object.  Can anyone help?
> >
> > Thanks,
> > Stephen.
> >
> > ---
> > Stephen Pascoe  +44 (0)1235 445980
> > British Atmospheric Data Centre
> > Rutherford Appleton Laboratory
> >
> > ----------------------------------------------------------------------
> > --- This SF.net email is sponsored by: Splunk Inc.
> > Still grepping through log files to find problems?  Stop.
> > Now Search log events and configuration files using AJAX and a
> browser.
> > Download your FREE copy of Splunk now >>  http://get.splunk.com/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>

[OpenBabel-scripting] Fwd: Developping in Python and problem import pybel modules

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

(For the record, this has been resolved by reinstalling)

---------- Forwarded message ----------
From: David Lagorce <dav...@un...>
Date: 01-Aug-2007 13:32
Subject: Re: [OpenBabel-scripting] Developping in Python and problem
import pybel modules
To: Noel O'Boyle <bao...@gm...>


Ok Noel,

I succeeded to install everything on Fedora 6. With your advices I have
deleted all the "OPenBabel stuff" and I have re-installed the last
package. Have re-compiled the pybel module....
No probs to import openbabel and pybel !

For the CentOS xml is not a problem...I wanted right your opinion for
these errors=85


Thanks a lot for these advices and the speed of your response...

Best Regards

David Lagorce







Noel O'Boyle wrote:

>On 01/08/07, David Lagorce <dav...@un...> wrote:
>
>
>>I installed these two distributions, that I got from the official
>>distributions websites, in two separate computers.
>>
>>
>OK, I was just wondering whether you got them from your package manager.
>
>
>
>>With root permissions I compiled in "/usr/local/programs/" the last
>>package Openbabel 2.1.1 that I downloaded on Openbabel SourceForge websit=
e.
>>In the /scripts/python directory, with root permissions I compiled the
>>pybel module.
>>I declared the LD_LIBRARY_PATH in my bash_profile in "/usr/local/lib"
>>(checked, there are here...)
>>
>>
>Usually, you shouldn't compile anything as root. You should just
>install as root. It's possible that there is some problem with the
>permissions due to this. If this is true, I cannot really help fix it.
>
>For the moment, let's assume that permissions are not the problem.
>
>On the CentOS system, it looks like everything is working except for
>two file formats. Both of these file formats are XML-based file
>formats. This means that they need libxml, a library for reading and
>writing XML files. You should look at the output of configure. Was it
>able to find libxml? If so, I don't know why it is unable to find it
>now.
>
>On Fedora 5, the error you describe is typically due to a mixup
>between the installed OpenBabel and the OpenBabel you compile the
>Python bindings against. There are many ways this can happen, but if
>you delete everything, and start again, it should work.
>
>The normal way of compiling things is to make a folder in your home
>directory, run configure and make. Then, as root, run "make install".
>Then, exit from root, and compile the Python bindings. Then as root,
>install the Python bindings.
>
>Hope this helps. Overall, I recommend that you delete everything with
>the word OpenBabel on your system, and follow through the instructions
>once more, keeping a copy of all of the output. It really should work!
>
>Noel
>
>
>
>>
>>
>>
>>
>>
>>>Where did you install these from? Did you compile them yourself from
>>>the latest distributions?
>>>
>>>On 31/07/07, Lagorce David <dav...@un...> wrote:
>>>
>>>
>>>
>>>
>>>>Hi,
>>>>I want to use the openbabel and pybel modules but I have some different=
s
>>>>problems when I import them.
>>>>It depend on the OS I use:
>>>>
>>>>1) install on Fedora 6 up to date
>>>>
>>>>Python 2.5 (r25:51908, Jan 30 2007, 17:11:32)
>>>>[GCC 4.1.1 20070105 (Red Hat 4.1.1-51)] on linux2
>>>>Type "help", "copyright", "credits" or "license" for more information.
>>>>
>>>>
>>>>
>>>>
>>>>>>>import openbabel
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>Traceback (most recent call last):
>>>> File "<stdin>", line 1, in <module>
>>>> File "openbabel.py", line 11, in <module>
>>>>   import _openbabel
>>>>ImportError: /usr/local/lib/python2.5/site-packages/_openbabel.so:
>>>>undefined symbol: _ZN9OpenBabel5ResNoE
>>>>
>>>>
>>>>
>>>>
>>>>>>>import pybel
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>Traceback (most recent call last):
>>>> File "<stdin>", line 1, in <module>
>>>> File "/usr/local/lib/python2.5/site-packages/pybel.py", line 1, in <mo=
dule>
>>>>   import openbabel as ob
>>>> File "/usr/local/lib/python2.5/site-packages/openbabel.py", line 11, i=
n
>>>><module>
>>>>   import _openbabel
>>>>ImportError: /usr/local/lib/python2.5/site-packages/_openbabel.so:
>>>>undefined symbol: _ZN9OpenBabel5ResNoE
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>>>
>>>>>>>
>>>>2) install on CentOS 5 up to date
>>>>
>>>>Python 2.5.1 (r251:54863, Jul 27 2007, 15:51:54)
>>>>[GCC 4.1.1 20070105 (Red Hat 4.1.1-52)] on linux2
>>>>Type "help", "copyright", "credits" or "license" for more information.
>>>>
>>>>
>>>>
>>>>
>>>>>>>import openbabel
>>>>>>>import pybel
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
>>>>*** Open Babel Error  in LoadFormatFiles
>>>> /usr/local/lib/openbabel/chemdrawformat.so did not load properly
>>>>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
>>>>*** Open Babel Error  in LoadFormatFiles
>>>> /usr/local/lib/openbabel/xcmlformat.so did not load properly
>>>>
>>>>
>>>>what is wrong ??
>>>>
>>>>thanks a lot
>>>>
>>>>David
>>>>
>>>>
>>>>
>>>>
>>>>-----------------------------------------------------------------------=
--
>>>>This SF.net email is sponsored by: Splunk Inc.
>>>>Still grepping through log files to find problems?  Stop.
>>>>Now Search log events and configuration files using AJAX and a browser.
>>>>Download your FREE copy of Splunk now >>  http://get.splunk.com/
>>>>_______________________________________________
>>>>OpenBabel-scripting mailing list
>>>>Ope...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>
>

Re: [OpenBabel-scripting] FastSearchIndexer from python

[Pascoe, S \(Stephen\) <S.P...@rl...>]

I have a MySQL database containing SMILES strings and want to do
substructure search on them.  I decided that the best way to do this
would be to build a FastSearch index file that mirrors the information
in the database.

Of course I could dump the SMILES string to a file and use the babel
command line program but I was hoping that it would be possible to do
completely within the python bindings.

I read that FastSearch uses fingerprints but I have no idea how these
are used.  Maybe there is a way to store fingerprints in MySQL for use
in substructure searching?

Many Thanks,
Stephen.


---
Stephen Pascoe  +44 (0)1235 445980
British Atmospheric Data Centre
Rutherford Appleton Laboratory

-----Original Message-----
From: Noel O'Boyle [mailto:bao...@gm...]=20
Sent: 01 August 2007 13:30
To: Pascoe, S (Stephen)
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] FastSearchIndexer from python

Python doesn't do streams, at least not in the C++ sense. So the current
FastSearchIndexer is a no go. However, perhaps you could describe the
exact problem and I can try to help you up with a general solution from
Python.

Noel

On 01/08/07, Pascoe, S (Stephen) <S.P...@rl...> wrote:
> I am trying to build a FastSearch index file from Python.  There=20
> appears to be a openbabel.FastSearchIndexer class but I have so far=20
> failed to instantiate it.  The class requires an ostream object, which

> I recognise from C++ but don't know how to create in python.  E.g.
>
> >>> fs =3D openbabel.FastSearchIndexer('test.smi', fh, 'FP2', 0)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/opt/python-2.5.1/lib/python2.5/site-packages/openbabel.py",
> line 2115, in __init__
>
> _openbabel.FastSearchIndexer_swiginit(self,_openbabel.new_FastSearchIn
> de
> xer(*args))
> NotImplementedError: Wrong number of arguments for overloaded function

> 'new_FastSearchIndexer'.
>   Possible C/C++ prototypes are:
>     OpenBabel::FastSearchIndexer(std::string &,std::ostream=20
> *,std::string &,int)
>     OpenBabel::FastSearchIndexer(std::string &,std::ostream=20
> *,std::string &)
>     OpenBabel::FastSearchIndexer(OpenBabel::FptIndex *,std::ostream *)
>
> Where fh is a python file object.  Can anyone help?
>
> Thanks,
> Stephen.
>
> ---
> Stephen Pascoe  +44 (0)1235 445980
> British Atmospheric Data Centre
> Rutherford Appleton Laboratory
>
> ----------------------------------------------------------------------
> --- This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a
browser.
> Download your FREE copy of Splunk now >>  http://get.splunk.com/=20
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] FastSearchIndexer from python

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

Python doesn't do streams, at least not in the C++ sense. So the
current FastSearchIndexer is a no go. However, perhaps you could
describe the exact problem and I can try to help you up with a general
solution from Python.

Noel

On 01/08/07, Pascoe, S (Stephen) <S.P...@rl...> wrote:
> I am trying to build a FastSearch index file from Python.  There appears
> to be a openbabel.FastSearchIndexer class but I have so far failed to
> instantiate it.  The class requires an ostream object, which I recognise
> from C++ but don't know how to create in python.  E.g.
>
> >>> fs = openbabel.FastSearchIndexer('test.smi', fh, 'FP2', 0)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/opt/python-2.5.1/lib/python2.5/site-packages/openbabel.py",
> line 2115, in __init__
>
> _openbabel.FastSearchIndexer_swiginit(self,_openbabel.new_FastSearchInde
> xer(*args))
> NotImplementedError: Wrong number of arguments for overloaded function
> 'new_FastSearchIndexer'.
>   Possible C/C++ prototypes are:
>     OpenBabel::FastSearchIndexer(std::string &,std::ostream
> *,std::string &,int)
>     OpenBabel::FastSearchIndexer(std::string &,std::ostream
> *,std::string &)
>     OpenBabel::FastSearchIndexer(OpenBabel::FptIndex *,std::ostream *)
>
> Where fh is a python file object.  Can anyone help?
>
> Thanks,
> Stephen.
>
> ---
> Stephen Pascoe  +44 (0)1235 445980
> British Atmospheric Data Centre
> Rutherford Appleton Laboratory
>
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[OpenBabel-scripting] FastSearchIndexer from python

[Pascoe, S \(Stephen\) <S.P...@rl...>]

I am trying to build a FastSearch index file from Python.  There appears
to be a openbabel.FastSearchIndexer class but I have so far failed to
instantiate it.  The class requires an ostream object, which I recognise
from C++ but don't know how to create in python.  E.g.
=20
>>> fs =3D openbabel.FastSearchIndexer('test.smi', fh, 'FP2', 0)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/python-2.5.1/lib/python2.5/site-packages/openbabel.py",
line 2115, in __init__
=20
_openbabel.FastSearchIndexer_swiginit(self,_openbabel.new_FastSearchInde
xer(*args))
NotImplementedError: Wrong number of arguments for overloaded function
'new_FastSearchIndexer'.
  Possible C/C++ prototypes are:
    OpenBabel::FastSearchIndexer(std::string &,std::ostream
*,std::string &,int)
    OpenBabel::FastSearchIndexer(std::string &,std::ostream
*,std::string &)
    OpenBabel::FastSearchIndexer(OpenBabel::FptIndex *,std::ostream *)

Where fh is a python file object.  Can anyone help?

Thanks,
Stephen.
=20
---
Stephen Pascoe  +44 (0)1235 445980
British Atmospheric Data Centre
Rutherford Appleton Laboratory

[OpenBabel-scripting] WriteMapList using Perl

[Duangrudee T. <DT...@ca...>]

Hi All,



I am trying to print out a list of atom index and a mol2 file containing =
the substructure which matches the SMARTS query.=20



Below is what I have written so far:=20



 my $file_to_read =3D "test.pdb";

 my $obMol =3D new Chemistry::OpenBabel::OBMol;

 my $obConverter =3D new Chemistry::OpenBabel::OBConversion;

 $obConverter->SetInAndOutFormats("pdb","mol2");

 $obConverter->ReadFile($obMol,$file_to_read);


 my $obsmartpattern =3D new Chemistry::OpenBabel::OBSmartsPattern;

 $obsmartpattern->Init('n1c2ccccc2ccc1');

 $obsmartpattern->Match($obMol);



I guess the next step should be:



 my $maplist =3D $obsmartpattern->GetUMapList();



However, I have no success in iterating through the maplist to print out =
which atoms match the SMARTS by using Perl. Any suggestion of how to =
print out the atoms would be greatly appreciated.

=20

Duangrudee

=20

Re: [OpenBabel-scripting] Developping in Python and problem import pybel modules

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

Where did you install these from? Did you compile them yourself from
the latest distributions?

On 31/07/07, Lagorce David <dav...@un...> wrote:
> Hi,
> I want to use the openbabel and pybel modules but I have some differents
> problems when I import them.
> It depend on the OS I use:
>
> 1) install on Fedora 6 up to date
>
> Python 2.5 (r25:51908, Jan 30 2007, 17:11:32)
> [GCC 4.1.1 20070105 (Red Hat 4.1.1-51)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import openbabel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "openbabel.py", line 11, in <module>
>     import _openbabel
> ImportError: /usr/local/lib/python2.5/site-packages/_openbabel.so:
> undefined symbol: _ZN9OpenBabel5ResNoE
> >>>
> >>> import pybel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.5/site-packages/pybel.py", line 1, in <module>
>     import openbabel as ob
>   File "/usr/local/lib/python2.5/site-packages/openbabel.py", line 11, in
> <module>
>     import _openbabel
> ImportError: /usr/local/lib/python2.5/site-packages/_openbabel.so:
> undefined symbol: _ZN9OpenBabel5ResNoE
>
> >>>
> >>>
>
>
> 2) install on CentOS 5 up to date
>
> Python 2.5.1 (r251:54863, Jul 27 2007, 15:51:54)
> [GCC 4.1.1 20070105 (Red Hat 4.1.1-52)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import openbabel
> >>> import pybel
> ==============================
> *** Open Babel Error  in LoadFormatFiles
>   /usr/local/lib/openbabel/chemdrawformat.so did not load properly
> ==============================
> *** Open Babel Error  in LoadFormatFiles
>   /usr/local/lib/openbabel/xcmlformat.so did not load properly
> >>>
>
>
> what is wrong ??
>
> thanks a lot
>
> David
>
>
>
>
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[OpenBabel-scripting] Developping in Python and problem import pybel modules

[Lagorce D. <dav...@un...>]

Hi,
I want to use the openbabel and pybel modules but I have some differents
problems when I import them.
It depend on the OS I use:

1) install on Fedora 6 up to date

Python 2.5 (r25:51908, Jan 30 2007, 17:11:32)
[GCC 4.1.1 20070105 (Red Hat 4.1.1-51)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "openbabel.py", line 11, in <module>
    import _openbabel
ImportError: /usr/local/lib/python2.5/site-packages/_openbabel.so:
undefined symbol: _ZN9OpenBabel5ResNoE
>>>
>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.5/site-packages/pybel.py", line 1, in <module>
    import openbabel as ob
  File "/usr/local/lib/python2.5/site-packages/openbabel.py", line 11, in
<module>
    import _openbabel
ImportError: /usr/local/lib/python2.5/site-packages/_openbabel.so:
undefined symbol: _ZN9OpenBabel5ResNoE

>>>
>>>


2) install on CentOS 5 up to date

Python 2.5.1 (r251:54863, Jul 27 2007, 15:51:54)
[GCC 4.1.1 20070105 (Red Hat 4.1.1-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import openbabel
>>> import pybel
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemdrawformat.so did not load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xcmlformat.so did not load properly
>>>


what is wrong ??

thanks a lot

David

Re: [OpenBabel-scripting] .debs for 2.1.0 with scripting support built?

[Andrew F. <fa...@po...>]

Thanks Noel,
    I was worried about which version of the shared objects the perl and python
wrappers would find.  (I've been burned once too often by LD_LIBRARY_PATH parse
issues).  Thanks for the heads up on the debchem people.  I had seen information
about debian science, but I had missed that there was a chemistry specific group
as well.

Thanks again.
	Andy

Noel O'Boyle wrote:
> I don't think there'd be any difference between installing a .deb and
> compiling it yourself. If you follow the instructions on the OpenBabel
> install page, there's a recipe for local installation. This won't
> interfere with the official .deb installation, and will allow you to
> use the scripting support.
> 
> Otherwise, the debichem people are working on getting 2.1.1 into
> Ubuntu/Debian, so they might be able to help:
>    http://lists.alioth.debian.org/mailman/listinfo/debichem-devel
> 
> Noel

Re: [OpenBabel-scripting] .debs for 2.1.0 with scripting support built?

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

I don't think there'd be any difference between installing a .deb and
compiling it yourself. If you follow the instructions on the OpenBabel
install page, there's a recipe for local installation. This won't
interfere with the official .deb installation, and will allow you to
use the scripting support.

Otherwise, the debichem people are working on getting 2.1.1 into
Ubuntu/Debian, so they might be able to help:
    http://lists.alioth.debian.org/mailman/listinfo/debichem-devel

Noel

On 16/07/07, Andrew D. Fant <fa...@po...> wrote:
> Perchance, does anyone have a .deb kicking around for openbabel 2.1 with
> the scripting support installed?  I've started using Ubuntu to try it
> for an upcoming project. Sadly its package for openbabel is old enough
> that scripting support isn't included.  I'd just build it and install it
> myself, but there are a few other applications that I need that have
> openbabel as a prerequsite and I don't want to have to build them from
> scratch as well.
>
> Thanks,
>         Andy
>
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>

[OpenBabel-scripting] .debs for 2.1.0 with scripting support built?

[Andrew D. F. <fa...@po...>]

Perchance, does anyone have a .deb kicking around for openbabel 2.1 with
the scripting support installed?  I've started using Ubuntu to try it
for an upcoming project. Sadly its package for openbabel is old enough
that scripting support isn't included.  I'd just build it and install it
myself, but there are a few other applications that I need that have
openbabel as a prerequsite and I don't want to have to build them from
scratch as well.

Thanks,
	Andy