openbabel-scripting Mailing List for Open Babel (Page 34)

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On May 25, 2006, at 10:53 AM, Noel O'Boyle wrote:

> I've been reading up on C++, and so can finally make some sense of the
> code. What does mol.ReserveAtoms(natom) do though? The API is  
> silent on
> this matter, and the inline code is slightly obaque.

Ah. I'll make a note to update the docs on that.

In C++, the vector type is a re-sizable array. That means if you  
start adding objects, it resizes when needed, right? When it resizes,  
and how much space it adds is an implementation issue. But if you're  
adding 1,000 atoms at once, chances are good that the vector will  
resize a few times -- copying data, allocating more memory, etc.

If you know ahead of time that you're going to be adding 1,000 atoms,  
you can improve performance and memory use by allocating that vector  
right at the beginning:

mol.ReserveAtoms(1000);
...

Cheers,
-Geoff

On Thu, 2006-05-25 at 10:25 -0400, Geoffrey Hutchison wrote:
> On May 25, 2006, at 5:08 AM, Noel O'Boyle wrote:
> 
> > Given a set of atom coordinates and corresponding atomic numbers,  
> > is the
> > following function sufficient to create an OBMol suitable for  
> > writing to
> > a file as a PDB, for example?
> 
> Sure. If you look at the xyzformat code, that's pretty much what you  
> get.

Thanks - 

I've been reading up on C++, and so can finally make some sense of the
code. What does mol.ReserveAtoms(natom) do though? The API is silent on
this matter, and the inline code is slightly obaque. Does this have an
effect on subsequent uses of mol.NewAtom() ?

Regards,
 Noel

On May 25, 2006, at 5:08 AM, Noel O'Boyle wrote:

> Given a set of atom coordinates and corresponding atomic numbers,  
> is the
> following function sufficient to create an OBMol suitable for  
> writing to
> a file as a PDB, for example?

Sure. If you look at the xyzformat code, that's pretty much what you  
get.

Cheers,
-Geoff

Given a set of atom coordinates and corresponding atomic numbers, is the
following function sufficient to create an OBMol suitable for writing to
a file as a PDB, for example?

def createopenbabel(atomcoords,atomnos):
    """Create an open babel molecule."""

    obmol = ob.OBMol()
    for coords,atomno in zip(atomcoords,atomnos):
        obatom = ob.OBAtom()
        obatom.SetAtomicNum(atomno)
        obatom.SetVector(*coords)
        obmol.AddAtom(obatom)
    obmol.ConnectTheDots()
    obmol.PerceiveBondOrders()
    return obmol

(I see that I've neglected to include the molecular charge, but apart
from that, how does it look? Do I have to handle aromaticity in some
way?)

Regards,
 Noel

On Apr 24, 2006, at 10:55 AM, Noel O'Boyle wrote:

>>> How can I access the data fields in an SD file? Such as...
>> data = mymol.GetData("Mol weight");   // returns type OBPairData
>> data.GetValue()                       // returns 1234.567 or whatever
>
> I think OB is misbehaving, then. mymol.GetData("NSC") returns None  
> (the
> Python object) and mymol.HasData("NSC") returns False.

I thought I had e-mailed you, but evidently not. Could you submit a  
bug report with a test file? Let's make sure this is fixed ASAP.

Thanks,
-Geoff

Ok, moving swiftly on from my previous non-bug, I have in fact identified 
an unexpected feature. I was a bit confused why you referred to OBPairData 
in the example below, as in Python it's an OBGenericData that's actually 
returned.

As a result, there's no GetValue() method and it's not possible to access 
the field value (I previously was accessing GetDataType() which was 
returning '1' which coincidentally happened to be the value of my data 
field and so I thought that everything was fine).

I'll submit a bug report.

Regards,
 Noel

On May 6 2006, Geoffrey Hutchison wrote:

>
>On Apr 24, 2006, at 10:55 AM, Noel O'Boyle wrote:
>
>>>> How can I access the data fields in an SD file? Such as...
>>> data = mymol.GetData("Mol weight");   // returns type OBPairData
>>> data.GetValue()                       // returns 1234.567 or whatever
>>
>> I think OB is misbehaving, then. mymol.GetData("NSC") returns None  
>> (the
>> Python object) and mymol.HasData("NSC") returns False.
>
>I thought I had e-mailed you, but evidently not. Could you submit a  
>bug report with a test file? Let's make sure this is fixed ASAP.
>
>Thanks,
>-Geoff
>

>> I think OB is misbehaving, then. mymol.GetData("NSC") returns None  
>> (the
>> Python object) and mymol.HasData("NSC") returns False.
>
>I thought I had e-mailed you, but evidently not. Could you submit a  
>bug report with a test file? Let's make sure this is fixed ASAP.

Hmmmm....you see, the strange thing is that it works fine now (egg on 
face). I don't have a copy of my original test code so I guess I probably 
had a typo either with the field name or was opening a file without the 
field.

In any case, sorry for 'bugging' you about this. Having this working, means 
that I can continue with my tutorial on using open source tools to 
manipulate SD files.

Noel

P.S.GetDataType() is the method name for getting the value out of the 
OBGenericData that's returned. Wouldn't GetValue() be more appropriate?

On May 6, 2006, at 2:22 PM, Dr N. O'Boyle wrote:

> Having this working, means that I can continue with my tutorial on  
> using open source tools to manipulate SD files.

Speaking of which, I've been meaning to ask if there's interest in a  
"contributed script archive" for Open Babel. The idea would be to  
have a set of scripts that folks can download for examples of the OB  
wrappers or to simply run.

For example, I have a Perl script which outputs a CSV text file  
suitable for a spreadsheet with a variety of molecular properties,  
e.g. like the obprop C++ tool.

Cheers,
-Geoff

On Mon, 2006-04-24 at 10:45 -0400, Geoffrey Hutchison wrote:
> On Apr 24, 2006, at 10:36 AM, Noel O'Boyle wrote:
> 
> > How can I access the data fields in an SD file? Such as...
> > ...
> > I am guessing that mymol.GetData() should do this, but it doesn't  
> > appear
> > to.
> 
> You're right. It should. But I haven't looked at how the wrapper  
> works. Probably...
> 
> data = mymol.GetData("Mol weight");   // returns type OBPairData
> data.GetValue()                       // returns 1234.567 or whatever

I think OB is misbehaving, then. mymol.GetData("NSC") returns None (the
Python object) and mymol.HasData("NSC") returns False.

> I need to write up some of those tutorials, don't I? Anyone have a  
> 25th hour?

How about an 11th hour? Did you see my email regarding the existence of
http://www.redbrick.dcu.ie/~noel/parseSD.html? Once I get a few more
examples together, it should give some sort of introduction for
cheminformaticians (although with a bias on Python and SD files).

> Cheers,
> -Geoff

On Apr 24, 2006, at 10:36 AM, Noel O'Boyle wrote:

> How can I access the data fields in an SD file? Such as...
> ...
> I am guessing that mymol.GetData() should do this, but it doesn't  
> appear
> to.

You're right. It should. But I haven't looked at how the wrapper  
works. Probably...

data = mymol.GetData("Mol weight");   // returns type OBPairData
data.GetValue()                       // returns 1234.567 or whatever

I need to write up some of those tutorials, don't I? Anyone have a  
25th hour?

Cheers,
-Geoff

How can I access the data fields in an SD file? Such as...

> <Mol weight>
2423.3434

I am guessing that mymol.GetData() should do this, but it doesn't appear
to.

Regards,
 Noel

Hello all,

Sorry for the crossposting, but some of you may be interested in looking
at http://www.redbrick.dcu.ie/~noel/parseSD.html where I compare the
performance of frowns, CDK and OB, in calculating the molecular weights
of all of the molecules in a 100K molecule SD file.

This is more from the point of view of creating examples of the use of
these programs than to compare performace.

Regards,
 Noel

The Open Babel project is extremely proud to announce the release of  
Open Babel 2.0.1, 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 improved memory usage, fixes for compilation  
problems on AIX, Solaris, Fedora Core, and with the new GCC-4.1  
compiler. Several crashes were fixed, and significantly improved  
scripting wrappers for Perl and Python are available. Support for  
Cygwin and countless bug fixes are also included.

What's new? See the full release notes at:
  http://openbabel.sourceforge.net/wiki/Open_Babel_2.0.1

To download, see:
  http://sourceforge.net/project/showfiles.php? 
group_id=40728&package_id=32894&release_id=410464

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.  
Particular thanks go to (in no particular order) Craig James, Mikael  
Johansson, Chris Morley, Noel O'Boyle and Kevin Parkes.

Cheers,
-Geoff

I apologize in advance to those receiving this message multiple times.

However, the 2.0.1 release does offer significant improvements for  
scripting access, and wanted to make this clear on the scripting list  
too.

> One of the difficulties in "stable" releases is leaving well enough  
> alone. Many times fixing a bug reveals 3 other related problems.  
> For this reason, as I'm finalizing the 2.0.1 release of Open Babel,  
> I have tried to make snapshots available for testing. As discussed  
> before and after the 2.0 release, we also didn't allow enough time  
> for a "freeze" before the release for people to test the 2.0  
> candidate, be sure the Windows and UNIX releases were in sync, and  
> make sure the source release had all files. (We managed to leave  
> out src/dlhandler_win32.cpp, for example.)
>
> So I've uploaded a 2.0.1 "release candidate" to SourceForge and  
> Chris and I are freezing the openbabel-2-0-x branch until the 2.0.1  
> release. This shouldn't be a big deal since no one except me has  
> actually checked code into that branch.
>
> Please try out the release candidate and send feedback. While it  
> doesn't fix every known bug, the remaining bugs are IMHO ones that  
> will require considerable debugging and coding to fix.
>
> http://sourceforge.net/project/showfiles.php? 
> group_id=40728&package_id=154019&release_id=409376
>
> If you uncover new bugs or would like to argue that a particular  
> bug needs to be fixed ASAP, now is a good time to speak up.  
> Otherwise, 2.0.1 should be released in the next week or so.

Cheers,
-Geoff

On Apr 12, 2006, at 3:24 AM, Steven Enoch wrote:

> Does anybody have any experience with getting the Perl bindings for  
> openbabel to work?  I have downloaded and installed OpenBabel 2.0,  
> I can get the C++ utilities to compile without any trouble, however  
> when I try and compile the Perl bindings I get the following errors  
> when I run make test:

It's the same bug -- the Perl and Python bindings worked just fine  
for me on Mac OS X, but it turns out that Linux has different options  
for loading shared plugins.

The "real solution" is in the 2.0.1 release, along with updated  
bindings for more classes and a pile of bug-fixes. I'd be happy to  
send anyone the release candidate -- it should be released in a week  
or two. If you want it, please e-mail me off-list.

A workaround in the meantime is to make a small change in OpenBabel.pm:

Find the line near the top:
@EXPORT = qw( );

Change it to read:
@EXPORT = qw( ); sub dl_load_flags { 0x01 }

Cheers,
-Geoff
This problem has been fixed in the development version of OpenBabel. You
can either check this out of CVS, or wait a week or so until Geoff has
released the next version of OpenBabel.

Regards,
 Noel

On Wed, 2006-04-12 at 08:24 +0100, Steven Enoch wrote:
> Hi,
>  
> Does anybody have any experience with getting the Perl bindings for
> openbabel to work?  I have downloaded and installed OpenBabel 2.0, I
> can get the C++ utilities to compile without any trouble, however when
> I try and compile the Perl bindings I get the following errors when I
> run make test:
>  
> /usr/local/lib/openbabel/<file>format.so did lot load properly
>  
> where <file> is every *.so file in the
> directory /usr/local/lib/openbabel
>  
> I have checked the /usr/local/lib/openbabel directory and the files
> definitely exists.  I am running Red Hat Enterprise WS4 version of
> Linux on an 32 bit dual processor Intel Xeon Dell machine.
>  
> I have 'Googled' for help but only come across the same problems
> relating to the Python bindings.
>  
> Any help would be appreciated,
>  
> Thanks, 
>  
> Steve
> 
> Dr Steve Enoch 
> Computational Chemist 
> Peakdale Molecular Ltd 
> Tel +44 (0) 1298 816741 
> ste...@pe... 
> 
>  
> 
> ********************************************************************** 
> 
> Peakdale Molecular Ltd 
> 
> Peakdale Science Park, Sheffield Road 
> 
> Chapel-en-le-Frith, High Peak, SK23 OPG, UK 
> 
> T: +44 1298 816700  E: in...@pe... 
> 
> F: +44 1298 816701  W: www.peakdale.co.uk 
> 
> This e-mail and any attachments hereto are: 
> 
> Strictly confidential and intended solely for the addressee.  If you
> are 
> 
> not the intended addressee you must not disclose, copy, distribute, or
> take 
> 
> any other action in reliance on this e-mail or attachments.  If you
> have 
> 
> received this e-mail in error, please notify the sender immediately. 
> 
> Addressees should check all attachments for viruses.  Peakdale
> Molecular Limited 
> 
> make no representations as regards the absence of viruses in
> attachments to this e-mail. 
> 
> **********************************************************************  
> 

Hi,
=20
Does anybody have any experience with getting the Perl bindings for
openbabel to work?  I have downloaded and installed OpenBabel 2.0, I can
get the C++ utilities to compile without any trouble, however when I try
and compile the Perl bindings I get the following errors when I run make
test:
=20
/usr/local/lib/openbabel/<file>format.so did lot load properly
=20
where <file> is every *.so file in the directory
/usr/local/lib/openbabel
=20
I have checked the /usr/local/lib/openbabel directory and the files
definitely exists.  I am running Red Hat Enterprise WS4 version of Linux
on an 32 bit dual processor Intel Xeon Dell machine.
=20
I have 'Googled' for help but only come across the same problems
relating to the Python bindings.
=20
Any help would be appreciated,
=20
Thanks,=20
=20
Steve

Dr Steve Enoch=20
Computational Chemist=20
Peakdale Molecular Ltd=20
Tel +44 (0) 1298 816741=20
ste...@pe...=20

=20

**********************************************************************
Peakdale Molecular Ltd
Peakdale Science Park, Sheffield Road
Chapel-en-le-Frith, High Peak, SK23 OPG, UK

T: +44 1298 816700=A0 E: in...@pe...
F: +44 1298 816701=A0 W: www.peakdale.co.uk
This e-mail and any attachments hereto are:

Strictly confidential and intended solely for the addressee.=A0 If you are
not the intended addressee you must not disclose, copy, distribute, or take
any other action in reliance on this e-mail or attachments.=A0 If you have
received this e-mail in error, please notify the sender immediately.

Addressees should check all attachments for viruses.=A0 Peakdale Molecular =
Limited
make no representations as regards the absence of viruses in attachments to=
 this e-mail.
**********************************************************************

On Apr 6, 2006, at 4:21 AM, Noel O'Boyle wrote:

> I may have missed something here, and if so, I recommend moving to the
> CVS version.

Actually, I recommend moving to the 2.0.1 CVS version, which will  
soon be released. The CVS "head" version for 2.1 is still a bit  
thorny in places. I've certainly had problems getting it to work from  
time to time.

On the other hand, the 2.0.1 version should fix many of the problems  
with 2.0. I'd be glad to send snapshots to people as needed.

> Please let us know if you have any more problems/questions with the
> scripting module as we are keen to improve it.

Indeed!

Cheers,
-Geoff

Hello Seth,

First of all, as the OB scripting modules in particular are young and
under active development, you may want to consider using the CVS version
of openbabel rather than the last release. (You also will have the
chance to test out the pyopenbabel module as somewhat described on the
openbabel website)

To answer your question, this bug has been fixed in CVS. It is caused by
Python's confusion between openbabel.so (a C extension) and openbabel.py
in /usr/lib/Python2.4/site-packages (on my system).

What you need to do is:
(1) Change "import openbabel" to "import _openbabel" at the start of
your own openbabel.py (in openbabel/scripts/python)
(2) change Extension('openbabel' to Extension('_openbabel' in
openbabel/scripts/python/setup.py.
(3) remove /usr/lib/Python2.4/site-packages/openbabel.so
(4) rerun "python setup.py install"
(/usr/lib/Python2.4/site-packages should now contain _openbabel.so and
openbabel.py)

I may have missed something here, and if so, I recommend moving to the
CVS version.

Please let us know if you have any more problems/questions with the
scripting module as we are keen to improve it.

Regards,
 Noel

On Thu, 2006-04-06 at 14:34 +1000, Dr. Seth Olsen wrote:
> 
> Hi OBScripters,
> 
> I built the python module from OB 2.0.0, but when I 'import
> openbabel', it fails with the following error:
> ImportErrr: dynamic module does not define init function
> (initopenbabel)
> 
> What did I do wrong?  Does anybody know?
> 
> Cheers,
> 
> Seth
> 
> -- 
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> 
> Dr Seth Olsen, PhD
> Postdoctoral Fellow, Biomolecular Modeling Group
> Centre for Computational Molecular Science
> Chemistry Building,
> The University of Queensland
> Qld 4072, Brisbane, Australia
> 
> tel (617) 33653732
> fax (617) 33654623
> email: s.o...@uq...
> Web: www.ccms.uq.edu.au 
> 
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> 

Hi OBScripters,

I built the python module from OB 2.0.0, but when I 'import openbabel', it
fails with the following error:
ImportErrr: dynamic module does not define init function (initopenbabel)

What did I do wrong?  Does anybody know?

Cheers,

Seth

--
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Biomolecular Modeling Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.o...@uq...
Web: www.ccms.uq.edu.au

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Regarding the wrapping of streams, you may find the following interesting: 
http://embedded.eecs.berkeley.edu/Alumni/pinhong/scriptEDA/pyTypemapFAQ.html#8

It appears to show a way of wrapping them.

Regards,
 Noel

On Mar 16 2006, Noel O'Boyle wrote:

>I'm not having great luck with this method.
>
>Attempt 1 Using Read after ReadFile
>=========
>from openbabel import *
>
>myfile = "3d.head.sdf"
>obConversion = OBConversion()
>obConversion.SetInFormat("sdf")
>
>mymol = OBMol()
>obConversion.ReadFile(mymol,myfile)
>print mymol.GetMolWt()
>print obConversion.Read(mymol)
>print "The program segfaults before this line"
>
>Attempt 2 Using Read after ReadString
>=========
>from openbabel import *
>
>myfilestring = open("3d.head.sdf","r").read()
>obConversion = OBConversion()
>obConversion.SetInFormat("sdf")
>
>mymol = OBMol()
>obConversion.ReadString(mymol,myfilestring)
>print mymol.GetMolWt()
>print obConversion.Read(mymol)
>print "The program aborts before this line"
>
>>From the python point of view, what is needed is a function that when
>repeatedly called, will return additional molecules. This doesn't need
>to be in the main openbabel library, but can be in the SWIG wrapper
>somewhere.
>
>Regards,
> Noel
>
>On Wed, 2006-03-15 at 14:18 -0500, Geoffrey Hutchison wrote:
>> On Mar 15, 2006, at 5:18 AM, Noel O'Boyle wrote:
>> 
>> > It seems that OBConversion.ReadFile(OBMolecule) just reads in the  
>> > first
>> > molecule, and I cannot see a way of iterating over the molecules.
>> 
>> The OBConversion.Read(OBMol) function should continue to read from  
>> the same file. However, since Python and Perl have no concept of  
>> "streams", it's not possible to use OBConversion.Read() to set up the  
>> input file or string.
>> 
>> So something like this (sorry, I haven't written much Python, so the  
>> syntax might be off):
>> 
>> import openbabel
>> 
>> mol = openbabel.OBMol()
>> conv = openbabel.OBConversion()
>> conv.SetInAndOutFormats("sdf", "sdf")
>> obConversion.ReadString(mol, "test.sdf")
>> 
>> while (obConversion.Read(mol))
>> ...
>> 
>> 
>> Cheers,
>> -Geoff
>
>
>
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I'm not having great luck with this method.

Attempt 1 Using Read after ReadFile
=========
from openbabel import *

myfile = "3d.head.sdf"
obConversion = OBConversion()
obConversion.SetInFormat("sdf")

mymol = OBMol()
obConversion.ReadFile(mymol,myfile)
print mymol.GetMolWt()
print obConversion.Read(mymol)
print "The program segfaults before this line"

Attempt 2 Using Read after ReadString
=========
from openbabel import *

myfilestring = open("3d.head.sdf","r").read()
obConversion = OBConversion()
obConversion.SetInFormat("sdf")

mymol = OBMol()
obConversion.ReadString(mymol,myfilestring)
print mymol.GetMolWt()
print obConversion.Read(mymol)
print "The program aborts before this line"

>From the python point of view, what is needed is a function that when
repeatedly called, will return additional molecules. This doesn't need
to be in the main openbabel library, but can be in the SWIG wrapper
somewhere.

Regards,
 Noel

On Wed, 2006-03-15 at 14:18 -0500, Geoffrey Hutchison wrote:
> On Mar 15, 2006, at 5:18 AM, Noel O'Boyle wrote:
> 
> > It seems that OBConversion.ReadFile(OBMolecule) just reads in the  
> > first
> > molecule, and I cannot see a way of iterating over the molecules.
> 
> The OBConversion.Read(OBMol) function should continue to read from  
> the same file. However, since Python and Perl have no concept of  
> "streams", it's not possible to use OBConversion.Read() to set up the  
> input file or string.
> 
> So something like this (sorry, I haven't written much Python, so the  
> syntax might be off):
> 
> import openbabel
> 
> mol = openbabel.OBMol()
> conv = openbabel.OBConversion()
> conv.SetInAndOutFormats("sdf", "sdf")
> obConversion.ReadString(mol, "test.sdf")
> 
> while (obConversion.Read(mol))
> ...
> 
> 
> Cheers,
> -Geoff

I have a question about the behaviour of ReadFile.

The following code repeatedly reads the first molecule in 3d.head.sdf
and prints out 122.12134 twice:
"""
from openbabel import *

myfile = "3d.head.sdf"
obConversion = OBConversion()
obConversion.SetInFormat("sdf")
mymol = OBMol()                      # Initialise for the first time
obConversion.ReadFile(mymol,myfile)
print mymol.GetMolWt()               # 122.12134
mymol = OBMol()                      # Initialise for the second time
obConversion.ReadFile(mymol,myfile)
print mymol.GetMolWt()               # 122.12134
"""

*but* the following code, appears to append the new molecule to the old
molecule -- is this the expected behaviour?

"""
from openbabel import *

myfile = "3d.head.sdf"
obConversion = OBConversion()
obConversion.SetInFormat("sdf")
mymol = OBMol()                      # Initialise once only
obConversion.ReadFile(mymol,myfile)
print mymol.GetMolWt()               # 122.12134
obConversion.ReadFile(mymol,myfile)
print mymol.GetMolWt()               # 244.24268 (=122.12134*2)
"""

Regards,
 Noel

On Mar 15, 2006, at 5:18 AM, Noel O'Boyle wrote:

> It seems that OBConversion.ReadFile(OBMolecule) just reads in the  
> first
> molecule, and I cannot see a way of iterating over the molecules.

The OBConversion.Read(OBMol) function should continue to read from  
the same file. However, since Python and Perl have no concept of  
"streams", it's not possible to use OBConversion.Read() to set up the  
input file or string.

So something like this (sorry, I haven't written much Python, so the  
syntax might be off):

import openbabel

mol = openbabel.OBMol()
conv = openbabel.OBConversion()
conv.SetInAndOutFormats("sdf", "sdf")
obConversion.ReadString(mol, "test.sdf")

while (obConversion.Read(mol))
...

Cheers,
-Geoff

2005	Jan	Feb	Mar	Apr	May	Jun (5)	Jul (1)	Aug	Sep	Oct (1)	Nov (10)	Dec (22)
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openbabel-scripting Mailing List for Open Babel (Page 34)

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