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Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

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

I need to get a linux compilation set up before I can contribute
usefully to your efforts. The first thing to do is to try merging the
recent changes in openbabel-python.i into openbabel-ruby.i (using "svn
merge" for example), and seeing whether this makes everything better.

Noel

On 16/01/2008, Joshua Ballanco <Jos...@st...> wrote:
> On Jan 16, 2008, at 10:42 AM, Noel O'Boyle wrote:
>
> > On 16/01/2008, Joshua Ballanco <Jos...@st...> wrote:
> >> I've tried fixing the OBGenericData and OBFormat scope issues in
> >> openbabel_ruby.cpp by hand (there's also 3 or so odd issues with
> >> making assignments to const values). I've gotten it to where the
> >> extension will compile, but like you, I run into errors with linking.
> >> I had thought it was my system (OS X Leopard, 10.5.1), but perhaps it
> >> goes deeper? Oh, and one last thing (don't know if this will help or
> >> not): If I use Ruby 1.9.0 instead of 1.8.6, then everything compiles
> >> and links without warning, but I get missing symbol lookup errors as
> >> soon as I start trying to use the extension in Ruby.
> >
> > Based on past experience, if we can get it to compile for one
> > scripting language, it will compile for all scripting languages. The
> > dependence on Ruby version number is strange though.
>
> I'm in the process of recompiling both Ruby and OpenBabel to try this
> again. I'll let you know if this discrepancy leads to any hints about
> what's going wrong.
>
> > I'm going to concentrate on sorting things out for Python first. Once
> > that's done we can start coordinating on Ruby, etc., as I don't know
> > how to test whether it's working, e.g. it might be a good idea to
> > write a short test program which we can use for this.
>
> Sounds good. I'll start thinking about some tests. I'm also curious
> how other's on the project feel about targeting Ruby 1.9? It's
> probably very early to be thinking along these lines, but the
> performance gains seem to be worth whatever headaches might pop up.
> Also, it doesn't seem that the interface for writing extensions has
> changed much.
>
> > Hope you don't mind if I cc the scripting list. Other scripting users
> > will probably be glad to hear that we are trying to sort out these
> > issues.
> >
>
> No problem. I was a tad reluctant to jump in, since I'm new to Babel
> (development that is, I've been using the cli utility for a few years
> now) and SWIG, but I'm willing to lend whatever help I can.
>
> Sincerely,
>
> Joshua Ballanco
> Graduate Student
> Department of Chemistry and Chemical Biology
> Stevens Institute of Technology
> Hoboken, NJ 07030
>
> E-mail: jba...@st...
>
>
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

[Joshua B. <Jos...@st...>]

On Jan 16, 2008, at 10:42 AM, Noel O'Boyle wrote:

> On 16/01/2008, Joshua Ballanco <Jos...@st...> wrote:
>> I've tried fixing the OBGenericData and OBFormat scope issues in
>> openbabel_ruby.cpp by hand (there's also 3 or so odd issues with
>> making assignments to const values). I've gotten it to where the
>> extension will compile, but like you, I run into errors with linking.
>> I had thought it was my system (OS X Leopard, 10.5.1), but perhaps it
>> goes deeper? Oh, and one last thing (don't know if this will help or
>> not): If I use Ruby 1.9.0 instead of 1.8.6, then everything compiles
>> and links without warning, but I get missing symbol lookup errors as
>> soon as I start trying to use the extension in Ruby.
>
> Based on past experience, if we can get it to compile for one
> scripting language, it will compile for all scripting languages. The
> dependence on Ruby version number is strange though.

I'm in the process of recompiling both Ruby and OpenBabel to try this  
again. I'll let you know if this discrepancy leads to any hints about  
what's going wrong.

> I'm going to concentrate on sorting things out for Python first. Once
> that's done we can start coordinating on Ruby, etc., as I don't know
> how to test whether it's working, e.g. it might be a good idea to
> write a short test program which we can use for this.

Sounds good. I'll start thinking about some tests. I'm also curious  
how other's on the project feel about targeting Ruby 1.9? It's  
probably very early to be thinking along these lines, but the  
performance gains seem to be worth whatever headaches might pop up.  
Also, it doesn't seem that the interface for writing extensions has  
changed much.

> Hope you don't mind if I cc the scripting list. Other scripting users
> will probably be glad to hear that we are trying to sort out these
> issues.
>

No problem. I was a tad reluctant to jump in, since I'm new to Babel  
(development that is, I've been using the cli utility for a few years  
now) and SWIG, but I'm willing to lend whatever help I can.

Sincerely,

Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030

E-mail: jba...@st...

Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

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

On 16/01/2008, Joshua Ballanco <Jos...@st...> wrote:
> Noel,
>
> I'm new to OpenBabel development, but I'm really interested in using
> it with Ruby for a couple of projects, so I thought I'd try to help
> out. The errors that you're getting? Is this with Python? I ask
> because I've been working through some eerily similar issues with Ruby.

Yes - they're with Python, but the inteface files are almost identical
for each of the languages. Once I get it to work for Python, I
generally merge the changes to the other ones without any problems.

> I've tried fixing the OBGenericData and OBFormat scope issues in
> openbabel_ruby.cpp by hand (there's also 3 or so odd issues with
> making assignments to const values). I've gotten it to where the
> extension will compile, but like you, I run into errors with linking.
> I had thought it was my system (OS X Leopard, 10.5.1), but perhaps it
> goes deeper? Oh, and one last thing (don't know if this will help or
> not): If I use Ruby 1.9.0 instead of 1.8.6, then everything compiles
> and links without warning, but I get missing symbol lookup errors as
> soon as I start trying to use the extension in Ruby.

Based on past experience, if we can get it to compile for one
scripting language, it will compile for all scripting languages. The
dependence on Ruby version number is strange though.

> If there's anything that I can do to help, just let me know. I'm not
> very familiar with Swig (picking it up as I go), but I've had some
> mild success with Ruby extensions in the past.

I'm going to concentrate on sorting things out for Python first. Once
that's done we can start coordinating on Ruby, etc., as I don't know
how to test whether it's working, e.g. it might be a good idea to
write a short test program which we can use for this.

Hope you don't mind if I cc the scripting list. Other scripting users
will probably be glad to hear that we are trying to sort out these
issues.

Regards,
   Noel

> Sincerely,
>
> Joshua Ballanco
> Graduate Student
> Department of Chemistry and Chemical Biology
> Stevens Institute of Technology
> Hoboken, NJ 07030
>
> E-mail: jba...@st...
>
>
>
> On Jan 16, 2008, at 5:13 AM, Noel O'Boyle wrote:
>
> > I've solved one problem but I don't know now. The problem is described
> > in Part 1 and the solution in Part 2.
> >
> > ---Part 1
> > Now that we are in snapshot mode, it's time to sort out the scripting
> > language bindings. There appear to be two separate problems, one
> > relating to OBGenericData and another related to OBFormat. If we
> > concentrate on just the first problem:
> >
> > 1>../../include\openbabel\generic.h(44): Warning(401): Base class
> > 'OBGenericData' undefined.
> > 1>../../include\openbabel\base.h(164): Warning(401): 'OBGenericData'
> > must be defined before it is used as a base class.
> >
> > These warnings appear several times in the SWIG output. Compilation
> > subsequently fails with an error message apparently related to this.
> > If the SWIG directive "%include <openbabel/generic.h>" is commented
> > out, these warnings and that compilation error disappears.
> >
> > So the problem appears to be in generic.h. Why does it think at line
> > 44 that OBGenericData is undefined? Is this a problem with SWIG? Is it
> > something we can find a workaround for on the SWIG mailing list?
> >
> > Noel (compiling off the trunk on Windows)
> >
> > --Part 2
> > Just before I sent off the email, I tried something and fixed this
> > problem. I switched the order of:
> > %include <openbabel/generic.h>
> > %include <openbabel/base.h>
> >
> > in the SWIG interface file so that base.h came before generic.h.
> >
> > The order of these "includes" has never had an effect previously.
> > Could someone speculate on why this is, and whether there are other
> > cases where we need to consider the order also?
> >
> > Noel
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2008.
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-Devel mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
>

Re: [OpenBabel-scripting] Trouble getting data fields from an SD file with pybel

[Hassan T. M. <HMa...@Pr...>]

Hello Noel

Thanks for your reply, I thought I had checked for that problem, but obviou=
sly I was wrong... a revision of os.path has sorted that out.  Everything w=
orks as it should now.

Cheers

Hassan

-----Original Message-----
From: Noel O'Boyle [mailto:bao...@gm...]
Sent: 15 January 2008 16:34
To: Hassan Thomas Mamdani
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] Trouble getting data fields from an SD f=
ile with pybel

On 15/01/2008, Hassan Thomas Mamdani <HMa...@pr...> wro=
te:
>
> Hi
Hello Hassan,
>
> I'm rather new to python and babel, but I'm trying return the data fields
> from and SD file.  I have adapted the code snippet on Noel O'Boyle's site
> (http://baoilleach.blogspot.com/search/label/python).  The
> code is as follows

Sorry about this problem. It's my fault. Pybel should say
"FileNotFound". I think you will find that the file "TopLigsScreened"
does not exist. Perhaps you have a file called "TopLigsScreened.sd".

Thanks for reporting this problem. I fix this in the next release. And
good to hear from someone else in Cambridge! :-)

Let us know if you have any further problems.

Noel

>
>
> import pybel
>
>
>
> inputfile=3Dpybel.readfile("sd","TopLigsScreened")
>
>
>
> datafile=3Dopen("TopLigsScreenedData.txt", "w")
>
>
>
> mol=3Dinputfile.next()
>
> datafile.write("%s\n" %("\t".join(mol.data.keys())))
>
>
>
> for mol in inputfile:
>
>     datafile.write("%s\n" %("\t".join(mol.data.values())))
>
>
>
> datafile.close()
>
>
>
>
>
> When I run it, the program fails with a StopIteration exception.  When I =
go
> through the steps at the interactive prompt, I get the StopIteration
> exception when I run mol =3D inputfile.next()
>
>
>
> The error message is:
>
>
>
> Traceback (most recent call last):
>
>   File "<interactive input>", line 1, in ?
>
> StopIteration
>
>
>
> I'm rather at loss, though I'm not very experienced with Python yet.  Any
> help would be appreciated.
>
>
>
> Kind Regards
>
> Hassan
>
>
>
> Hassan Mamdani MSci MPhil MRSC
>
> Research Scientist, Computational Chemistry
>
>
>
> ProMetic BioSciences Ltd
>
> 211 Cambridge Science Park
>
> Milton Rd
>
> Cambridge
>
> CB4 0WA
>
>
>
> 01223 433861
>
> hma...@pr...
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

Re: [OpenBabel-scripting] Trouble getting data fields from an SD file with pybel

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

On 15/01/2008, Hassan Thomas Mamdani <HMa...@pr...> wrote:
>
> Hi
Hello Hassan,
>
> I'm rather new to python and babel, but I'm trying return the data fields
> from and SD file.  I have adapted the code snippet on Noel O'Boyle's site
> (http://baoilleach.blogspot.com/search/label/python).  The
> code is as follows

Sorry about this problem. It's my fault. Pybel should say
"FileNotFound". I think you will find that the file "TopLigsScreened"
does not exist. Perhaps you have a file called "TopLigsScreened.sd".

Thanks for reporting this problem. I fix this in the next release. And
good to hear from someone else in Cambridge! :-)

Let us know if you have any further problems.

Noel

>
>
> import pybel
>
>
>
> inputfile=pybel.readfile("sd","TopLigsScreened")
>
>
>
> datafile=open("TopLigsScreenedData.txt", "w")
>
>
>
> mol=inputfile.next()
>
> datafile.write("%s\n" %("\t".join(mol.data.keys())))
>
>
>
> for mol in inputfile:
>
>     datafile.write("%s\n" %("\t".join(mol.data.values())))
>
>
>
> datafile.close()
>
>
>
>
>
> When I run it, the program fails with a StopIteration exception.  When I go
> through the steps at the interactive prompt, I get the StopIteration
> exception when I run mol = inputfile.next()
>
>
>
> The error message is:
>
>
>
> Traceback (most recent call last):
>
>   File "<interactive input>", line 1, in ?
>
> StopIteration
>
>
>
> I'm rather at loss, though I'm not very experienced with Python yet.  Any
> help would be appreciated.
>
>
>
> Kind Regards
>
> Hassan
>
>
>
> Hassan Mamdani MSci MPhil MRSC
>
> Research Scientist, Computational Chemistry
>
>
>
> ProMetic BioSciences Ltd
>
> 211 Cambridge Science Park
>
> Milton Rd
>
> Cambridge
>
> CB4 0WA
>
>
>
> 01223 433861
>
> hma...@pr...
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] Trouble getting data fields from an SD file with pybel

[Hassan T. M. <HMa...@Pr...>]

Hi

I'm rather new to python and babel, but I'm trying return the data fields f=
rom and SD file.  I have adapted the code snippet on Noel O'Boyle's site (h=
ttp://baoilleach.blogspot.com/search/label/python).  The code is as follows

import pybel

inputfile=3Dpybel.readfile("sd","TopLigsScreened")

datafile=3Dopen("TopLigsScreenedData.txt", "w")

mol=3Dinputfile.next()
datafile.write("%s\n" %("\t".join(mol.data.keys())))

for mol in inputfile:
    datafile.write("%s\n" %("\t".join(mol.data.values())))

datafile.close()


When I run it, the program fails with a StopIteration exception.  When I go=
 through the steps at the interactive prompt, I get the StopIteration excep=
tion when I run mol =3D inputfile.next()

The error message is:

Traceback (most recent call last):
  File "<interactive input>", line 1, in ?
StopIteration

I'm rather at loss, though I'm not very experienced with Python yet.  Any h=
elp would be appreciated.

Kind Regards
Hassan

Hassan Mamdani MSci MPhil MRSC
Research Scientist, Computational Chemistry

ProMetic BioSciences Ltd
211 Cambridge Science Park
Milton Rd
Cambridge
CB4 0WA

01223 433861
hma...@pr...

Re: [OpenBabel-scripting] [openbabel-scripting] MMFF94 Force field

[<ge...@ge...>]

Dear Nehru,

Welcome to Open Babel. Yes, for the 2.1.x releases, we were only able to
validate the Ghemical (Tripos-5.2-like) force field. When we release
2.2.0, we will include MMFF94 and UFF implementations. There is not much
interest in MM2 (since the other force fields perform better) so that will
not be released.

I suspect that a 2.2 release will be made in early 2008, but we have not
planned a specific release date yet.

I am not sure what files you are referring to -- that link is an extremely
general search for anything in the Open Babel project. Yes, there are
validation routines for force field in the SVN trunk (developer version).

Hope that helps!
-Geoff

> Hi all,
> I'm new to babel. I started using openbabel-2.1.1.
> I found  that i'm able to use only Ghemical force field.
> I heared that MM2 and MMFF94 force filed would be incorporated in the new
> release
> so can  anyone tell me when it is.
>
> also i found some codes in the link
> http://www.krugle.org/kse/files?query=&lang=C%2B%2B&project=%22Open%20Babel%22#7
>
> is it the validation for the force field?
>
> Thanks for any help,
> Nehru Viji

[OpenBabel-scripting] [openbabel-scripting] MMFF94 Force field

[Nehru <vij...@gm...>]

Hi all,
I'm new to babel. I started using openbabel-2.1.1.
I found  that i'm able to use only Ghemical force field.
I heared that MM2 and MMFF94 force filed would be incorporated in the new
release
so can  anyone tell me when it is.

also i found some codes in the link
http://www.krugle.org/kse/files?query=&lang=C%2B%2B&project=%22Open%20Babel%22#7

is it the validation for the force field?

Thanks for any help,
Nehru Viji


-- 
View this message in context: http://www.nabble.com/MMFF94-Force-field-tp14522372p14522372.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] mandatory hydrogen?

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

Thanks for the explanation, Jeff. I guess I am muddling SMILES and SMARTS; I
want c1ccnc1 to mean "a five membered, aromatic ring with one nitrogen,
which may be connected hydrogen but may be connected to something else".  I
guess I need to do that SMILES-to-SMARTS conversion manually.
Thanks,

Dave.

On Dec 13, 2007 10:33 AM, Geoffrey Hutchison <ge...@ge...>
wrote:

>
> On Dec 13, 2007, at 9:44 AM, David Rose wrote:
>
> > c1cc[nH]c1
>
> This is pyrrole. The [nH] is necessary in the aromatic SMILES form to
> indicate the protonation in the aromatic nitrogen. This makes pyrrole
> distinct from say:
>
> C1=CC=NC1
>
> Same formula (C4H5N) but very different compounds. Some other
> "mandatory hydrogens" come with chiral atoms, e.g.:
>
> Cl[C@H](C)CC
>
> Here the H atom must stay explicit to indicate the chirality of the C
> atom.
>
> Cheers,
> -Geoff
>

Re: [OpenBabel-scripting] mandatory hydrogen?

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

On Dec 13, 2007, at 9:44 AM, David Rose wrote:

> c1cc[nH]c1

This is pyrrole. The [nH] is necessary in the aromatic SMILES form to  
indicate the protonation in the aromatic nitrogen. This makes pyrrole  
distinct from say:

C1=CC=NC1

Same formula (C4H5N) but very different compounds. Some other  
"mandatory hydrogens" come with chiral atoms, e.g.:

Cl[C@H](C)CC

Here the H atom must stay explicit to indicate the chirality of the C  
atom.

Cheers,
-Geoff

[OpenBabel-scripting] mandatory hydrogen?

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

Greetings,
  Can anyone explain the following behavior?

The script:

use Chemistry::OpenBabel;
my $file = "./mol7.mol";
system("cat $file");
my $mol = Chemistry::OpenBabel::OBMol->new();
my $conv = Chemistry::OpenBabel::OBConversion->new();
$conv->SetInAndOutFormats("mol","smi");
$conv->ReadFile($mol,$file);
print "Before deleting H's: ",$conv->WriteString($mol);
$mol->DeleteHydrogens();
print "After deleting H's: ",$conv->WriteString($mol);

The output:

myMol
JME 2003.12 Wed Dec 12 10:06:59 EST 2007

  5  5  0  0  0  0  0  0  0  0999 V2000
    2.2652    1.3315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1326    2.1544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8326    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.3315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4326    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
Before deleting H's: c1cc[nH]c1 myMol
After deleting H's: c1cc[nH]c1  myMol

So, original molecule has no explicit hydrogens.  Conversion to SMILES adds
an explicit hydrogen on the N (but nowhere else).  This explicit hydrogen is
not removed by DeleteHydrogens.   Is this a bug, or the expected behavior?
 If the latter, why?  And, is there a way to remove all hydrogens?  I want
to use the SMILES as a SMARTS to do a substructure search, and because of
that H the search fails for molecules that have other things (e.g. a methyl
or phenyl) on that nitrogen.

Many thanks,
David Rose.

Re: [OpenBabel-scripting] Fingerprints

[Noel O'B. <bao...@gm...>]
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[OpenBabel-scripting] extconf.rb problem in MacOSX/iBookG4

[Masaaki K. <ko...@tc...>]

Hi. I have been trying to install OBRuby into my MacOSX/iBookG4, but stil=
l
without success. It seems extconf.rb can't find header files, and we coul=
dn't
find the same problem in the mailing list. A friend of mine also has exac=
tly
the same problem, and he tried something to improve the situation. We wou=
ld
really appreciate it if you gave us a suggestion.

The followings are what he tried:

I tried adding /usr/local/include/openbabel-2.0/openbabel to the Makefile
(created at the "ruby extconf.rb" step):

CPPFLAGS =3D -I. -I$(topdir) -I$(hdrdir) -I$(srcdir)
-I/usr/local/include/openbabel-2.0/openbabel

Then I ran make again

$ make >& errors

$ cat errors | head -n 3

g++ -fno-common -g -Os -pipe -fno-common -pipe  -fno-common -pipe -fno-co=
mmon =20
-I. -I/usr/lib/ruby/1.8/universal-darwin8.0
-I/usr/lib/ruby/1.8/universal-darwin8.0 -I.
-I/usr/local/include/openbabel-2.0/openbabel -c openbabel.cpp
In file included from openbabel.cpp:1696:
/usr/local/include/openbabel-2.0/openbabel/obutil.h:23:35: error:
openbabel/babelconfig.h: No such file or directory
When I looked in /usr/local/include/openbabel-2.0/openbabel/obutil.h it t=
ries to
include openbabel/babelconfig.h, when that file is in the same directory!=
  I
don't understand this, but then I'm not a C++ programmer...

So I tried adding

-I/usr/local/include/openbabel-2.0

to CPPFLAGS and this now gives me 384 lines of errors when I run 'make'
(compared with 35007 errors previously!) but now there seems to be some
redundancy:

g++ -fno-common -g -Os -pipe -fno-common -pipe  -fno-common -pipe -fno-co=
mmon =20
-I. -I/usr/lib/ruby/1.8/universal-darwin8.0
-I/usr/lib/ruby/1.8/universal-darwin8.0 -I.
-I/usr/local/include/openbabel-2.0/openbabel -I/usr/local/include/openbab=
el-2.0
 -c openbabel.cpp
In file included from /usr/local/include/openbabel-2.0/openbabel/obutil.h=
:23,
                 from openbabel.cpp:1696:
/usr/local/include/openbabel-2.0/openbabel/babelconfig.h:18:1: warning: "=
EXTERN"
redefined
In file included from /usr/lib/ruby/1.8/universal-darwin8.0/ruby.h:22,
                 from openbabel.cpp:809:
/usr/lib/ruby/1.8/universal-darwin8.0/defines.h:210:1: warning: this is t=
he
location of the previous definition


Best wishes,
Masaaki Kotera


--- Forwarded message ---
Hello Masaaki,

Thanks for your feedback. I don't have access to a OSX
system, so it's hard for me to diagnose your problem.

Have you tried the instructions in this more recent
article?:

http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-=
open-babel

Geoff Hutchison says that these instructions work on
his OSX system.

If you still aren't able to get Ruby Open Babel
working, I'd suggest posting to the
openbabel-scripting list:

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

Either way, could you let me know how it goes for you?

Cheers,
Rich

--- Masaaki Kotera <ko...@tc...> wrote:

> Dear Mr. Richard L. Apodaca,
>
> I have been trying to install OBRuby into my
> MacOSX/iBookG4,
> but currently without success.
>
> I followed the instruction from this webpage:
>
http://depth-first.com/articles/2006/10/31/obruby-a-ruby-interface-to-ope=
n-babel
>
> There seems no ldconfig in MacOSX, so I skipped
> (This might be the cause of the problem).
>
> Then, I get a long error message beginning with the
> followings:
>
> In file included from
>
/usr/local/include/openbabel-2.0/openbabel/obutil.h:23,
> from openbabel.cpp:1696:
>
/usr/local/include/openbabel-2.0/openbabel/babelconfig.h:18:1:
> warning: "EXTERN"
> redefined
> In file included from
> /usr/lib/ruby/1.8/powerpc-darwin8.0/ruby.h:22,
> from openbabel.cpp:809:
> /usr/lib/ruby/1.8/powerpc-darwin8.0/defines.h:207:1:
> warning: this is the
> location of the previous definition
> openbabel.cpp: In function `VALUE
> _wrap_open_datafile(int, VALUE*, VALUE)':
> openbabel.cpp:9180: error: ???OpenDatafile??? is not
> a member of ???OpenBabel???
> openbabel.cpp: In function `VALUE
> _wrap_Vector3_is_approx(int, VALUE*, VALUE)':
> openbabel.cpp:10422: error: ???const class
> OpenBabel::vector3??? has no member
> named ???IsApprox???
> openbabel.cpp: In function `VALUE
> _wrap_Vector3_as_array(int, VALUE*, VALUE)':
> openbabel.cpp:10446: error: ???class
> OpenBabel::vector3??? has no member named
> ???AsArray???
>
> I wonder if you would kindly give me a suggestion
> about this problem.
>
> All the best,
>
> Masaaki Kotera
> Biochemistry Department, Trinity College Dublin
>

[OpenBabel-scripting] Ruby Open Babel in 2.1.1

[richard a. <ric...@ya...>]

Looks like there was a change in the Ruby Open Babel
wrapper from version 2.1.0 (which worked) to 2.1.1
(which does not work).

The symptom (after installing Ruby Open Babel as
described in
http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel):

$ irb
irb(main):001:0> require 'openbabel'
LoadError:
/usr/local/lib/ruby/site_ruby/1.8/i686-linux/openbabel.so:
undefined symbol: Init_openbabel -
/usr/local/lib/ruby/site_ruby/1.8/i686-linux/openbabel.so
        from
/usr/local/lib/ruby/site_ruby/1.8/i686-linux/openbabel.so
        from (irb):1
        from :0

The fix is simple:

on line 87617 of openbabel_ruby.cpp, change:

Init_OpenBabel

to:

Init_openbabel

Then make and make install.

Cheers,
Rich

___________________________________

Richard L. Apodaca

http://depth-first.com      Blog
http://metamolecular.com    Company

Re: [OpenBabel-scripting] Aromatic error

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

> '*** Open Babel Warning in ParseComplex
>      Illegal aromatic element '
> What could be the cause of this as well as a solution to the cause.

Well, the message comes up in SMILES parsing when there's a non- 
aromatic element written in lowercase. For example, if you submit the  
string "b1cccc1" this will bring up this string -- boron is not  
designated as an aromatic element in SMILES, even though some people  
use it that way.

This is simply a warning -- Open Babel is letting you know that the  
input is against the specification, but continues to process anyway.

Cheers,
-Geoff

[OpenBabel-scripting] Aromatic error

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

SGkgYWxsCgpDYW4gc29tZW9uZSBzaGluZSBhIGxpZ2h0IG9uIHRoZSBmb2xsb3dpbmcuCkkgZ2V0
IHRoZSBmb2xsb3dpbmcgZXJyb3Igd2l0aCBhIHB5YmVsIGFuZCBvcGVuYmFiZWwgcHl0aG9uIHNj
cmlwdDoKCicqKiogT3BlbiBCYWJlbCBXYXJuaW5nIGluIFBhcnNlQ29tcGxleAogICAgIElsbGVn
YWwgYXJvbWF0aWMgZWxlbWVudCAnCgpXaGF0IGNvdWxkIGJlIHRoZSBjYXVzZSBvZiB0aGlzIGFz
IHdlbGwgYXMgYSBzb2x1dGlvbiB0byB0aGUgY2F1c2UuCgpUaGFueAoKLS0gClJlZ2FyZHMvR3Jv
ZXRlL01pdCBmcmV1bmRsaWNoZW4gR3LDvMOfZW4vcmVjdWVyZG9zL21laWxsZXVyZXMgc2FsdXRh
dGlvbnMvCmRpc3RpbnRpIHNhbHV0aS9zaW9uZy9kdcOsIHnDui/Qv9GA0LjQstC10YIKCkp1cmdl
bnMgZGUgQnJ1aW4K

Re: [OpenBabel-scripting] [openbabel-scripting] finding different molecules inside a file from python

[Manuel M. F. <man...@gm...>]

Dear Noel,

First thanks so much for your help, It works, it does what I want.

There is a small strange problem, whenever I run my software with the
following file (which contains only one molecule) it breaks
(segmentation fault) in the separate part.

It is not a problem for me, but ...

best regards

Manu



On Nov 6, 2007 10:20 AM, Noel O'Boyle <bao...@gm...> wrote:
> Dear Manuel,
>
> If you look at the documentation for OBMol at:
> http://openbabel.sourceforge.net/api/2.1.0/classOpenBabel_1_1OBMol.shtml#1e5c6955a32c0ec2317a8de12ab7ba5a
> you will see that there is a method called OBMol::Separate() which
> will do exactly what you wish.
>
> For example, given the PDB file below:
> >>> import pybel
> >>> input_molecule = pybel.readfile("pdb", "example.pdb").next()
> >>> separate_mols = input_molecule.OBMol.Separate()
> >>> pybel_mols = [pybel.Molecule(x) for x in separate_mols]
> >>> print pybel_mols[0].atoms[0].coords
> (8.0389999999999997, 5.8680000000000003, 0.49299999999999999)
>
> You can access the second molecule with pybel_mols[1], and you can
> find the number of molecules with len(pybel_mols), etc.
>
> Regards,
>    Noel
>
>
> On 06/11/2007, Manuel Melle Franco <man...@gm...> wrote:
> > Thanks for the prompt answer,
> >
> > Sorry, I guess I am using the wrong terminology here.
> > For instace this  a file containing two molecules of water:
> >
> > An easy input in pdb:
> > HEADER    two water molecules
> > COMPND
> > SOURCE
> > HETATM    1  O     1     1       8.039   5.868   0.493
> > HETATM    2  H     2     1       7.581   5.023   0.404
> > HETATM    3  H     2     1       8.287   6.062  -0.397
> > HETATM    4  O     1     2       0.115  -8.877   6.446
> > HETATM    5  H     2     2       0.959  -8.446   6.405
> > HETATM    6  H     2     2       0.247  -9.794   6.138
> > CONECT    1    2    3
> > CONECT    2    1
> > CONECT    3    1
> > CONECT    4    5    6
> > CONECT    5    4
> > CONECT    6    4
> > END
> >
> >
> > atoms 1 2 3 are part of molecule 1
> > atoms 4 5 6 are part of molecule 2
> >
> > actually now that I think about I could make one file for each
> > molecule and that would
> > solve the problem, since I have  only few molecules in this case. This
> > would not be
> >
> >
> > best regards, and thanks
> >
> > Manu
> >
> > On 11/5/07, Noel O'Boyle <bao...@gm...> wrote:
> > > Can you give an example of your input file? I've never used a file
> > > format containing multiple molecules...
> > >
> > > Noel
> > >
> > > On 05/11/2007, manulinho72 <man...@gm...> wrote:
> > > >
> > > > Dear All,
> > > >
> > > > I am pretty new to openbabel, so hope this is not a too silly question.
> > > >
> > > > I have a file with a number of molecules ( as shown but their connectivity).
> > > >
> > > > I've got an algorithm that tells me how many molecules there are an index
> > > > each atom
> > > > as corresponding to one molecule. However, my system is quite large and in
> > > > python this it is very slow. I could try another algorithm but maybe there
> > > > is something already implemented in the libraries I can try.
> > > >
> > > > The idea is, for instance I have to water molecules, I would get an array
> > > > with values
> > > >
> > > > H1 1
> > > > O1 1
> > > > H1 1
> > > > H2 2
> > > > O2 2
> > > > H2 2
> > > >
> > > > Thanks in advance.
> > > >
> > > > regards
> > > >
> > > > Manu
> > > > --
> > > > View this message in context: http://www.nabble.com/finding-different-molecules-inside-a-file-from-python-tf4752415.html#a13589313
> > > > Sent from the openbabel-scripting mailing list archive at Nabble.com.
> > > >
> > > >
> > > > -------------------------------------------------------------------------
> > > > 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
> > > >
> > >
> >
> >
> > --
> > ____________________________________________________________
> >
> > Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
> > him how he could so freely contradict this week what he had said just
> > last week.  The great man replied that it was because this week he knew
> > better.
> > ____________________________________________________________
> >
> > Manuel Melle-Franco, Ph.D.
> > Dip. di Chimica "G. Ciamician"
> > Universita Di Bologna
> > via Selmi 2, I-40126
> > Bologna, Italy
> > ---------------------------------------------------------
> > Fax   :   +39-051-2099456
> > Phone :  +39-051-2099578 *NEW NUMBER 09/07*
> > ---------------------------------------------------------
> >
>



-- 
____________________________________________________________

Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
him how he could so freely contradict this week what he had said just
last week.  The great man replied that it was because this week he knew
better.
____________________________________________________________

Manuel Melle-Franco, Ph.D.
Dip. di Chimica "G. Ciamician"
Universita Di Bologna
via Selmi 2, I-40126
Bologna, Italy
---------------------------------------------------------
Fax   :   +39-051-2099456
Phone :  +39-051-2099578 *NEW NUMBER 09/07*
---------------------------------------------------------

Re: [OpenBabel-scripting] Surface

[Noel O'B. <bao...@gm...>]
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Re: [OpenBabel-scripting] [openbabel-scripting] finding different molecules inside a file from python

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

Dear Manuel,

If you look at the documentation for OBMol at:
http://openbabel.sourceforge.net/api/2.1.0/classOpenBabel_1_1OBMol.shtml#1e5c6955a32c0ec2317a8de12ab7ba5a
you will see that there is a method called OBMol::Separate() which
will do exactly what you wish.

For example, given the PDB file below:
>>> import pybel
>>> input_molecule = pybel.readfile("pdb", "example.pdb").next()
>>> separate_mols = input_molecule.OBMol.Separate()
>>> pybel_mols = [pybel.Molecule(x) for x in separate_mols]
>>> print pybel_mols[0].atoms[0].coords
(8.0389999999999997, 5.8680000000000003, 0.49299999999999999)

You can access the second molecule with pybel_mols[1], and you can
find the number of molecules with len(pybel_mols), etc.

Regards,
   Noel

On 06/11/2007, Manuel Melle Franco <man...@gm...> wrote:
> Thanks for the prompt answer,
>
> Sorry, I guess I am using the wrong terminology here.
> For instace this  a file containing two molecules of water:
>
> An easy input in pdb:
> HEADER    two water molecules
> COMPND
> SOURCE
> HETATM    1  O     1     1       8.039   5.868   0.493
> HETATM    2  H     2     1       7.581   5.023   0.404
> HETATM    3  H     2     1       8.287   6.062  -0.397
> HETATM    4  O     1     2       0.115  -8.877   6.446
> HETATM    5  H     2     2       0.959  -8.446   6.405
> HETATM    6  H     2     2       0.247  -9.794   6.138
> CONECT    1    2    3
> CONECT    2    1
> CONECT    3    1
> CONECT    4    5    6
> CONECT    5    4
> CONECT    6    4
> END
>
>
> atoms 1 2 3 are part of molecule 1
> atoms 4 5 6 are part of molecule 2
>
> actually now that I think about I could make one file for each
> molecule and that would
> solve the problem, since I have  only few molecules in this case. This
> would not be
>
>
> best regards, and thanks
>
> Manu
>
> On 11/5/07, Noel O'Boyle <bao...@gm...> wrote:
> > Can you give an example of your input file? I've never used a file
> > format containing multiple molecules...
> >
> > Noel
> >
> > On 05/11/2007, manulinho72 <man...@gm...> wrote:
> > >
> > > Dear All,
> > >
> > > I am pretty new to openbabel, so hope this is not a too silly question.
> > >
> > > I have a file with a number of molecules ( as shown but their connectivity).
> > >
> > > I've got an algorithm that tells me how many molecules there are an index
> > > each atom
> > > as corresponding to one molecule. However, my system is quite large and in
> > > python this it is very slow. I could try another algorithm but maybe there
> > > is something already implemented in the libraries I can try.
> > >
> > > The idea is, for instance I have to water molecules, I would get an array
> > > with values
> > >
> > > H1 1
> > > O1 1
> > > H1 1
> > > H2 2
> > > O2 2
> > > H2 2
> > >
> > > Thanks in advance.
> > >
> > > regards
> > >
> > > Manu
> > > --
> > > View this message in context: http://www.nabble.com/finding-different-molecules-inside-a-file-from-python-tf4752415.html#a13589313
> > > Sent from the openbabel-scripting mailing list archive at Nabble.com.
> > >
> > >
> > > -------------------------------------------------------------------------
> > > 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
> > >
> >
>
>
> --
> ____________________________________________________________
>
> Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
> him how he could so freely contradict this week what he had said just
> last week.  The great man replied that it was because this week he knew
> better.
> ____________________________________________________________
>
> Manuel Melle-Franco, Ph.D.
> Dip. di Chimica "G. Ciamician"
> Universita Di Bologna
> via Selmi 2, I-40126
> Bologna, Italy
> ---------------------------------------------------------
> Fax   :   +39-051-2099456
> Phone :  +39-051-2099578 *NEW NUMBER 09/07*
> ---------------------------------------------------------
>

[OpenBabel-scripting] Surface

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

SGkKCkkga25vdyB0aGF0IE9CIGNhbiBjYWxjdWxhdGUgdGhlIFBTQSBvZiBhIG1vbGVjdWxlLiBJ
IHdhcyB3b25kZXJpbmcgaWYgdGhpcwppcyB0aGUgb25seSBzdXJmYWNlIG1lYXN1cmVtZW50IHRo
YXQgY2FuIGJlIGNhbGN1bGF0ZWQuCgpUaGFua3MKCi0tIApSZWdhcmRzL0dyb2V0ZS9NaXQgZnJl
dW5kbGljaGVuIEdyw7zDn2VuL3JlY3VlcmRvcy9tZWlsbGV1cmVzIHNhbHV0YXRpb25zLwpkaXN0
aW50aSBzYWx1dGkvc2lvbmcvZHXDrCB5w7ov0L/RgNC40LLQtdGCCgpKdXJnZW5zIGRlIEJydWlu
Cg==

Re: [OpenBabel-scripting] [openbabel-scripting] finding different molecules inside a file from python

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

Can you give an example of your input file? I've never used a file
format containing multiple molecules...

Noel

On 05/11/2007, manulinho72 <man...@gm...> wrote:
>
> Dear All,
>
> I am pretty new to openbabel, so hope this is not a too silly question.
>
> I have a file with a number of molecules ( as shown but their connectivity).
>
> I've got an algorithm that tells me how many molecules there are an index
> each atom
> as corresponding to one molecule. However, my system is quite large and in
> python this it is very slow. I could try another algorithm but maybe there
> is something already implemented in the libraries I can try.
>
> The idea is, for instance I have to water molecules, I would get an array
> with values
>
> H1 1
> O1 1
> H1 1
> H2 2
> O2 2
> H2 2
>
> Thanks in advance.
>
> regards
>
> Manu
> --
> View this message in context: http://www.nabble.com/finding-different-molecules-inside-a-file-from-python-tf4752415.html#a13589313
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
>
> -------------------------------------------------------------------------
> 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] [openbabel-scripting] finding different molecules inside a file from python

[manulinho72 <man...@gm...>]

Dear All, 

I am pretty new to openbabel, so hope this is not a too silly question. 

I have a file with a number of molecules ( as shown but their connectivity). 

I've got an algorithm that tells me how many molecules there are an index
each atom
as corresponding to one molecule. However, my system is quite large and in
python this it is very slow. I could try another algorithm but maybe there
is something already implemented in the libraries I can try. 

The idea is, for instance I have to water molecules, I would get an array
with values

H1 1
O1 1
H1 1
H2 2
O2 2
H2 2

Thanks in advance. 

regards

Manu
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Re: [OpenBabel-scripting] SMILES

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

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[OpenBabel-scripting] SMILES

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

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Re: [OpenBabel-scripting] distributing python binaries with py2app

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

On Oct 28, 2007, at 1:55 PM, Adam Tenderholt wrote:

> dynamic file format modules to work correctly. Does anyone know where
> these should be copied?

As you might know, I cheat. I install everything Open Babel into /usr/ 
local much like on UNIX. This is even true for Avogadro,  
ChemSpotlight, iBabel, etc. It's arguably a decent solution -- several  
packages all use the same libopenbabel.dylib,

Alternatively, you can always tell Open Babel to look for dynamic file  
formats using BABEL_LIBDIR and BABEL_DATADIR environment variables.

On the Mac, you can create .mpkg files which have multiple install  
packages. See ChemSpotlight or Avogadro packages for an example. You  
can simply re-use my OpenBabel.pkg file. For those of us with OB  
already installed, it will discover it and not bother to re-install.

> way to compile openbabel so that only a couple of supported formats
> are included instead of everything? I really only need XYZ, PDB, and
> MOL.

The easiest way is to use dynamic modules and delete the ones you  
don't want. You can also hack the Makefile.am in src/formats and  
disable some.

Cheers,
-Geoff