[Open Babel] 2D or 3D

[Jochen Schreiber]

Hello guys,

i need a fast answer.

Is the similarity search in babel 2D or 3D?

Greetz,

Jochen Schreiber

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Re: [Open Babel] 2D or 3D

[Maciek Wójcikowski]

Fingerprints are 1D therefore similarity search is 1D. To
my knowledge there is no shape similarity search in OB.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


W dniu 23 kwietnia 2012 09:20 użytkownik Jochen Schreiber <
joc...@googlemail.com> napisał:

> Hello guys,
>
> i need a fast answer.
>
> Is the similarity search in babel 2D or 3D?
>
> Greetz,
>
> Jochen Schreiber
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
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[Open Babel] Energy Minimization of complex of two molecules

[Чугунов Антон]

 Dear Open Babel users, I'm writing a script to reconstruct a complex of two peptides. I employ OB python interface and also Pybel to make necessary transformations of both peptides, but finally I have to perform energy minimization of the whole complex to avoid bumping of side chains.It seems to be possible, since when I load two molecules from one PDB file, OB can optimize them. But here I don't know how to combine two molecules into one object that I could apply energy-minimization routine for the system.Can you help, please?PS. Let's say, molecules are defined as the following:H1 = pybel.readfile('pdb', 'pep1.pdb').next()H2 = pybel.readfile('pdb', 'pep2.pdb').next() 

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Re: [Open Babel] Energy Minimization of complex of two molecules

[Maciek Wójcikowski]

Have you tried "H1 + H2"? Actually this wasn't working for me in perl, but
it's supposed to be working in Python.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


W dniu 23 kwietnia 2012 13:52 użytkownik Чугунов Антон
napisał:

>
> Dear Open Babel users,
> I'm writing a script to reconstruct a complex of two peptides. I employ OB
> python interface and also Pybel to make necessary transformations of both
> peptides, but finally I have to perform energy minimization of the whole
> complex to avoid bumping of side chains.
> It seems to be possible, since when I load two molecules from one PDB
> file, OB can optimize them. But here I don't know how to combine two
> molecules into one object that I could apply energy-minimization routine
> for the system.
> Can you help, please?
>
> PS. Let's say, molecules are defined as the following:
> H1 = pybel.readfile('pdb', 'pep1.pdb').next()
> H2 = pybel.readfile('pdb', 'pep2.pdb').next()
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
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>
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>
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Re: [Open Babel] 2D or 3D

[Geoffrey Hutchison]

> Fingerprints are 1D therefore similarity search is 1D. To my knowledge there 
> is no shape similarity search in OB.

The Spectrophore techniques are shape dependent.
http://openbabel.org/docs/current/Fingerprints/spectrophore.html

-Geoff
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[Open Babel] Tautomer issue

[Jörg Kurt Wegner]

Hi all,

I am trying to get my head around the tautomer function. Here a few issues,
could you help me getting into touch with Tim, or someone else being able
to help with the tautomerization functionality?

First, the canonical tautomer function is less tautomeric than I would wish
for.
The following molecules are not normalized correctly, I get two different
tautomeric versions. Test file and debugging log files are attached.
In both cases I would expect: CC(=O)Cc1c1


Second, the full enumeration is just not working. In the case of NOT
defining "-c" I would expect to get all possible tautomers as defined by
the Functor class
class Functor : public OpenBabel::TautomerFunctor
but I just get one structure all the time? Any clues what goes wrong?

Cheers
/.Joerg
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CC(=O)Cc1c1 
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  --> LeafNode reached...
Change?
8 
D 
  Change 8 to Acceptor
-> Rule 5: Assign 1-2 Double
-> Rule 5: Assign 7-8 Double
-> Rule 4: Assign 2-3 Single
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-> Rule 5: Assign 3-4 Double
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invalid Acceptor/Hybridized 1
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  Backtrack... 8
CC(=Cc1c1)O 


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-> Rule 5: Assi

[Open Babel] libopenbabel.so versions

[Craig James]

I'm (finally) moving to the latest version of OpenBabel.  I discovered
that after compiling, the .so version number is still
libopenbabel.so.4 -- the same name as OpenBabel 2.2.x.  By my
understanding of .so libraries, this means OpenBabel 2.3.1 is 100% ABI
compatible with code compiled against OpenBabel 2.2.x.

Is that right?  (If that's true, it's great news.)

Thanks,
Craig

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Re: [Open Babel] libopenbabel.so versions

[Michael Banck]

Hi,

On Mon, Apr 23, 2012 at 02:11:05PM -0700, Craig James wrote:
> I'm (finally) moving to the latest version of OpenBabel.  I discovered
> that after compiling, the .so version number is still
> libopenbabel.so.4 -- the same name as OpenBabel 2.2.x.  By my
> understanding of .so libraries, this means OpenBabel 2.3.1 is 100% ABI
> compatible with code compiled against OpenBabel 2.2.x.
> 
> Is that right?  (If that's true, it's great news.)

IIRC 2.2.x had libopenbabel.so.3 as SONAME, see e.g.

http://packages.debian.org/search?keywords=libopenbabel3


Cheers,

Michael

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Re: [Open Babel] libopenbabel.so versions

[Craig James]

On Mon, Apr 23, 2012 at 3:20 PM, Michael Banck  wrote:
>> I'm (finally) moving to the latest version of OpenBabel.  I discovered
>> that after compiling, the .so version number is still
>> libopenbabel.so.4 -- the same name as OpenBabel 2.2.x.  By my
>> understanding of .so libraries, this means OpenBabel 2.3.1 is 100% ABI
>> compatible with code compiled against OpenBabel 2.2.x.
>>
>> Is that right?  (If that's true, it's great news.)
>
> IIRC 2.2.x had libopenbabel.so.3 as SONAME, see e.g.
>
> http://packages.debian.org/search?keywords=libopenbabel3

Thanks for the link ... so why is it that my version of OpenBabel
2.2.x uses libopenbabel.4.0.0?  It was a developer's release, not a
stable version.  I guess the .so version must have changed a long time
before the official 2.3.x release.

Thanks,
Craig

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Re: [Open Babel] libopenbabel.so versions

[Michael Banck]

On Mon, Apr 23, 2012 at 03:26:22PM -0700, Craig James wrote:
> On Mon, Apr 23, 2012 at 3:20 PM, Michael Banck  wrote:
> >> I'm (finally) moving to the latest version of OpenBabel.  I discovered
> >> that after compiling, the .so version number is still
> >> libopenbabel.so.4 -- the same name as OpenBabel 2.2.x.  By my
> >> understanding of .so libraries, this means OpenBabel 2.3.1 is 100% ABI
> >> compatible with code compiled against OpenBabel 2.2.x.
> >>
> >> Is that right?  (If that's true, it's great news.)
> >
> > IIRC 2.2.x had libopenbabel.so.3 as SONAME, see e.g.
> >
> > http://packages.debian.org/search?keywords=libopenbabel3
> 
> Thanks for the link ... so why is it that my version of OpenBabel
> 2.2.x uses libopenbabel.4.0.0?  It was a developer's release, not a
> stable version.  I guess the .so version must have changed a long time
> before the official 2.3.x release.

That's it probably.  I believe it is customary to bump the SONAME once
the actual API break occurs.

OpenBabel does not use the odd/even numbering scheme to designate
developer and stable versions, so this complicates things slightly as
the bump has to happen at some point before the major version is
changed/released.


Michael

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