[Open Babel] 2D or 3D

2012-04-23 Thread Jochen Schreiber
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. Monitor Your

[Open Babel] Energy Minimization of complex of two molecules

2012-04-23 Thread 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

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

2012-04-23 Thread 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 batc...@yandex.runapisał: Dear Open Babel users,

Re: [Open Babel] 2D or 3D

2012-04-23 Thread 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

[Open Babel] Tautomer issue

2012-04-23 Thread 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

[Open Babel] libopenbabel.so versions

2012-04-23 Thread 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

Re: [Open Babel] libopenbabel.so versions

2012-04-23 Thread Craig James
On Mon, Apr 23, 2012 at 3:20 PM, Michael Banck mba...@gmx.net 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

Re: [Open Babel] libopenbabel.so versions

2012-04-23 Thread 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 mba...@gmx.net 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