With the 2.3.1 release and using obabel instead babel, the problem persists.
Best regards.
> Hello, is available an example about how to process pdqt files using a dlg
> input file
>
> babel -L pdbqt
> One of the formats
> pdbqt -- Autodock Protein Data Bank
> (...)
> d Input file is in dlg (d
I'm agree to what is said above: calculating molecular similarity basing on
SMILES alignment is not a good idea. A so better alternative, already
explored by several researcher is the "lingo method", which can accurately
calculate molecular similarity with SMILES, but it's not based on an
alignment
Hi guys,
I've a problem using the last Open Babel 2.3.1 in an GNU/Linux ubuntu OS.
When I convert an sdf file to a mol2 (or whatever other format) using the
"--partialcharge gasteiger" option, I obtain molecules with wrong partial
charges.
case A) obabel -isdf mols_charged.sdf -omol2 --partialcha
That may not be of much help, but the same happens to me with Java bindings and
the provided OBTest.java snippet.
OBConversion c = new OBConversion();
OBMol mol = new OBMol();
System.out.println("Mol: "+mol);
System.out.println(c.SetInFormat("SMILES"));
System.out.println(c.ReadStrin
Hi Geoff,
thank you very much, that was actually the problem, now the OBForceField object
is set. Sadly, I encountered a new problem: I have OpenBabel installed locally
so I did the following:
export BABEL_DATADIR=/home/aklenner/workspace/openBabel/openbabel-2.3.1/data/
export BABEL_LIBDIR=/hom
Hello OB Team, I am trying to use OpenBabel with Perl bindings in my project. OpenBabel compiled fine, and Perl bindings seem to work. Scripts which create molecules atom by atom work as expected. However, we have a problem when trying to use obConversion. I have tried to use obConversion in differ
