I've wrote short script to replicate that problem.
#!/usr/bin/perl
use Chemistry::OpenBabel;
my $mol1 = new Chemistry::OpenBabel::OBMol;
my $mol2 = new Chemistry::OpenBabel::OBMol;
#my $mol3 = new Chemistry::OpenBabel::OBMol; # should not be necesary
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInFormat("smi");
$obConversion->ReadString($mol1, "C1=CC=CS1");
$obConversion->ReadString($mol2, "CCO");
print "Mol1: ".$mol1->NumAtoms()."\n";
print "Mol2: ".$mol2->NumAtoms()."\n";
$mol3 = $mol2;
print "Mol3 step one: ".$mol3->NumAtoms()."\n";
### there you go
#$mol3 += $mol1; # doesn't work, throws error
$mol3 -> add($mol1); # this does what above should.
###
print "Mol3 step two: ".$mol3->NumAtoms()."\n";
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 28 marca 2012 16:48 użytkownik Noel O'Boyle
<baoille...@gmail.com>napisał:
> Can you provide a short script that reproduces the problem? For
> example, with SMILES strings.
>
> - Noel
>
> On 26 March 2012 11:28, mwojcikowski <mac...@wojcikowski.pl> wrote:
> > I've done some extra testing, when I wanted to write the simplest script
> to
> > recreate that problem. It seams it was my fault, and Setup does work
> > (although the weird error). I found out by the way that += operator on
> OBmol
> > class doesn't work resulting empty value. How would you recommend to
> append
> > ligand to pocket structure in perl instead of:
> > $mol = $mol_pocket;
> > $mol += $mol_ligand;
> > where every variable is initialized OBmol object and both prefixed ones
> are
> > read from files.
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/OBForceField-in-Perl-tp4503052p4505342.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
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