C , 2012-06-07 11:04 -0700, Craig James rakstīja:
> On Thu, Jun 7, 2012 at 8:29 AM, My Th wrote:
> Now I got to the real culprits of this issue - previousState and
> previousBondState. They are vectors of integers holding the state of
> each atom and bond in molecule at the beg
C , 2012-06-07 12:02 -0400, Geoffrey Hutchison rakstīja:
> > +size_t idx1 = mol->GetBond(bond_idx)->GetBeginAtom()->GetIdx();
> > +size_t idx2 = mol->GetBond(bond_idx)->GetEndAtom()->GetIdx();
> >
> > Still crashed for default max stack size. I'm not sure if this kind of
> > optimization i
On Thu, Jun 7, 2012 at 8:29 AM, My Th wrote:
> Hi!
>
> I was looking at bug #3508648 and it turns out that it segfaults in
> expandKekulize() due to stack overflow. The routine in question uses
> recursive algorithm to assign bond orders for aromatic systems. For
> large molecules (1bxr has almos
> +size_t idx1 = mol->GetBond(bond_idx)->GetBeginAtom()->GetIdx();
> +size_t idx2 = mol->GetBond(bond_idx)->GetEndAtom()->GetIdx();
>
> Still crashed for default max stack size. I'm not sure if this kind of
> optimization is useful at all since compiler should realize that bond,
> atom1 an
Hi!
I was looking at bug #3508648 and it turns out that it segfaults in
expandKekulize() due to stack overflow. The routine in question uses
recursive algorithm to assign bond orders for aromatic systems. For
large molecules (1bxr has almost 50k atoms) it means that the stack can
grow quite a bit
nevermind...
I succeded modifying the method signature in openbabel-java.cpp from
SWIGEXPORT void JNICALL
Java_org_openbabel_openbabel_1javaJNI_OBAtom_1SetType
to
SWIGEXPORT void JNICALL
Java_org_openbabel_openbabel_1javaJNI_OBAtom_1SetType_1_1SWIG_10
mimicking other methods that present overlo
I compiled the JNI binding following the instructions (with some
modification) on linux and everything is working fine, except this single
command: SetType in OBAtom, that gives the following error:
Exception in thread "main" java.lang.UnsatisfiedLinkError:
org.openbabel.openbabel_javaJNI.OBAtom_
