Well I'm not quite sure what the issue is to be honest (also not very sure if
this fix will even work, so thought it best to ask).
The work round is:
ROMol *tempMol= static_cast<ROMol *>(new RWMol(mol));
tempMol = MolOps::addHs(*tempMol);
mol = static_cast<RWMol>(*tempMol);
However this is returning an error at the compilation:
Undefined symbols for architecture x86_64:
"RDKit::ROMol::operator=(RDKit::ROMol const&)", referenced from:
RDKit::RWMol::operator=(RDKit::RWMol const&)in ccnK7Flz.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
And I can't think why I'm getting this error, I'm 90% sure I've included all
the correct libraries and linked them.
Best,
Nick
Nicholas Firth, Ph.D. Student
Institute of Cancer Research
15 Cotswold Road
Belmont
Surrey
SM2 5NG
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On 6 Jun 2012, at 12:42, Paul Emsley wrote:
On 06/06/12 13:37, Paul Emsley wrote:
On 06/06/12 12:27, Nicholas Firth wrote:
Hi All,
I'm having some issues with getting some more 'interesting' ring systems to
kekulize. I'm creating the molecule in RDKit by individually adding all the
atoms and bonds from a graph. However I have found similar issue when trying to
initialise a molecule from smiles.
Two examples of molecules which won't kekulize are:
n1nnnn1
c1cccp1
however, when adding hydrogens to these smiles, so
n1n[nH]nn1
c1ccc[pH]1
These will work perfectly fine. This is a problem as the graph structure I have
does not include any hydrogens. For a fix I have tried to addHs to my molecule,
however I'm having issue with these functions because I'm writing in C++ and
want to return this value, so don't have any pointers as this results in a
memory leak.
I guess I'm missing something. addHs() returns an ROMol - it is not clear to me
why that gives you pointer issues/problems.
Argh. Just missed the Cancel Button in time.
Yes, ROMol does indeed return a pointer. Why does that cause a problem? I
guess we need to look at the details...?
Paul.
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