Sorry, I thought I was clear about this. You could, in principal change the
maximum number of bonds in data/elements.txt (e.g. that you want to allow up to
3 bonds to an oxygen).
ConnectTheDots would respect this.
But I don’t think it’s a good general idea, because you’d frequently get
spuriou
On 11/01/16 16:56, Geoffrey Hutchison wrote:
>> for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB
>> does detect all bonds.
>
> I would assume you mean “does not” detect all bonds.
Indeed.
>
> The maximum number of bonds for a particular element is defined in
> data/elements.t
> for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB
> does detect all bonds.
I would assume you mean “does not” detect all bonds.
The maximum number of bonds for a particular element is defined in
data/elements.txt (i.e. OBElement::MaxBonds()
http://openbabel.org/dev-api/c
On 11/01/16 15:42, Craig James wrote:
> It would be helpful if you could be very specific. Are you reading a
> file, or creating a molecule via a C++ program? What sort of output are
> you looking at, a particular file (like SMILES, SDF, or PDB)? The best
> way is to give a concrete example with sa
It would be helpful if you could be very specific. Are you reading a file,
or creating a molecule via a C++ program? What sort of output are you
looking at, a particular file (like SMILES, SDF, or PDB)? The best way is
to give a concrete example with sample files that will allow others to
repeat yo
Hi,
for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB
does detect all bonds. Is this determined by input files (like
bondtyp.txt) or by the code itself? Suggestions for how I can fix it?
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Bio
