Below is a test program, highly stripped down, that illustrates a problem I
can't figure out. The idea is to find ions that are neutral and show them
with a charge (don't worry about the chemistry behind this; this is highly
stripped down from the real code and just illustrates the
I haven't looked into the details of your code (but I will if no-one
else does), but regarding the relationship between different things,
you may find the following notes I have made useful:
In the Open Babel world, the valence methods of an atom refer to the
number of bonds, rather than the sum
Sorry - irrespective of the issue here, I should add that I have some
code that fixes the overall handling of implicit valence for SMILES
reading and writing. I'll check it into a git branch (but it's not
ready for production as it requires a rejigging of the kekulization
code). In short, we
Noel - Thanks for all the feedback/info. I have to head home and the next
two days are going to be crazy with some personal business I have to attend
to, but I'll try to get the info you requested. The real key here that I
can't figure out is why B, Al, and Si behave differently from the other
One more detail: It's nothing to do with SMILES, because it does the exact
same thing if I modify the program to read SD files.
Craig
On Tue, Mar 19, 2013 at 3:12 PM, Noel O'Boyle baoille...@gmail.com wrote:
I haven't looked into the details of your code (but I will if no-one
else does), but
Here's another very simple test program. It starts with [AlH3], delete the
hydrogens, then adds hydrogens back one by one. It will never print less
than three hydrogens, but will print correctly once you exceed the original
three hydrogens. A program is attached below; here is its output.
