[adding the list back to the recipient list]
On Mon, Jan 19, 2015 at 10:02 AM, Naeem Attari <[email protected]>
wrote:
> Can't we derive the bond order and connectivity information from distance
> matrix (which can be derived from coordinates)?
>
Assuming all hydrogens and charges are present in the file, the geometry is
a good one, and the structure is made up of octet-complete atoms from the
"organic subset", getting >90% of the bonds correct is almost certainly
doable without too much effort. The last bit will be problematic. If you
remove any of the above constraints, you're left with a research problem.
Here's a recent publication on the topic:
http://pubs.acs.org/doi/abs/10.1021/ci300358c
This isn't an attempt to discourage you from doing an implementation for
your own purposes, just an explanation of why something that is seemingly
simple is not present in the RDKit.
-greg
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