Yes, I understand that. I think the original workflow was first to
establish the bonds ("single" by default) and then use valency information
and hoping that the structure makes sense (no hydrogens missing), etc. The
book has a follow up section on that second step. But I agree with your
doubt
On Jan 20, 2021, at 07:37, Egon Willighagen wrote:
> Jmol had code to deduce bonds (for files which only have coordinates and no
> bond info, like XYZ), which was ported at some point to the CDK. Here's some
> example code: https://egonw.github.io/cdkbook/missing.html#reconnecting-atoms
Thanks
On Tue, Jan 19, 2021 at 11:50 PM Andrew Dalke
wrote:
> BTW, I had to drop support for some of the formats, like XYZ and PDB,
> because I couldn't figure out how to use them to read a structure into a
> form that could be use to generate fingerprints. If anyone needs them and
> can tell me how to
Hi all,
I've just release chemfp-3.5b1 with more complete support for CDK in chemfp.
I'm looking for friendly users to try it out and provide feedback.
For installation directions see
https://chemfp.com/chemfp-35b1-is-available.html .
Most of the additional work since the experimental
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