Hi,
I’m an OpenBabel newbie so I apologize for this very basic question, but I
can’t seem to find the answer in the documentation or the discussion list
archives.
I’m also not a chemistry expert so that probably doesn’t help.
Does OBIsomorphismMapper consider the atomic numbers of the atoms
PS. As synchronisity would have it, one of my users needed to generate
an SVG from a smiles string (copied from CAS) today and got a "scrambled
egg" depiction similar to what I reported back in June ("Broken svg" posts).
She then found a smiles -> sdf converter online (cactvs), generated an
svg fr
Hi everyone,
Thanks for the suggestions – I realize that by starting with the SMILES string
and not the 3D structure I might have caused some confusion.
My main goal is actually to draw the 2D representation from the 3D structure,
attached again here (I’m a quantum chemist); the SMILES st
Hi,
For carbon monoxyde, try this smile: [C-]#[O+]
Regards,
Pascal
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The H atoms are drawn intentionally. See the docs for the 'a' option:
a draw all carbon atoms
So propane would display as H3C-CH2-CH3
What you want is an additional option that draws the C's but not the
H's. I don't have time now to do development, but it should be pretty
easy to see where o
You can put brackets around the carbon in carbon monoxide and not get the
hydrogen. Otherwise, smiles specifies that carbon must have 4 bonds, so you
need a hydrogen to fill the fourth bond.
Note, you'll probably now have a little dot next to the carbon. I have no
idea how to get rid of that.
On
