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
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
Hi,
For carbon monoxyde, try this smile: [C-]#[O+]
Regards,
Pascal
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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
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,
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
