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 option 'a' is in the C++ code and add a new option
to do as you suggest. Perhaps you, or someone else reading this, would
like to try this.
- Noel
On 26 September 2014 04:34, Lee-Ping Wang <leep...@stanford.edu> wrote:
> Hi there,
>
> I'm using the Python interface to OpenBabel to create 2D representations of
> my molecules. I'm having a great time except when it decides to draw extra
> hydrogens. I'm quite sure these hydrogens are not supposed to be drawn. In
> the attached image, the "CH" on carbon monoxide is not numbered; I think this
> means it's not explicitly represented in the OBMol object, but the SVG writer
> decides to draw it anyway. In the SVG file, the text comes out as "CH" in a
> single element.
>
> I've tried almost all combinations of add/delete, implicit/explicit hydrogens
> in the input and output options. If I set {"C":True} in write(), it won't
> draw the "CH" on carbon monoxide - in fact it doesn't draw any atoms to the
> right of the triple bond, but I do want it to draw "C". I could just edit
> the .svg file manually, but that's probably not the best solution.
>
> Generally speaking, all I want is for OpenBabel to draw exactly the same
> atoms that I gave it! :)
>
> In [1]: import pybel
> In [2]: mol = pybel.readfile('can', 'can.txt', opt={"h":True})
> In [3]: mol.next().write("svg", "can.svg", opt={"a":True,"P":600,"i":True},
> overwrite=True)
>
> Thanks,
>
> - Lee-Ping
>
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