Turn off wedge and hash bonds

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Turn off wedge and hash bonds

Samo Lešnik
I am using obabel to create a number of 2D depictions of molecules. However, I don't want to display wedge and hash bond (only general single bonds).

An example of my command is:

obabel input.pdb  --gen2d -d -O output.svg -xd.

So how would I be able to turn of wedges and hashed?


Regards.

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Re: Turn off wedge and hash bonds

Noel O'Boyle
Administrator
Apart from editing the source code, you could generate SMILES with the
"i" option (see "obabel -Hsmi") to remove chiral symbols.
Alternatively, you could write a script to remove the stereochemistry
programmatically after reading it in from the PDB file.

By the way, try to avoid PDB files if possible.

Regards,
- Noel

On 3 February 2017 at 13:03, Samo Lešnik <[hidden email]> wrote:

> I am using obabel to create a number of 2D depictions of molecules. However,
> I don't want to display wedge and hash bond (only general single bonds).
>
> An example of my command is:
>
> obabel input.pdb  --gen2d -d -O output.svg -xd.
>
> So how would I be able to turn of wedges and hashed?
>
>
> Regards.
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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