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 string is derived from the 3D structure and I think it’s correct, though I could be wrong about that. This is a more general problem – often I want to draw carbenes, radicals, and isolated atoms from the 3D structure where the hydrogens are there (though the octet rule may not be satisfied) – thus I don’t want the program to interpret the molecules chemically and fill in hydrogens that it thinks is missing. I don’t think the OBMol object is adding any extra atoms because it corresponds to the 3D structure, but when I draw the SVG the extra hydrogens show up. Note that the added unnumbered hydrogens appear as “CH” rather than “C-H”, so they are different from the hydrogens that I explicitly added when creating the OBMol object from the 3D structure. Noel: I do want explicit hydrogens to be displayed, but only the hydrogens that I explicitly have. I don’t want carbon monoxide to be shown as O#CH since my starting point is the CO in the 3D structure. If you could point me to the correct file, I could write the code myself. I’m a bit new to the code base so I might have some questions along the way. Thanks, - Lee-Ping From: Pascal Muller [mailto:pascal.jm.mul...@gmail.com] Sent: Friday, September 26, 2014 3:03 AM Cc: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] SVG draws unwanted extra hydrogens Hi, For carbon monoxyde, try this smile: [C-]#[O+] Regards, Pascal
coords.xyz
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