1. When converting a sdf file (see attached) for carbon monoxide to smi The SDF says it came through Open Babel.. presumably from some other format. It gives formal charges: M CHG 2 1 -1 2 1 This gives a -1 charge to the carbon and +1 to the oxygen:  Certainly the SMILES has an issue (why it protonated the oxygen) — the current development version gives: [C-]#[O+] 2. Hydrogens are inserted when converting the smiles P#P for the Indeed, there's clearly an issue with the valence for triple-bonded phosphorous. There's no case for this in OB's atom typing, so it falls back to an implicit valence of 3 (i.e., one connection to the P plus 2 hydrogens). You can correct this by adding the following line to the atomtyp.txt file: IMPVAL [$([#15]#*)] 1 # for P#P -Geoff |
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