Re: [Open Babel] File conversion adds unwanted hydrogens

2014-03-03 Thread Tim Vandermeersch
Hi, While testing the changes to correctly canonicalize multi-fragment SMILES, I noticed the same problem and it seems to only occur for multi-fragment molecules. I reported this on the openbabel-devel mailing list with title "More multi-fragment canonical SMILES tests". I'm not sure where things

[Open Babel] File conversion adds unwanted hydrogens

2014-03-01 Thread Lee-Ping Wang
Hi there,I'm converting some molecules to 2D format, and some of them are extremely small and/or uncommon in normal chemistry (e.g. nitrogen atoms).  I'm running into an issue where sometimes it automatically adds hydrogen atoms.  For example, I have a reaction where NH is split into N and H atoms,