I have what may be a simple question. I'm taking the 2D molfile for Naproxen:
[cid:image001.png@01CD5F96.2CB3DAD0] When I convert this to a 3D molfile with "add explicit H" checked in the OpenBabel GUI or I try the same in code the OH seems to become O- (O with a negative charge). Even if I use Cheshire to sprout explicit H everywhere necessary first, including the OH abbreviation I still get an O- in the resulting 3D molfile from OpenBabel: [cid:image002.png@01CD5F96.2CB3DAD0] Do you know why that is and how I can prevent it? A customer of yours and ours has seen the Draw add-ins I have written with other 3D geometry calculators and asked if I could do this with OpenBabel and I'm almost there. Best Regards, James [cid:image003.jpg@01CD5F96.2CB3DAD0] James Jack PhD. Principal Solutions Architect, ELM Solution Architects Team Accelrys Ltd 7 Hill Rise, Measham, Swadlincote, DE12 7NZ, United Kingdom Mobile: 07590258058 Home Office: 01530 220906 Smarter Science. Better Business. Stay Connected with Accelrys and the Scientific & Engineering Community Website<http://accelrys.com/> | Communities<https://community.accelrys.com/> | Blog<http://blog.accelrys.com/> | Twitter<http://twitter.com/accelrys> | LinkedIn<http://www.linkedin.com/companies/accelrys> | Facebook<http://www.facebook.com/Accelrys> ________________________________ Accelrys Limited (http://accelrys.com) Registered office: 334 Cambridge Science Park, Cambridge, CB4 0WN, UK Registered in England: 2326316
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