Hi Eric, On Wed, Dec 21, 2011 at 9:30 PM, Eric Jang <[email protected]> wrote: > How are formal charges calculated for atom containers in CDK? Where can I > find the iterative algorithm?
At this moment, not really... practically, the atom type perception takes care of that, but not quite... atom types have associated formal charges, but without that set, the right atom type will not be recognized... it depends a bit on the input, but what I have been doing in the past is when no atom type is perceived (e.g. for a neutral four-coordinate nitrogen) is to increase/decrease the charge by one, and try again... But this was rather ad hoc, and just for those nitrogens... we recently discussed this (on the list?), and I am not sure how well this scales to any element and to any charge. Algorithmically this can be done, but we would need to run a good test to see what the false 'charge' rate is... Community, comments please... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
