2011/1/18 Angel Herráez <[email protected]>: > Just my 2 cents: > >> Evidently, a fair number of PubChem's sdf's have partial charge data. > > I see aproblem here. The format shown in your example is not > according to SDF spec (I think it does not suppor partial charge, > only formal charge).
How so? The file looks fine to me. The partial charges are stored in custom data fields... > So if Jmol is made to support reading that, it is not really SDF > import. That should be made clear. Now, PubChem is that common that it would not be bad to add support for the 'PUBCHEM_MMFF94_PARTIAL_CHARGES' data field... If peope are worried that there will be an explosion of supported common data fields, then it may be an option later to use Jmol script to tell the SD file reader to parse fields as such; something like: set symyxSDreadPropertyAs PUBCHEM_MMFF94_PARTIAL_CHARGES partialCharge (I guess partialCharge will match an existing script keyword reflecting the partial charge, but too lazy right now to look up the exact phrase...) While certainly possible, it is indeed a bit ridiculous to not read these partial charges, and having to use a JS SD files parser for that... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet 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 ------------------------------------------------------------------------------ Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
