Hens wrote: >>Q: Is there value in having this column support 'partialCharge' in >>addition to 'formalCharge'? >> > There is, if we are ever going to make use of it, as in calculating and > displaying ESP coloured surfaces.
Jmol uses this value today. One can say 'color atoms partialCharge' or 'color atoms formalCharge' At this point I cannot remember which file formats support which types of charges. > What about the partial charges listed in CML files, are they read and > stored somewhere? Yes, they are read and used. CML may be one of the few formats that supports both formal charge and partial charge. The CML spec defines 'formalCharge'. Egon defined "jmol:charge" for partial charge. >>Q: Please confirm that the range of values for partial charges is > -1 && >> < 1 >> >> > Partial charges depend on the method to calculate them. > Among the many methods there is one, AIM, that sometimes produces > partial charges larger than 1. > (Which is why organic chemists distrust AIM). The internals of the jmol code assume that partial charge is in the range -1 .. 1 I believe that values outside that range get clamped to either -1 or 1 >>Q: Please confirm that I could use the following algorithm to distinguish >>between partial charge and formal charge for the 'charge' value in (for >>example) an XYZ file: >> >> if (value > -1 && value < 1) >> partial charge >> else if (value is an integer value >= -4 && <= 7) >> formal charge >> else >> error >> >> >> > In 99+ % of the cases this would work; see remark above. OK. Q: Please confirm that if I put in support for partial charges in the range (-1 < partialCharge < 1) inside the XyzReader then you will test and use this capability. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
