How's this for MOL implementation?
switch (order) {
case 4:
case 6: //1.25 ??
case 7: //1.75 ??
order = JmolAdapter.ORDER_AROMATIC;
break;
case 5:
order = JmolAdapter.ORDER_PARTIAL12;
break;
}
The idea being that those 1.25/1.75 are probably aromatic. Or we could
move 1.25 down to 1 and 1.75 up to 2?
switch (order) {
case 4:
order = JmolAdapter.ORDER_AROMATIC;
break;
case 6: //1.25 ??
order = 1;
break;
case 7: //1.75 ??
order = 2;
break;
case 5:
order = JmolAdapter.ORDER_PARTIAL12;
break;
}
Angel Herraez wrote:
>Bob's and Nick's comments reminded me of a limitation I found out
>this summer: 1,5 order bond order is not recognized from MDL MOL
>files.
>To summarize current state (tested in 11.3.26):
>
>Bond order 0.5:
> "partial" in connect and bondOrder commands
> unavailable in MOL, but could be type 8 ("any"); Jmol already
>renders 8 as partial.
>
>Bond order 1:
> "single"
> type 1 in MOL
>
>Bond order 1.25:
> not implemented in Jmol
> type 6 in MOL, "single/aromatic" [[ I don't think there is need to
>support this ]]
>
>Bond order 1.5:
> "partialDouble"
> type 5 in MOL, but fails in Jmol, no bond is drawn [[ this must be
>fixed, I see it as a bug ]]
>
>Bond order 1.5 also:
> "aromatic"
> type 4 in MOL
>
>Bond order 1.75:
> not implemented in Jmol
> type 7 in MOL, "double/aromatic" [[ I don't think there is need to
>support this]]
>
>Bond order 2:
> "double"
> type 2 in MOL
>
>Bond order 2.5:
> not implemented in Jmol, but requested
> not available in MOL
>
>Bond order 3:
> "triple"
> type 3 in MOL
>
>Bond order 4:
> "quadruple"
> not available in MOL
>
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Splunk Inc.
>Still grepping through log files to find problems? Stop.
>Now Search log events and configuration files using AJAX and a browser.
>Download your FREE copy of Splunk now >> http://get.splunk.com/
>_______________________________________________
>Jmol-users mailing list
>[email protected]
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-------------------------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
