Bugs item #2808700, was opened at 2009-06-18 17:31
Message generated for change (Comment added) made by hansonr
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Category: File Input/Output
Group: None
Status: Closed
Resolution: Out of Date
Priority: 5
Private: No
Submitted By: Gregory Magoon (gmagoon)
Assigned to: Miguel (migueljmol)
Summary: Partial bonds from CML
Initial Comment:
It seems that certain partial bonds in CML are not rendered by Jmol. In
particular, I have tried CML files with order="partial12", indicating a bond
order between single and double, and Jmol Version 11.6.24 does not display the
bond.
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>Comment By: Bob Hanson (hansonr)
Date: 2009-06-18 23:55
Message:
I reproduce the code from the CML reader here for reference. You will need
to pick one of the options supported. Basically anything that starts with
"P" will be read as "partial12".
int parseBondToken(String str) {
float floatOrder = parseFloat(str);
if (Float.isNaN(floatOrder) && str.length() >= 1) {
str = str.toUpperCase();
switch (str.charAt(0)) {
case 'S':
return JmolAdapter.ORDER_COVALENT_SINGLE;
case 'D':
return JmolAdapter.ORDER_COVALENT_DOUBLE;
case 'T':
return JmolAdapter.ORDER_COVALENT_TRIPLE;
case 'A':
return JmolAdapter.ORDER_AROMATIC;
case 'P':
//TODO: Note, this could be elaborated more specifically
return JmolAdapter.ORDER_PARTIAL12;
}
return parseInt(str);
}
if (floatOrder == 1.5)
return JmolAdapter.ORDER_AROMATIC;
if (floatOrder == 2)
return JmolAdapter.ORDER_COVALENT_DOUBLE;
if (floatOrder == 3)
return JmolAdapter.ORDER_COVALENT_TRIPLE;
return JmolAdapter.ORDER_COVALENT_SINGLE;
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Comment By: Gregory Magoon (gmagoon)
Date: 2009-06-18 18:34
Message:
Great...in that case it is not an issue, then. My apologies.
----------------------------------------------------------------------
Comment By: Angel Herraez (aherraez)
Date: 2009-06-18 18:11
Message:
'partial12' was implemented in Jmol 11.7.32
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629
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