From: SourceForge.net <no...@so...> - 2009-06-18 22:31:22
|
Bugs item #2808700, was opened at 2009-06-18 18:31 Message generated for change (Tracker Item Submitted) made by gmagoon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None 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. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629 |
From: SourceForge.net <no...@so...> - 2009-06-18 23:11:07
|
Bugs item #2808700, was opened at 2009-06-19 00:31 Message generated for change (Comment added) made by aherraez You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None 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. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2009-06-19 01:11 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 |
From: SourceForge.net <no...@so...> - 2009-06-18 23:34:03
|
Bugs item #2808700, was opened at 2009-06-18 18:31 Message generated for change (Comment added) made by gmagoon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None 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. ---------------------------------------------------------------------- Comment By: Gregory Magoon (gmagoon) Date: 2009-06-18 19:34 Message: Great...in that case it is not an issue, then. My apologies. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2009-06-18 19:11 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 |
From: SourceForge.net <no...@so...> - 2009-06-18 23:34:21
|
Bugs item #2808700, was opened at 2009-06-18 18:31 Message generated for change (Settings changed) made by gmagoon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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. ---------------------------------------------------------------------- Comment By: Gregory Magoon (gmagoon) Date: 2009-06-18 19:34 Message: Great...in that case it is not an issue, then. My apologies. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2009-06-18 19:11 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 |
From: SourceForge.net <no...@so...> - 2009-06-19 04:55:56
|
Bugs item #2808700, was opened at 2009-06-18 17:31 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2808700&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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. ---------------------------------------------------------------------- >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; ---------------------------------------------------------------------- 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 |