From: SourceForge.net <no...@so...> - 2003-09-30 16:39:30
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Feature Requests item #815253, was opened at 2003-09-30 16:39 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 Category: cdk.render Group: None Status: Open Priority: 5 Submitted By: Anatoli Krassavine (akrassavine) Assigned to: Nobody/Anonymous (nobody) Summary: An utility to convert aromatic bonds into Kekule structure Initial Comment: It will be useful to have a static library to assign alternating single and double bond orders to bonds within a given aromatic molecular entity (such as naphthalene or phananthrene). The utility should retain aromaticity flag and simply tweak bond orders on relevant bonds. The situation is especially relevant if the original data came from SMILES with aromaticity specified. Example: If I load a fused ring structure from SMILES c1cccc(cccc2)c12 (naphthalene), I want to force correct allocation on double bonds on it. Notes: 1) This functionality is a complimentary functionality to explicit aromatic bond depiction - it does not replace it. I also appreciate that this is less useful for editor, but much more useful for renderer. 2) The library should operate on the whole molecule. 3)The method should throw exception if single/double bonds cannot be meaningfully assigned. 4) In most cases several equivalent Kekule structures could be generated for any specific aromatic system. The library is not expected to make any guarantees about which of the equivalent structures will be generated - just produce the first legal one. 5) the method should override any existing single/double bonds flags for the bonds affected (it could be made conditional). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 |
From: SourceForge.net <no...@so...> - 2004-01-20 15:20:24
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Feature Requests item #815253, was opened at 2003-09-30 18:39 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 >Category: None Group: None Status: Open Priority: 5 Submitted By: Anatoli Krassavine (akrassavine) >Assigned to: Egon Willighagen (egonw) Summary: An utility to convert aromatic bonds into Kekule structure Initial Comment: It will be useful to have a static library to assign alternating single and double bond orders to bonds within a given aromatic molecular entity (such as naphthalene or phananthrene). The utility should retain aromaticity flag and simply tweak bond orders on relevant bonds. The situation is especially relevant if the original data came from SMILES with aromaticity specified. Example: If I load a fused ring structure from SMILES c1cccc(cccc2)c12 (naphthalene), I want to force correct allocation on double bonds on it. Notes: 1) This functionality is a complimentary functionality to explicit aromatic bond depiction - it does not replace it. I also appreciate that this is less useful for editor, but much more useful for renderer. 2) The library should operate on the whole molecule. 3)The method should throw exception if single/double bonds cannot be meaningfully assigned. 4) In most cases several equivalent Kekule structures could be generated for any specific aromatic system. The library is not expected to make any guarantees about which of the equivalent structures will be generated - just produce the first legal one. 5) the method should override any existing single/double bonds flags for the bonds affected (it could be made conditional). ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2004-01-20 16:20 Message: Logged In: YES user_id=25678 This can be achieved using the cdk.tools.SaturationChecker.saturate() which adjusts the bond orders for a molecule. So, it's a two step process: 1. set aromatic bonds to order 1 2. run the SaturationChecker.saturate() on the molecule ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 |
From: SourceForge.net <no...@so...> - 2004-02-24 12:24:23
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Feature Requests item #815253, was opened at 2003-09-30 18:39 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 Category: None Group: None Status: Open Priority: 5 Submitted By: Anatoli Krassavine (akrassavine) >Assigned to: Nobody/Anonymous (nobody) Summary: An utility to convert aromatic bonds into Kekule structure Initial Comment: It will be useful to have a static library to assign alternating single and double bond orders to bonds within a given aromatic molecular entity (such as naphthalene or phananthrene). The utility should retain aromaticity flag and simply tweak bond orders on relevant bonds. The situation is especially relevant if the original data came from SMILES with aromaticity specified. Example: If I load a fused ring structure from SMILES c1cccc(cccc2)c12 (naphthalene), I want to force correct allocation on double bonds on it. Notes: 1) This functionality is a complimentary functionality to explicit aromatic bond depiction - it does not replace it. I also appreciate that this is less useful for editor, but much more useful for renderer. 2) The library should operate on the whole molecule. 3)The method should throw exception if single/double bonds cannot be meaningfully assigned. 4) In most cases several equivalent Kekule structures could be generated for any specific aromatic system. The library is not expected to make any guarantees about which of the equivalent structures will be generated - just produce the first legal one. 5) the method should override any existing single/double bonds flags for the bonds affected (it could be made conditional). ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2004-02-24 13:13 Message: Logged In: YES user_id=25678 Don't have time any soon. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2004-01-20 16:20 Message: Logged In: YES user_id=25678 This can be achieved using the cdk.tools.SaturationChecker.saturate() which adjusts the bond orders for a molecule. So, it's a two step process: 1. set aromatic bonds to order 1 2. run the SaturationChecker.saturate() on the molecule ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 |
From: SourceForge.net <no...@so...> - 2004-05-27 17:35:06
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Feature Requests item #815253, was opened at 2003-09-30 18:39 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 >Category: cdk.tools Group: None >Status: Closed Priority: 5 Submitted By: Anatoli Krassavine (akrassavine) >Assigned to: Egon Willighagen (egonw) Summary: An utility to convert aromatic bonds into Kekule structure Initial Comment: It will be useful to have a static library to assign alternating single and double bond orders to bonds within a given aromatic molecular entity (such as naphthalene or phananthrene). The utility should retain aromaticity flag and simply tweak bond orders on relevant bonds. The situation is especially relevant if the original data came from SMILES with aromaticity specified. Example: If I load a fused ring structure from SMILES c1cccc(cccc2)c12 (naphthalene), I want to force correct allocation on double bonds on it. Notes: 1) This functionality is a complimentary functionality to explicit aromatic bond depiction - it does not replace it. I also appreciate that this is less useful for editor, but much more useful for renderer. 2) The library should operate on the whole molecule. 3)The method should throw exception if single/double bonds cannot be meaningfully assigned. 4) In most cases several equivalent Kekule structures could be generated for any specific aromatic system. The library is not expected to make any guarantees about which of the equivalent structures will be generated - just produce the first legal one. 5) the method should override any existing single/double bonds flags for the bonds affected (it could be made conditional). ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2004-05-27 19:35 Message: Logged In: YES user_id=25678 Use the mechanism described at 2004-01-20 16:20, and also check the ValencyChecker.saturate() method. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2004-02-24 13:13 Message: Logged In: YES user_id=25678 Don't have time any soon. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2004-01-20 16:20 Message: Logged In: YES user_id=25678 This can be achieved using the cdk.tools.SaturationChecker.saturate() which adjusts the bond orders for a molecule. So, it's a two step process: 1. set aromatic bonds to order 1 2. run the SaturationChecker.saturate() on the molecule ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=370024&aid=815253&group_id=20024 |