From: SourceForge.net <no...@so...> - 2003-02-25 12:55:55
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Bugs item #692871, was opened at 2003-02-25 14:05 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 Category: org.openscience.cdk.renderer Group: None Status: Open Resolution: None Priority: 5 Submitted By: Stefan Kuhn (shk3) Assigned to: Nobody/Anonymous (nobody) Summary: Strange behaviour of Renderer2D with Hs Initial Comment: If I render the same molecule with Renderer2D with the implicit Hs as explicit atoms the result looks strange. The molecule I used was the following without Hs (as mdl): 10 10 0 0 0 0 0 0 0 0 1 V2000 42.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49.0000 13.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 0 0 6 4 1 0 0 0 0 6 5 1 0 0 0 0 7 1 1 0 0 0 0 7 4 1 0 0 0 0 8 1 1 0 0 0 0 9 2 1 0 0 0 0 9 3 1 0 0 0 0 9 8 1 0 0 0 0 10 1 2 0 0 0 0 M END All works fine. The same with Hs: 23 23 0 0 0 0 0 0 0 0 1 V2000 42.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49.0000 13.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 0 0 6 4 1 0 0 0 0 6 5 1 0 0 0 0 7 1 1 0 0 0 0 7 4 1 0 0 0 0 8 1 1 0 0 0 0 9 2 1 0 0 0 0 9 3 1 0 0 0 0 9 8 1 0 0 0 0 10 1 2 0 0 0 0 2 11 1 0 0 0 0 2 12 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 3 15 1 0 0 0 0 3 16 1 0 0 0 0 4 17 1 0 0 0 0 5 18 1 0 0 0 0 5 19 1 0 0 0 0 6 20 1 0 0 0 0 6 21 1 0 0 0 0 7 22 1 0 0 0 0 8 23 1 0 0 0 0 M END and the result gets bad looking. Notice that the coordinates for the Hs are the same as for their "parent" atom, but this should just lead to atoms painted at the same place. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 |
From: SourceForge.net <no...@so...> - 2003-08-29 08:36:51
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Bugs item #692871, was opened at 2003-02-25 14:05 Message generated for change (Settings changed) made by steinbeck You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 Category: org.openscience.cdk.renderer Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Stefan Kuhn (shk3) >Assigned to: Christoph Steinbeck (steinbeck) Summary: Strange behaviour of Renderer2D with Hs Initial Comment: If I render the same molecule with Renderer2D with the implicit Hs as explicit atoms the result looks strange. The molecule I used was the following without Hs (as mdl): 10 10 0 0 0 0 0 0 0 0 1 V2000 42.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49.0000 13.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 0 0 6 4 1 0 0 0 0 6 5 1 0 0 0 0 7 1 1 0 0 0 0 7 4 1 0 0 0 0 8 1 1 0 0 0 0 9 2 1 0 0 0 0 9 3 1 0 0 0 0 9 8 1 0 0 0 0 10 1 2 0 0 0 0 M END All works fine. The same with Hs: 23 23 0 0 0 0 0 0 0 0 1 V2000 42.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49.0000 13.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 0 0 6 4 1 0 0 0 0 6 5 1 0 0 0 0 7 1 1 0 0 0 0 7 4 1 0 0 0 0 8 1 1 0 0 0 0 9 2 1 0 0 0 0 9 3 1 0 0 0 0 9 8 1 0 0 0 0 10 1 2 0 0 0 0 2 11 1 0 0 0 0 2 12 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 3 15 1 0 0 0 0 3 16 1 0 0 0 0 4 17 1 0 0 0 0 5 18 1 0 0 0 0 5 19 1 0 0 0 0 6 20 1 0 0 0 0 6 21 1 0 0 0 0 7 22 1 0 0 0 0 8 23 1 0 0 0 0 M END and the result gets bad looking. Notice that the coordinates for the Hs are the same as for their "parent" atom, but this should just lead to atoms painted at the same place. ---------------------------------------------------------------------- >Comment By: Christoph Steinbeck (steinbeck) Date: 2003-08-29 10:36 Message: Logged In: YES user_id=54358 This bug has become obsolete with the new working version of HydrogenPlacer. If you have a 2D model with coordinates without hydrogens, you can simply use the HydrogenAdder.addExplicitHydrogensToSatisfyValency(Molecule molecule) to get hydrogens added to the molecule and have them layouted. If you have a molecule without coordinates and hydrogens, make a layout of it and then use HydrogenAdder.addExplicitHydrogensToSatisfyValency(Molecule molecule). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 |
From: SourceForge.net <no...@so...> - 2003-08-29 08:57:39
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Bugs item #692871, was opened at 2003-02-25 14:05 Message generated for change (Comment added) made by steinbeck You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 Category: org.openscience.cdk.renderer Group: None Status: Closed Resolution: Fixed Priority: 5 Submitted By: Stefan Kuhn (shk3) Assigned to: Christoph Steinbeck (steinbeck) Summary: Strange behaviour of Renderer2D with Hs Initial Comment: If I render the same molecule with Renderer2D with the implicit Hs as explicit atoms the result looks strange. The molecule I used was the following without Hs (as mdl): 10 10 0 0 0 0 0 0 0 0 1 V2000 42.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49.0000 13.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 0 0 6 4 1 0 0 0 0 6 5 1 0 0 0 0 7 1 1 0 0 0 0 7 4 1 0 0 0 0 8 1 1 0 0 0 0 9 2 1 0 0 0 0 9 3 1 0 0 0 0 9 8 1 0 0 0 0 10 1 2 0 0 0 0 M END All works fine. The same with Hs: 23 23 0 0 0 0 0 0 0 0 1 V2000 42.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0000 7.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49.0000 13.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 3.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 10.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 65.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 79.0000 12.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 53.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 31.0000 7.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 0 0 6 4 1 0 0 0 0 6 5 1 0 0 0 0 7 1 1 0 0 0 0 7 4 1 0 0 0 0 8 1 1 0 0 0 0 9 2 1 0 0 0 0 9 3 1 0 0 0 0 9 8 1 0 0 0 0 10 1 2 0 0 0 0 2 11 1 0 0 0 0 2 12 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 3 15 1 0 0 0 0 3 16 1 0 0 0 0 4 17 1 0 0 0 0 5 18 1 0 0 0 0 5 19 1 0 0 0 0 6 20 1 0 0 0 0 6 21 1 0 0 0 0 7 22 1 0 0 0 0 8 23 1 0 0 0 0 M END and the result gets bad looking. Notice that the coordinates for the Hs are the same as for their "parent" atom, but this should just lead to atoms painted at the same place. ---------------------------------------------------------------------- >Comment By: Christoph Steinbeck (steinbeck) Date: 2003-08-29 10:57 Message: Logged In: YES user_id=54358 Here is a screenshot of the behavious of the fix, based on the orignal example given in the bug report. Please note that the bad layout at the N is another bug :-) ---------------------------------------------------------------------- Comment By: Christoph Steinbeck (steinbeck) Date: 2003-08-29 10:36 Message: Logged In: YES user_id=54358 This bug has become obsolete with the new working version of HydrogenPlacer. If you have a 2D model with coordinates without hydrogens, you can simply use the HydrogenAdder.addExplicitHydrogensToSatisfyValency(Molecule molecule) to get hydrogens added to the molecule and have them layouted. If you have a molecule without coordinates and hydrogens, make a layout of it and then use HydrogenAdder.addExplicitHydrogensToSatisfyValency(Molecule molecule). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 |
From: Egon W. <el...@ca...> - 2003-02-25 13:38:49
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On Tuesday 25 February 2003 1:05 pm, SourceForge.net wrote: > Bugs item #692871, was opened at 2003-02-25 14:05 > You can respond by visiting: > https://sf.net/tracker/?func=detail&atid=120024&aid=692871&group_id=20024 > > Submitted By: Stefan Kuhn (shk3) > Summary: Strange behaviour of Renderer2D with Hs > > Initial Comment: > If I render the same molecule with Renderer2D with the > implicit Hs as explicit atoms the result looks strange. > The molecule I used was the following without Hs (as mdl): <snip> > All works fine. The same with Hs: <snip> > and the result gets bad looking. Notice that the > coordinates for the Hs are the same as for their > "parent" atom, but this should just lead to atoms > painted at the same place. The feature causing this is the fact that the hydrogen adder should not generate new coordinates... that is done with the layout engine... Therefore, it is not a bug but a feature... Agreed? Egon |