From: <no...@so...> - 2002-11-22 18:46:14
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Bugs item #642456, was opened at 2002-11-22 18:46 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 Category: None Group: None Status: Open Resolution: None Priority: 5 Submitted By: Peter Murray-Rust (petermr) Assigned to: Nobody/Anonymous (nobody) Summary: IChI reader does not map atoms Initial Comment: The IChI reader (V1.3) does not appear to read the <atom.orig-nbr> element so that atoms in the final structure are garbled. This means that IChI does not output correct connection tables. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 |
From: <no...@so...> - 2002-11-22 19:59:35
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Bugs item #642456, was opened at 2002-11-22 19:46 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 >Category: org.openscience.cdk.io Group: None Status: Open Resolution: None Priority: 5 Submitted By: Peter Murray-Rust (petermr) >Assigned to: Egon Willighagen (egonw) Summary: IChI reader does not map atoms Initial Comment: The IChI reader (V1.3) does not appear to read the <atom.orig-nbr> element so that atoms in the final structure are garbled. This means that IChI does not output correct connection tables. ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2002-11-22 20:59 Message: Logged In: YES user_id=25678 The documentation states that this informaion is auxiliary. As such it should not be necessary for the identifier itself. Description of the <basic> element describes how atoms are numbered. The output by the IChI program even says "Auxiliary info is not a part of the identifier, it is not unique". In any case, v1.3 does indeed not read <atom.orig-nbr>. Could you elaborate why this is a bug, i.e. explain why the garbling is actually caused by the missing <atom.orig-nbr>? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 |
From: Peter Murray-R. <pm...@ca...> - 2002-11-23 13:52:28
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At 11:59 22/11/2002 -0800, no...@so... wrote: >Bugs item #642456, was opened at 2002-11-22 19:46 >You can respond by visiting: >https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 > > >Category: org.openscience.cdk.io >Group: None >Status: Open >Resolution: None >Priority: 5 >Submitted By: Peter Murray-Rust (petermr) > >Assigned to: Egon Willighagen (egonw) >Summary: IChI reader does not map atoms > >Initial Comment: >The IChI reader (V1.3) does not appear to read the ><atom.orig-nbr> >element so that atoms in the final structure are garbled. This >means that IChI does not output correct connection tables. > > > >---------------------------------------------------------------------- > > >Comment By: Egon Willighagen (egonw) >Date: 2002-11-22 20:59 > >Message: >Logged In: YES >user_id=25678 First, I am using IChI V0.9beta. Is this what you have used? >The documentation states that this informaion is auxiliary. >As such it should not be necessary for the identifier >itself. agreed > Description of the <basic> element describes how >atoms are numbered. The output by the IChI program even says >"Auxiliary info is not a part of the identifier, it is not >unique". agreed >In any case, v1.3 does indeed not read ><atom.orig-nbr>. Could you elaborate why this is a bug, i.e. >explain why the garbling is actually caused by the missing ><atom.orig-nbr>? We created a number of files using IChI where the dbonds did not map onto the given bonds and appeared to require the atom.orig-nbr. I agree that this shouldn't be necessary. Here is a file distributed with IChI which shows a dbond (8-7-) not originally in the bond list: --------------------8<-------------- <IChI version="0.9Beta"> <structure number="1" id.name="" id.value=""> <identifier version="0.9Beta" tautomeric="0"> <basic>C*6C1*16CC, 2-1 4-3 6-5 7-1 8-2 9-3 10-4 11-7 12-8 13-9 14-10 15-11 16-12 17-13 18-14 19-15 20-16 21-17 22-18 23-5-19-21 24-6-20-22</basic> <charge></charge> <stereo> <dbond>8-7- 13-9- 14-10- 15-11+ 16-12+ 21-17+ 22-18+ 23-19+ 24-20+</dbond> <sp3></sp3> </stereo> </identifier> <identifier.auxiliary-info version="0.9Beta" tautomeric="0"> <!-- Auxiliary info is not a part of the identifier, it is not unique --> <atom.orig-nbr>13 14 23 24 10 11 9 15 1 22 8 18 2 21 7 17 3 20 6 16 4 19 5 12</atom.orig-nbr> <atom.equivalence>(1 2 3 4)(5 6)(7 8 9 10)(11 12 13 14)(15 16 17 18)(19 20 21 22)(23 24)</atom.equivalence> </identifier.auxiliary-info> </structure> </IChI> --------------------8<-------------- I have a suspicion that this is a problem with IChIV0.9beta . It suggests that there needs to be more error checking in an IChIReader. I do not have the problem files with me but should be able to send some samples on Monday. I suspect this may also be responsible for one of the other bugs I reported. It also emphasises the need to have test sets that are available so that we can agree on what are bugs and whose responsibility it P. >---------------------------------------------------------------------- > >You can respond by visiting: >https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 > > >------------------------------------------------------- >This sf.net email is sponsored by:ThinkGeek >Welcome to geek heaven. >http://thinkgeek.com/sf >_______________________________________________ >Cdk-devel mailing list >Cdk...@li... >https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: E.L. W. <eg...@sc...> - 2002-11-23 16:23:12
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> I have a suspicion that this is a problem with IChIV0.9beta . It suggests > that there needs to be more error checking in an IChIReader. Yes, I believe the IChI beta is not without bugs... i encountered one in the past too... > I do not have the problem files with me but should be able to send some > samples on Monday. I suspect this may also be responsible for one of the > other bugs I reported. It also emphasises the need to have test sets that > are available so that we can agree on what are bugs and whose > responsibility it Indeed. Egon |
From: <no...@so...> - 2002-11-22 20:52:24
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Bugs item #642456, was opened at 2002-11-22 19:46 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 Category: org.openscience.cdk.io Group: None >Status: Pending Resolution: None Priority: 5 Submitted By: Peter Murray-Rust (petermr) Assigned to: Egon Willighagen (egonw) Summary: IChI reader does not map atoms Initial Comment: The IChI reader (V1.3) does not appear to read the <atom.orig-nbr> element so that atoms in the final structure are garbled. This means that IChI does not output correct connection tables. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2002-11-22 20:59 Message: Logged In: YES user_id=25678 The documentation states that this informaion is auxiliary. As such it should not be necessary for the identifier itself. Description of the <basic> element describes how atoms are numbered. The output by the IChI program even says "Auxiliary info is not a part of the identifier, it is not unique". In any case, v1.3 does indeed not read <atom.orig-nbr>. Could you elaborate why this is a bug, i.e. explain why the garbling is actually caused by the missing <atom.orig-nbr>? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=642456&group_id=20024 |