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[Cdk-devel] [ cdk-Patches-3482689 ] MDLV2000 Read Atom Parity
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From: SourceForge.net <no...@so...> - 2012-02-04 19:07:22
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Patches item #3482689, was opened at 2012-02-01 04:10 Message generated for change (Comment added) made by jwmay You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3482689&group_id=20024 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: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: John May (jwmay) Assigned to: Nobody/Anonymous (nobody) Summary: MDLV2000 Read Atom Parity Initial Comment: Minor change that allows MDLV2000 to read the atom parity from atom block. ---------------------------------------------------------------------- >Comment By: John May (jwmay) Date: 2012-02-04 11:07 Message: Oh yes, just did a quick search and found org.openscience.cdk.stereo.StereoTool with a "getHandedness" and getStereo methods :-). These look like they do what I need. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-02-04 10:50 Message: There might be such functionality already... I think Stefan Kuhn did work in this area too, but don't remember the details right now... that should be explored first... ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-04 10:19 Message: Hi Egon, I can't seem to find the code from patch in the current MDLV2000Reader, was it pushed? I can rewrite the patch on Monday so support relaxed/strict. Do you think it would be good to have the algorithm to calculate the stereo parity when only up/down bond's are set? Found a nice bit of linear algebra to do it, here (bit old but the method makes sense): http://www.mdpi.org/molecules/papers/61100915/61100915.htm. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-02-03 13:29 Message: John, can you have a quick look at my patch of a while back? I was merely reading the bit, not the value, and marking the atom as chiral... needed that at the time... https://sourceforge.net/tracker/?func=detail&aid=3043782&group_id=20024&atid=320024 I'm leaning towards supporting it... which we can do in the same way as we support other non-default features... accept in RELAXED mode and trigger a warning, and throw an error in STRICT mode... ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-02 03:44 Message: Looking into the CTFile format it seems that the stereo parity should be ignored when read, invalidating this patch I guess. However I need the parity for a project and have found an algorithm to determine the parity. If I wanted to include this would a method : "AtomContainerManipulator.assignStereoParity(IAtomContainer)" be appropriate? The format doesn't given any justification, would be interested if anyone know why you wouldn't want to read it? Spec: http://www.idea2ic.com/File_Formats/CTfile%20Formats.pdf ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-02-02 01:31 Message: Yeah, I did not get around to replying on it ... I though I had approved your first email too, but it seems I did something wrong there. Both alternative email addresses should now be automatically approved. ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-01 11:50 Message: Apologies, just realised I sent from the wrong email. Not with it today, thanks Egon :-). ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-01 09:42 Message: I'm getting bounced... but I'm on the list and rejoined just to confirm :-s. .. Your mail to 'Cdk-patches' with the subject Fwd: Read/Write Atom Parity - MDLV2000 (patch files) Is being held until the list moderator can review it for approval. The reason it is being held: Post by non-member to a members-only list Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: https://lists.sourceforge.net/lists/confirm/cdk-patches/2abb51196e11ce89009fbfda99717c48f3f40522 ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-01 06:54 Message: Have sent the cdk-patches list. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-02-01 05:58 Message: John, if that is too much effort, you can also send the patch to the cdk-patches mailing list: https://lists.sourceforge.net/lists/listinfo/cdk-patches ---------------------------------------------------------------------- Comment By: Rajarshi Guha (rajarshi) Date: 2012-02-01 05:47 Message: I can't download these patchs - SF.net is screwing up. Can you publish a Git branch for me to pull from? ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-01 04:40 Message: Wasn't closing the unit test ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3482689&group_id=20024 |