addImplicitHydrogens and helpers

[lpatiny]

@thsa I have a problem that after adding implicit hydrogens the cHelpers array for neighbour is not correct anymore.

https://github.com/Actelion/openchemlib/blob/master/src/main/java/com/actelion/research/chem/contrib/HydrogenHandler.java#L280-L286

What would be the best way ? Recalculate at the end of the function the helper array ?

So adding

molecule.ensureHelperArrays(Molecule.cHelperNeighbours);

Just before turning from the function ?

[thsa]

the concept in OpenChemLib is the opposite. If you need the helpers in a method, then just call ensureHelperArrays() at the beginning of the method. Never call it at the end just in case somebody else might need correct helpers later.

…

________________________________ Von: Luc Patiny ***@***.***> Gesendet: Montag, 7. Februar 2022 15:26 An: Actelion/openchemlib ***@***.***> Cc: Thomas Sander ***@***.***>; Mention ***@***.***> Betreff: [Actelion/openchemlib] addImplicitHydrogens and helpers (Issue #67) @thsa<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fthsa&data=04%7C01%7Cthomas.sander%40idorsia.com%7Cf7b8cc13a6324d4ab95608d9ea45d4c6%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637798407903829738%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ZgnVPhPJqNEE%2BV1c8G8G6yDplV%2BFYhJWtdBvkfn7iq4%3D&reserved=0> I have a problem that after adding implicit hydrogens the cHelpers array for neighbour is not correct anymore. https://github.com/Actelion/openchemlib/blob/master/src/main/java/com/actelion/research/chem/contrib/HydrogenHandler.java#L280-L286<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FActelion%2Fopenchemlib%2Fblob%2Fmaster%2Fsrc%2Fmain%2Fjava%2Fcom%2Factelion%2Fresearch%2Fchem%2Fcontrib%2FHydrogenHandler.java%23L280-L286&data=04%7C01%7Cthomas.sander%40idorsia.com%7Cf7b8cc13a6324d4ab95608d9ea45d4c6%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637798407903829738%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=d1kKKIA%2FoX2VlsLw4xaiiqQL8BACyRFnpLf1MVUpbLA%3D&reserved=0> What would be the best way ? Recalculate at the end of the function the helper array ? So adding molecule.ensureHelperArrays(Molecule.cHelperNeighbours); Just before turning from the function ? — Reply to this email directly, view it on GitHub<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FActelion%2Fopenchemlib%2Fissues%2F67&data=04%7C01%7Cthomas.sander%40idorsia.com%7Cf7b8cc13a6324d4ab95608d9ea45d4c6%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637798407903829738%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0WT0aANBeOL5BVEgzfViNWcrE%2F6j%2FIesas1WeL%2B1lxg%3D&reserved=0>, or unsubscribe<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACNFEBXJZVQF3UZB3UBQR7LUZ7JBJANCNFSM5NXTJFLA&data=04%7C01%7Cthomas.sander%40idorsia.com%7Cf7b8cc13a6324d4ab95608d9ea45d4c6%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637798407903829738%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=PnaEbO1ScUl2zvRqqR2oAKReGJXzQA09Xi30tX3N2CM%3D&reserved=0>. Triage notifications on the go with GitHub Mobile for iOS<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cthomas.sander%40idorsia.com%7Cf7b8cc13a6324d4ab95608d9ea45d4c6%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637798407903829738%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=f8leRdif0WhuGsg%2BoFk3qjhSIXrXKSbdioLljVyY9Cw%3D&reserved=0> or Android<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cthomas.sander%40idorsia.com%7Cf7b8cc13a6324d4ab95608d9ea45d4c6%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637798407903829738%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=kIUPtKhV05aIAkAcECqxtqF3VXV5bhEVI%2BpqX8OSL%2FY%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***> The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorized to state them to be the views of the sender's company.