{"action":"created","issue":{"url":"https://api.github.com/repos/mcs07/MolVS/issues/20","repository_url":"https://api.github.com/repos/mcs07/MolVS","labels_url":"https://api.github.com/repos/mcs07/MolVS/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/mcs07/MolVS/issues/20/comments","events_url":"https://api.github.com/repos/mcs07/MolVS/issues/20/events","html_url":"https://github.com/mcs07/MolVS/issues/20","id":295644366,"number":20,"title":"TautomerCanonicalizer gives unexpected/forbidden form of phosphoric acid","user":{"login":"benbowen","id":810953,"avatar_url":"https://avatars0.githubusercontent.com/u/810953?v=4","gravatar_id":"","url":"https://api.github.com/users/benbowen","html_url":"https://github.com/benbowen","followers_url":"https://api.github.com/users/benbowen/followers","following_url":"https://api.github.com/users/benbowen/following{/other_user}","gists_url":"https://api.github.com/users/benbowen/gists{/gist_id}","starred_url":"https://api.github.com/users/benbowen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benbowen/subscriptions","organizations_url":"https://api.github.com/users/benbowen/orgs","repos_url":"https://api.github.com/users/benbowen/repos","events_url":"https://api.github.com/users/benbowen/events{/privacy}","received_events_url":"https://api.github.com/users/benbowen/received_events","type":"User","site_admin":false},"labels":[{"id":110571221,"url":"https://api.github.com/repos/mcs07/MolVS/labels/bug","name":"bug","color":"d93f0b","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-02-08T19:54:17Z","updated_at":"2018-02-09T17:57:56Z","closed_at":null,"author_association":"NONE","body":"I'm converting all the molecules in my database to canonical-tautomers and noticed that things like NADH looked weird.  You can see it most plainly for phosphoric acid.  I didn't expect the Hydrogen on the phosphorous.  Is this the correct/expected behavior?\r\n\r\n```python\r\nfrom rdkit import Chem\r\nfrom rdkit.Chem import Draw\r\nfrom molvs.tautomer import TautomerCanonicalizer\r\n\r\noriginal_smiles = 'OP(=O)(O)O'\r\n\r\noriginal_mol = Chem.MolFromSmiles(original_smiles)\r\ntautomerized_mol = TautomerCanonicalizer().canonicalize(original_mol)\r\n\r\nDraw.MolsToGridImage([original_mol,tautomerized_mol],\r\n                     molsPerRow=3,subImgSize=(200,200),\r\n                     legends=['original','tautomer'])\r\n```\r\n\r\n\r\n![image](https://user-images.githubusercontent.com/810953/35994767-4a5e3038-0cc6-11e8-9f03-d97fc5109515.png)\r\n"},"comment":{"url":"https://api.github.com/repos/mcs07/MolVS/issues/comments/364509445","html_url":"https://github.com/mcs07/MolVS/issues/20#issuecomment-364509445","issue_url":"https://api.github.com/repos/mcs07/MolVS/issues/20","id":364509445,"user":{"login":"benbowen","id":810953,"avatar_url":"https://avatars0.githubusercontent.com/u/810953?v=4","gravatar_id":"","url":"https://api.github.com/users/benbowen","html_url":"https://github.com/benbowen","followers_url":"https://api.github.com/users/benbowen/followers","following_url":"https://api.github.com/users/benbowen/following{/other_user}","gists_url":"https://api.github.com/users/benbowen/gists{/gist_id}","starred_url":"https://api.github.com/users/benbowen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benbowen/subscriptions","organizations_url":"https://api.github.com/users/benbowen/orgs","repos_url":"https://api.github.com/users/benbowen/repos","events_url":"https://api.github.com/users/benbowen/events{/privacy}","received_events_url":"https://api.github.com/users/benbowen/received_events","type":"User","site_admin":false},"created_at":"2018-02-09T17:57:56Z","updated_at":"2018-02-09T17:57:56Z","author_association":"NONE","body":"You are correct, removing that rule stops that moiety from being modified.  When you say, \"more strict\", you think specify an explicit number of bonds on the Phosphorous in the SMARTS pattern?\r\n\r\nWhy does rdkit allow 6 bonds on the phosphorous? Rdkit is a vast package, but looking at the definition of Phosphorous, it has[ max bonds of 5](https://github.com/rdkit/rdkit-orig/blob/master/rdkit/Chem/PeriodicTable.py#L37).\r\n\r\nIf I do SantizeMol, the hydrogen stays put.  When I paste the structure into ChemDraw, its not valid."}}
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