Daniel Lowe

Bingo tanimoto similarity can be over 1?

2

I'm using a version built from source on the 16th November 2017 against PostgreSQL 9.6. `select count(*) from bingo.chemdata where smiles @ ('0.95', '1', 'S(C1C=CC(=C(C2=NC(C3=C(C(CCC)=NN3C)N2)=O)C=1)OCC)(N1CCN(C)CC1)(=O)=O', 'Tanimoto')::bingo.sim` 9 `select count(*) from...

Calling molecularWeight() on an invalid isotope kills the JVM when called from Java

2

```java Indigo indigo = new Indigo(); IndigoObject mol = indigo.loadMolecule("[60C]"); double mw = mol.molecularWeight(); System.out.println(mw); ``` Crashes the JVM on v1.5.0 and v1.6.1 due to: ``` terminate called after throwing...

I have a probably rather niche use case, I'd like to create RunAutomatons, serialize them with `store`, then only once they're deserialized with `load` tabelize them. The reasoning being that...

e.g. 8-(3,5-Bis-trifluoromethyl-benzoyl)-3-furan-2-yl-methyl-1-o-tolyl-1,3,8-triaza-spiro[4.5]decane-2,4-dione should be treated as 8-(3,5-Bis-trifluoromethyl-benzoyl)-3-(furan-2-yl-methyl)-1-o-tolyl-1,3,8-triaza-spiro[4.5]decane-2,4-dione

This is used to indicate relative stereochemistry in meso cyclic compounds

Rejected: 1-phenyl-2-(pyrrolidin-1-yl){alkyl ketone}

2

**[Original report](https://bitbucket.org/dan2097/opsin/issue/116) by Steve Chapman (Bitbucket: [isomerdesign](https://bitbucket.org/isomerdesign), ).** ---------------------------------------- Rejects propanone and higher ketones with **Atom is in unphysical valency state! Element: C valency: 5** Accepts 1-phenyl-2-\(pyrrolidin-1-yl\)ethanone Accepts 1-phenyl-2-\(pyrrolidin-1-yl\)-1-propanone Accepts...

IUPAC systematic names for the naturally occurring diatomic do not parse

2

**[Original report](https://bitbucket.org/dan2097/opsin/issue/107) by Jason Sonnenberg (Bitbucket: [jsonnenb](https://bitbucket.org/jsonnenb), GitHub: [jsonnenb](https://github.com/jsonnenb)).** ---------------------------------------- For the seven elements (hydrogen, oxygen, nitrogen, fluorine, chlorine, bromine and iodine) that have diatomic allotropes at STP, the IUPAC...

**[Original report](https://bitbucket.org/dan2097/opsin/issue/85) by Daniel Lowe (Bitbucket: [dan2097](https://bitbucket.org/dan2097), GitHub: [dan2097](https://github.com/dan2097)).** ---------------------------------------- Element names are a closed set of Strings, so an enum would be more efficient and enforce usage of Strings...

can't convert 4'-Vinyluridine-5'-(O-phenyl-N-(S)-1-(isopropoxycarbonyl)ethyl phosphoramidate)

1

**[Original report](https://bitbucket.org/dan2097/opsin/issue/120) by Anonymous.** ---------------------------------------- can not convert 4'-Vinyluridine-5'-(O-phenyl-N-(S)-1-(isopropoxycarbonyl)ethyl phosphoramidate) but chemdraw can does this transform

**[Original report](https://bitbucket.org/dan2097/opsin/issue/113) by Daniel Lowe (Bitbucket: [dan2097](https://bitbucket.org/dan2097), GitHub: [dan2097](https://github.com/dan2097)).** ---------------------------------------- e.g. bromacetyl should be intepreted as bromo acetyl, not bromine replacement of cetyl (bug found by P Schwaller)