[Cdk-user] ([SMART_PARSER_IS_COMPLETE])*

the smart parser is on it's way. I have updated the files to svn. A big change in src\org\openscience\cdk\isomorphism\matchers package. and a updatedsrc\org\openscience\cdk\smiles\smarts\SMARTSParser.jj file We can now parse the operators expression like [C,N,Cl,Ca] or [!r5&x2] or any kind

[Cdk-user] SDF file with multiple newline characters

Hi all, Some softwares seem to produce SDF files, where new line delimiter include both unix (CR) and windows (CR/LF) characters, e.g. atom/bond blocks looks like below: -3.40370.41190. C 0 0 0 0 0 0 0 0 0 0 0 0[CR][CR/LF] -3.1119 -0.49550. C 0 0 0 0

Re: [Cdk-user] generating SMILES string for molecular fragments

> However it's not clear to me whether the generator could make use of > prior information at all. More specifically, if you have an > IAtomContainer X and then fragment it to an IAtomContainer[] Y. > > Say you had an ARF for X, there is no guarantee that the atoms/bonds in > the ARF for X would ma