On Wed, Jun 24, 2009 at 3:38 PM, Craig James <[email protected]>wrote:
> (Cross posted to OpenBabel-discuss and BlueObelisk-discuss) > > > --------------- > > a) The facility to have comment lines in SMILES files seems > > *very* useful and it would be a great shame to lose it. > > That's very true, and perhaps we should add something to the OpenSMILES > specification. Perhaps something like starting a line with '#' or '//', > like so many other languages. Or even starting a line with whitespace -- it > doesn't matter, as long as it's formally specified. > > As we used to say in my electrical engineering days: "The great thing about > standards is that there are so many to choose from!" In other words, a > standard isn't any good unless we all follow it. If OpenBabel treats these > lines as comments, it will produce files that other parsers can't read. On the assumption that Openbabel and the BlueObelisk are rapidly starting to become a place for the generation of de facto standards I support the motivation > > > Just to illustrate: Suppose someone else said, "I'm going to skip > whitespace that starts a line, and parse SMILES starting at the first > non-whitespace character." In other words, they'd parse indented SMILES. > This isn't hypothetical, I've seen people do this. They would try to parse > the lines that you think are comments, so this file: > > | This is a comment about > | CCO, the ethanol molecule, not to be mistaken with the > | CO methanol molecule. > |CCO > > would be interpreted by OpenBabel as one SMILES, and by the other guys as > three SMILES and one error. > --------------- > > So my proposal is to say that any line that starts with '#', '/', or ' ' > (space) should be treated as a comment line, and should be ignored > completely when processing the file, except that it may be copied to the > output if a program's output format supports comments. > Please, Please don't use whitespace. It is so easy to lose or to generate by mistake. It's generally a good idea NOT to use a character out of the language syntax for a comment. both hash and / are SMILES characters. There are a few others which I think are unused. P. -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069
------------------------------------------------------------------------------
_______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
