Hi Andrew, thanks for your comments.
On Sat, 23 Jan 2010 03:59:06 pm Andrew Dalke wrote: > > Out of curiosity, I see it's licensed as: > > This program is free software; you can redistribute it and/or modify > it under the terms of the GNU General Public License as published by > the Free Software Foundation version 2 of the License. > > Is there are reason you have it only under version 2? I know > the OB is GPLv2 only, because of OpenEye's original license, > but I suspect authors of new code should consider "v2 or later." No reason, I just overlooked it. That licence comes from exampleformat.cpp in OB. > I looked a few other parts of the code. Were it me I would fix > up some of the comments, like have > > //To use an output option > become > // To use an output option heheh, again, that style of commenting is left over from the example. > I also like code which fits into 80 columns, but I realize > that both this and the previous comment of mine are more > personal preferences, and not an OB standard convention. Yeah, I think if you can't tell your editor to autowrap code at your preferred width then you need a better editor. :) > I'm curious about if you've resolved this comment: > > // Will this need to recurse here? (Or does atomic numbering take care > of that?) I haven't, because the specification is not really clear. My plan is to send a beta version to the person that wrote the specification and see what they think. > I looked at the URLs but couldn't find the format definitions. Yeah, the problem is that the definition is in a journal that requires a subscription or a one-off fee per article that can be $20-$50. Maybe I should rewrite the definition on the OB wiki, cite the original article and refer to the wiki in the code? > Do you have examples, which could be added to the test cases? Yes, but only moderately trivial ones. I'll attach amitryptline as an example, with comments stripped out. Cheers. Jeremy
amitriptyline.mol
Description: MOL mdl chemical test
-C(-H(-C)-H(-C)-H(-C)-N(-C-C-C)) -N(-C(-H-H-H-N)-C(-H-H-H-N)-C(-H-H-C-N)) -C(-H(-C)-H(-C)-H(-C)-N(-C-C-C)) -C(-H(-C)-H(-C)-C(-H-H-C-C)-N(-C-C-C)) -C(-H(-C)-H(-C)-C(-H-H-C-N)-C(C-H-C)) -C(C(CC-C)-H(-C)-C(-H-H-C-C)) C(C(CCC)C(CCC)-C(C-H-C)) C(C(CC-C)C(CC-H)C(CCC)) C(C(CCC)C(CC-H)-H(C)) C(C(CC-H)C(CC-H)-H(C)) C(C(CC-H)C(CC-H)-H(C)) C(C(CC-H)C(CCC)-H(C)) C(C(CCC)C(CC-H)C(CC-H-H)) C(C(CCC)C(CC-H-H)-H(C)-H(C)) C(C(CC-H-H)C(CCC)-H(C)-H(C)) C(C(CC-H-H)C(CC-H)C(CCC)) C(C(CCC)C(CC-H)-H(C)) C(C(CC-H)C(CC-H)-H(C)) C(C(CC-H)C(CC-H)-H(C)) C(C(CC-H)C(CCC)-H(C)) C(C(CC-C)C(CCC)C(CC-H)) -H(-C(-H-H-H-N)) -H(-C(-H-H-H-N)) -H(-C(-H-H-H-N)) -H(-C(-H-H-H-N)) -H(-C(-H-H-H-N)) -H(-C(-H-H-H-N)) -H(-C(-H-H-C-N)) -H(-C(-H-H-C-N)) -H(-C(-H-H-C-C)) -H(-C(-H-H-C-C)) -H(-C(C-H-C)) -H(C(CC-H)) -H(C(CC-H)) -H(C(CC-H)) -H(C(CC-H)) -H(C(CC-H-H)) -H(C(CC-H-H)) -H(C(CC-H-H)) -H(C(CC-H-H)) -H(C(CC-H)) -H(C(CC-H)) -H(C(CC-H)) -H(C(CC-H))
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