#131 FP3 and FP4 use different file formats

[Andrew Dalke]

Two of the three fingerprinters are based on SMARTS patterns. The two files ("patterns.txt" and "SMARTS_InteLigand.txt") use different file formats. That doesn't make sense. Why not rewrite one so both use the same format? The decision code is in

bool ReadPatternFile(const string& filename, vector<string>& lines)
{
//Reads two types of file: SMARTS + comments and vice versa
//depending on whether the first line is #Comments after SMARTS
//Output strings in vector are SMARTS + comments

The lack of consistency makes it harder for someone to figure out how the formats work (because one is different than the other) and to add a new SMARTS-based definition (which format should someone use?)

[Geoff Hutchison]

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While I agree that consistency is a good aim, I'm going to move this to "Feature Requests" rather than an explicit bug.

I believe the difference is simply that the two files came from different sources and Chris attempted to retain the formatting for merging in future revisions.