Week 10

Last week! If there's one thing I've learned about bioinformatics (well, I've learned more than one thing, but that's besides the point) is that there are a million file formats, and everyone seems to have to have their own depending on the information they want. This makes for a lot of scripts to change from one file format to another. Sybyl uses a mol2 file, and we use our own file format, called admol. So after running the files through the barrage of scripts, and imputing the admols into our program, what does it do? Seg faults!

The first problem was that I did not renumber the atoms. The second problem is that at one point I remove lone pairs from the file. However, there was bond information between these lone pairs and the other atoms, and the script doesn't remove these bonds. The program was looking for atoms that longer existed. So right now I finally have admol files that I believe are correct. However, our program still seg faults. So far the bug has been elusive.

While my DMP term is now over, I will be able to continue working on this project through the school year, so I hope to finally get other test cases to work with our program.

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