Progress Report - 10 Aug 2007
1. What were my goals for this week?
- Try to generate motions on the beam PDB using Aaron's C-alpha program
- Determine if PointList.h is worth using
- Finish Sanity - bonds, etc
- Finish MotionSeg - spatial clustering, different types of motion clustering
2. What did I accomplish this week?
- Got odd motions on the beam PDB using the C-alpha program
- Constructed a bend motion by hand using the network spring program
- Implemented hierarchical spatial clustering in MotionSeg
- Met with CIBM group and discussed long-term class scheduling
- Completed Phase One of Madison Move 2007
3. Why are numbers 1 and 2 different?
Not quite sure whether PointList.h is going to be necessary - might try using it with a weighted, six-dimensional cluster at some point, but not yet; no decision has been made. Didn't get to Sanity's bonds, as MotionSeg's clustering took longer to debug than expected and I'm still unsure as to the best way to go about classifying the bonds for verification. As a side note, when loading in the beam PDB, MMDB got very angry with me for not having valid protein structure, though it did not yell at me for not having the appropriate atoms in each residue.
4. What are my goals for next week?
- Look at heuristic algorithms to cluster motions more quickly/intelligently
- See if I can optimize the hierarchical clustering
- Try other forms of clustering on the motions
- Figure out what to do with k-means outliers
- Implement affine fitting on the clusters
- Talk to Aaron about glyphs for static representation of motions!
5. How does this fit in my bigger picture?
Really getting somewhere with the project - might actually have some sort of results by the end of the week!
6. What did I read this week?
- McMurry, John, Organic Chemistry.
- Hays, James and Efros, Alexei A., Scene Completion Using Millions of Photographs.