============================================================================== === TO DO ================================================================== ============================================================================== Crash with 1h0v? Kin to show source? BUG with model numbers and TER records not having the same number?? ============================================================================== === CHANGE LOG ============================================================= ============================================================================== ### 1.12 ### - Added -*range flags to control what ranges to search on parameters. - Changed kin output to show PDB names of fragments. ### 1.11 ### - Usability enhancements: better file names, fragments in kins have PDB source identity info. - Added -tighter to give option for tighter parameters. ### 1.10 ### - Changed FragFiller to use new database setup, with each fragment length in a separate table. ### 1.09 ### - Added jiffiloop.changes and help files. - Added -fragment to limit number of fragments generated. - Added -sequence to keep residue name info. - Changed functionality to renumber and rename residues by default. ### 1.08 ### - Scorer function for scoring the jiffiloop-ness of a protein. - Output changed to spit out each individual gap score. ### 1.07 ### - Added option for superimposing using just N-term of a fragment. - Found some issues with residues/fragments not being complete. - Moved some exception handling around to be a little smarter and with more useful bug reports. ### 1.06 ### - Moved DatabaseManager to driftwood. ### 1.05 ### - Fixed a bug in database "select" construction. - Added a system.out for printing out gap parameters. ### 1.04 ### - Added a way to simulate gaps in structures. - Output pdbs get labeled with model name and chain. ### 1.03 ### - Input pdb gets output in the output kin. - Output pdbs include information past column 80 on where the files came from. - Added ability for tool to obtain fragment data from a database. - Added a ProteinGap class to hold all info on gaps. ### 1.02 ### - added a way to parse arguments, specifying locations for the libraries. - fixed bugs in how it deals with arguments. ### 1.01 ### - fixed main so it uses the absolute path of the arguments. ### 1.00 ### - initial build of fragment filler program, based on PatchGapPlugin