Added AptaFast.py, an optimised version of AptaMat with the same features but faster.
- Implemented double-list search with search-depth to find the nearest point.
- Replaced the file parser algorithm with a faster one.
- Parallelized file parsing and nearest point search.
- Implemented a new parameter to control greediness and speed:
speed -[slow|fast](slow by default). - Added a changelog with all changes and explanations + performance and accuracy tests.
Added random_gen.py a pseudo-realistic dotbracket sequence random generator for performance tests only.
- random_gen can create .fa files which can be input to AptaFast and AptaMat.
- 4 parameters can be changed : bias, density, length and number of structures (please see
CHANGELOG.mdfor in depth explanations) - random_gen verifies the structure created by the algorithm and then inputs it into a file.
- with each structure, a random weight is generated and input into the file.