gtfold/gtfold — pull request #64 by msoni3 (2012-01-30 00:37:20+00:00)
Title: rna-scoring, partition function, code update

1)rna-scoring code added
2)Partition function time, stochastic traceback time computation added
3)calculation of partition function in d0 mode is modified as discussed with Shel
4)integration of rna-scoring and gtfold (stochastic traceback and partition function) added
5)new option added (and corresponding code) in gtfold
./gtboltzmann --sample INT --dump [--dump_dir dump_dir_path] [--dump_summary dump_summery_file_name] seq_file_path,
Sample number of structures equal to INT and dump each structure to a ct file in dump_dir_path directory (if no value provided then use current directory value for this purpose) and also create a summary file with name stochastic_summery_file_name in dump_dir_path directory (if no value provided, use stochaSampleSummary.txt value for this purpose)
6)5)new option added (and corresponding code) in rna-scoring,
./RNAScoring --pf_test