Calculate INFs

files from another job e.g., 614e0a1b

target: filename of file to be used as the reference, if empty the first file dropped will be used

The INF csv output file can be found here inf.csv

The raw output files for each step of the pipeline can be found here and downloaded as a ZIP file here.


rna_calc_infs.py - a tool to calc inf_all (INF of all interactions), inf_stack (INF for stacking interaction), inf_WC (INF for Watson-Crick interactions), inf_nWC (INF for non-Watson-Crick interactions), SNS_WC (sensitivity for Watson-Crick interactions), PPV_WC (positive predictive values for Watson-Crick interactions), SNS_nWC (sensitivity for non-Watson-Crick interactions), PPV_nWC (positive predictive values for non-Watson-Crick) interactions between two structures (or one vs more)

If you still have problem with various number of atoms, check out this issue: get_rnapuzzle_ready see Tools

target              fn                        inf_all  inf_stack  inf_WC  inf_nWC  sns_WC  ppv_WC  sns_nWC  ppv_nWC
21_3dRNA_1_rpr.pdb  21_ChenHighLig_1_rpr.pdb  0.64     0.65       0.6     0.58     1.0     0.36    1.0      0.33
21_3dRNA_1_rpr.pdb  21_Adamiak_1_rpr.pdb      0.59     0.59       0.6     0.71     1.0     0.36    1.0      0.5
21_3dRNA_1_rpr.pdb  21_Das_1_rpr.pdb          0.57     0.62       0.6     0.3      1.0     0.36    1.0      0.09

T. Waleń, G. Chojnowski, P. Gierski, and J. M. Bujnicki, “ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.,” Nucleic Acids Research, vol. 42, no. 19, pp. e151–e151, Oct. 2014.

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