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README
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Please ensure that your input file contains at least three columns: The first two columns are the names of the mutation ligands, and the third colunm are their pair-wise energy.
Example:
1. Example with only three data columns: ligand1, ligand2 and pair-wise energy(Input file: Example/example_without_w).
Usage:
python wcc_main.py -f Example/example_without_w -r 3A -e -8.83
output:
Node dG_cc path_dependent_error path_independent_error
3K -9.6490 0.6800 0.3917
4M -9.2534 0.6800 0.3917
3N -7.2975 0.4600 0.2542
3A -8.8300 0.0000 0.2126
3M -9.3731 0.4600 0.2542
4P -9.5708 0.9300 0.3917
4L -8.2269 0.9300 0.3917
4N -8.4780 0.8500 0.2580
4I -7.7850 0.6800 0.2542
2. Example with five data columns: ligand1, ligand2, pair-wise energy, bar_std, slide_std(Input file: Example/example_with_w)
Usage:
python wcc_main.py -f Example/example_with_w -r 3A -e -8.83
output:
Node dG_cc dG_wcc1 dG_wcc2 path_dependent_error path_independent_error
3K -9.6490 -9.8057 -9.9030 0.6800 0.3917
4M -9.2534 -9.1101 -9.1422 0.6800 0.3917
3N -7.2975 -7.3467 -7.4097 0.4600 0.2542
3A -8.8300 -8.8300 -8.8300 0.0000 0.2126
3M -9.3731 -9.3372 -9.3444 0.4600 0.2542
4P -9.5708 -9.6788 -9.7445 0.9300 0.3917
4L -8.2269 -8.2082 -8.3992 0.9300 0.3917
4N -8.4780 -8.5057 -8.5536 0.8500 0.2580
4I -7.7850 -7.8019 -7.9035 0.6800 0.2542
3. If you want obtain pair-wise results after calculation, add "-p yes" option
Usage:
python wcc_main.py -f Example/example_with_w -r 3A -e -8.83 -p yes
output:
Printing Pairwise Energies:
Pair ddG_cc ddG_wcc1 ddG_wcc2 pair_error
3K-4M 0.3956 0.6956 0.7607 0.5600
3N-3A -1.5325 -1.4833 -1.4203 0.4600
3M-3A 0.5431 0.5072 0.5144 0.4600
3K-3N 2.3515 2.4590 2.4932 0.5000
4P-3K -0.0782 -0.1269 -0.1585 0.6300
4M-4P -0.3174 -0.5688 -0.6022 0.6300
3K-4L 1.4221 1.5975 1.5038 0.6300
4M-3M -0.1197 -0.2271 -0.2022 0.5000
4N-3K -1.1710 -1.3001 -1.3494 0.5100
4I-3N 0.4875 0.4552 0.4938 0.5000
4I-3M -1.5881 -1.5354 -1.4409 0.5000
4M-4L 1.0264 0.9018 0.7432 0.6300
4M-4N 0.7753 0.6043 0.5888 0.5100
****************************************************************************************************
Node dG_cc dG_wcc1 dG_wcc2 path_dependent_error path_independent_error
3K -9.6490 -9.8057 -9.9030 0.6800 0.3917
4M -9.2534 -9.1101 -9.1422 0.6800 0.3917
3N -7.2975 -7.3467 -7.4097 0.4600 0.2542
3A -8.8300 -8.8300 -8.8300 0.0000 0.2126
3M -9.3731 -9.3372 -9.3444 0.4600 0.2542
4P -9.5708 -9.6788 -9.7445 0.9300 0.3917
4L -8.2269 -8.2082 -8.3992 0.9300 0.3917
4N -8.4780 -8.5057 -8.5536 0.8500 0.2580
4I -7.7850 -7.8019 -7.9035 0.6800 0.2542
References
----------
Li, Yishui & Liu, Runduo & Liu, Jie & Luo, Haibin & Wu, Chengkun & Li, Zhe. An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations. Journal of Chemical Information and Modeling. 2023, 63, 2, 561–570
Refer to the publication above for a detailed description of the wcc method and the parameters and please cite it to support our work if you use this software in your research.