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Add dG obtaining code and showing how to shift the absolutes #86

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Merged
IAlibay merged 3 commits into from
Sep 15, 2023
Merged

Add dG obtaining code and showing how to shift the absolutes #86

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c1fc515
Add dG obtaining code and showing how to shift the absolutes
IAlibay Sep 15, 2023
8bdf31a
Update for new gather
IAlibay Sep 15, 2023
ba876c8
match things better with gather's output
IAlibay Sep 15, 2023
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237 changes: 185 additions & 52 deletions plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb
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38 changes: 10 additions & 28 deletions plotting_rbfes_with_cinnabar/final_results.tsv
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Original file line number Diff line number Diff line change
@@ -1,28 +1,10 @@
measurement type ligand_i ligand_j estimate (kcal/mol) uncertainty (kcal/mol)
DDGbind(lig_ejm_42, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_42 0.49 0.09
DDGbind(lig_ejm_46, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_46 -0.73 0.097
DDGbind(lig_ejm_47, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_47 0.016 0.15
DDGbind(lig_ejm_48, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_48 0.45 0.17
DDGbind(lig_ejm_50, lig_ejm_31) RBFE lig_ejm_31 lig_ejm_50 0.94 0.072
DDGbind(lig_ejm_43, lig_ejm_42) RBFE lig_ejm_42 lig_ejm_43 1.2 0.14
DDGbind(lig_jmc_23, lig_ejm_46) RBFE lig_ejm_46 lig_jmc_23 -0.39 0.046
DDGbind(lig_jmc_27, lig_ejm_46) RBFE lig_ejm_46 lig_jmc_27 -0.65 0.1
DDGbind(lig_jmc_28, lig_ejm_46) RBFE lig_ejm_46 lig_jmc_28 -0.12 0.044
DGcomplex(lig_ejm_31, lig_ejm_42) complex lig_ejm_31 lig_ejm_42 -19.0 0.088
DGsolvent(lig_ejm_31, lig_ejm_42) solvent lig_ejm_31 lig_ejm_42 -19.0 0.017
DGcomplex(lig_ejm_31, lig_ejm_46) complex lig_ejm_31 lig_ejm_46 -39.0 0.077
DGsolvent(lig_ejm_31, lig_ejm_46) solvent lig_ejm_31 lig_ejm_46 -38.0 0.059
DGcomplex(lig_ejm_31, lig_ejm_47) complex lig_ejm_31 lig_ejm_47 -27.0 0.11
DGsolvent(lig_ejm_31, lig_ejm_47) solvent lig_ejm_31 lig_ejm_47 -27.0 0.11
DGcomplex(lig_ejm_31, lig_ejm_48) complex lig_ejm_31 lig_ejm_48 -19.0 0.17
DGsolvent(lig_ejm_31, lig_ejm_48) solvent lig_ejm_31 lig_ejm_48 -20.0 0.043
DGcomplex(lig_ejm_31, lig_ejm_50) complex lig_ejm_31 lig_ejm_50 -54.0 0.072
DGsolvent(lig_ejm_31, lig_ejm_50) solvent lig_ejm_31 lig_ejm_50 -55.0 0.0072
DGcomplex(lig_ejm_42, lig_ejm_43) complex lig_ejm_42 lig_ejm_43 -13.0 0.14
DGsolvent(lig_ejm_42, lig_ejm_43) solvent lig_ejm_42 lig_ejm_43 -14.0 0.0046
DGcomplex(lig_ejm_46, lig_jmc_23) complex lig_ejm_46 lig_jmc_23 6.5 0.041
DGsolvent(lig_ejm_46, lig_jmc_23) solvent lig_ejm_46 lig_jmc_23 6.9 0.021
DGcomplex(lig_ejm_46, lig_jmc_27) complex lig_ejm_46 lig_jmc_27 7.6 0.1
DGsolvent(lig_ejm_46, lig_jmc_27) solvent lig_ejm_46 lig_jmc_27 8.3 0.0086
DGcomplex(lig_ejm_46, lig_jmc_28) complex lig_ejm_46 lig_jmc_28 14.0 0.0069
DGsolvent(lig_ejm_46, lig_jmc_28) solvent lig_ejm_46 lig_jmc_28 14.0 0.043
ligand_i ligand_j DDG(i->j) (kcal/mol) uncertainty (kcal/mol)
lig_ejm_31 lig_ejm_42 0.49 0.09
lig_ejm_31 lig_ejm_46 -0.73 0.10
lig_ejm_31 lig_ejm_47 0.0 0.2
lig_ejm_31 lig_ejm_48 0.5 0.2
lig_ejm_31 lig_ejm_50 0.94 0.07
lig_ejm_42 lig_ejm_43 1.2 0.1
lig_ejm_46 lig_jmc_23 -0.39 0.05
lig_ejm_46 lig_jmc_27 -0.6 0.1
lig_ejm_46 lig_jmc_28 -0.12 0.04