Merge pull request #86 from OpenFreeEnergy/more_plotting

Add dG obtaining code and showing how to shift the absolutes
OpenFreeEnergy · Sep 15, 2023 · e06c524 · e06c524
2 parents c973f6a + ba876c8
commit e06c524
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diff --git a/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb b/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb
diff --git a/plotting_rbfes_with_cinnabar/final_results.tsv b/plotting_rbfes_with_cinnabar/final_results.tsv
@@ -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