Merge pull request #78 from OpenFreeEnergy/Plotting

Add notebook for plotting out free energies using Cinnabar v0.3

Author: richardjgowers

plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb

@@ -0,0 +1,14 @@
+ligand	estimate (kcal/mol)	uncertainty (kcal/mol)
+lig_ejm_31	-9.57	0.18
+lig_ejm_42	-9.81	0.18
+lig_ejm_43	-8.29	0.18
+lig_ejm_45	-9.59	0.18
+lig_ejm_46	-11.35	0.17
+lig_ejm_47	-9.73	0.18
+lig_ejm_48	-9.03	0.18
+lig_ejm_50	-9.01	0.18
+lig_ejm_54	-10.57	0.18
+lig_ejm_55	-9.24	0.18
+lig_jmc_23	-11.74	0.18
+lig_jmc_27	-11.31	0.17
+lig_jmc_28	-11.01	0.18

plotting_rbfes_with_cinnabar/experimental.tsv

@@ -0,0 +1,28 @@
+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