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Author: hannahbaumann

abfe_tutorial/abfe_analysis.ipynb

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     "### Methods to extract and manipulate the ABFE results\n",
     "The next three methods allow you to extract ABFE results (extract_results_dict) and then manipulate them to get different types of results.\n",
     "\n",
-    "These include:\n",
+    "These manipulation methods include:\n",
     "\n",
     "- `generate_dg`: to get the dG values.\n",
     "- `generate_dg_raw`: to get the raw dG values for each individual legs in the ABFE transformation cycles."
    ]
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     "## Analyzing your results\n",
-    "Now that we have defined a set of methods to help us extract results. Let's analyze the results!\n",
+    "Now that we have defined a set of methods to help us extract results, let's analyze the results!\n",
     "\n",
     "### Specify result directories and gather results\n",
     "Let's start by gathering all our simulation results. First we define all the directories where our ABFE results exist. Here we assume that our simulation repeats sit in three different results directories under abfe_results, named from results_0 to results_2."
    ]
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-    "### Obtain the overall difference in binding affinity for all edges in the network\n",
+    "### Obtain the overall difference in binding affinity for all nodes in the network\n",
     "With these extracted results, we can now get the dG prediction between each ligand.\n",
     "\n",
     "Note: if only a single repeat was run, the MBAR error is used as uncertainty estimate, while the standard deviation is used when results from more than one repeat are provided."
    ]
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        "0      1        -18.36                   0.98"
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@@ -533,12 +533,12 @@
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     "### Obtain the raw DGs of every leg in the thermodynamic cycle\n",
-    "If needed, you can also get the individual dG results for each leg of the ABFE transformation cycles. This can be useful in various different situation, such as when trying to diagnose which part of your simulation has the highest uncertainty."
+    "If needed, you can also get the individual dG results for each leg of the ABFE transformation cycles. This can be useful in various different situation, such as when trying to diagnose which part of your simulation has the highest uncertainty. These include the DG of turning ligand interactions off in the `complex` and `solvent`, as well as the `standard_state_correction` that accounts for turning off the Boresch restraints between the non-interacting ligand and the protein and transferring the non-interacting ligand into the standard state."
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        "8  standard_state_correction      1          -9.0                    0.0"
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