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StollLab · Dec 26, 2024 · db746ad · db746ad
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diff --git a/README.md b/README.md
@@ -11,12 +11,13 @@
 </p>
 
 
-| **UPDATES**                                                                                                                   |
-|-------------------------------------------------------------------------------------------------------------------------------|
-| 2024.8.15 : chiLife 1.0 released!                                                                                             |
-| 2024.8.15 : chiLife can now be used to create arbitrary peptides with natural and NCAAs. Checkout the `make_peptide` function. |
-| 2024.8.15 : chiLife can make NCAA structures from smiles. Checkout `smiles2residue`. Note: Requires RDKit to be installed.    | 
-| chiLife now supports arbitrary backbone attachments including DNA and RNA labels and more!                                    | 
+| **UPDATES**                                                                                                                                                                                                                                                                  |
+|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 2024.12.26 : Changes to the "energy funciton" backend. forcefield, forgive factors, etc should all be parts of the energy function now, and not parts of a rotamer library  Checkout [Example_07](https://stolllab.github.io/chiLife/gallery/07-Custom_Energy_Function.html) |                                                                               
+| 2024.08.15 : chiLife 1.0 released!                                                                                                                                                                                                                                           |
+| 2024.08.15 : chiLife can now be used to create arbitrary peptides with natural and NCAAs. Checkout the `make_peptide` function.                                                                                                                                              |
+| 2024.08.15 : chiLife can make NCAA structures from smiles. Checkout `smiles2residue`. Note: Requires RDKit to be installed.                                                                                                                                                  | 
+| chiLife now supports arbitrary backbone attachments including DNA and RNA labels and more!                                                                                                                                                                                   | 
 
 
 

diff --git a/src/chilife/RotamerEnsemble.py b/src/chilife/RotamerEnsemble.py
@@ -62,12 +62,9 @@ class RotamerEnsemble:
             Name of the forcefield you wish to use to parameterize atoms for the energy function. Currently, supports
             `charmm` and `uff`
         energy_func : callable
-            Python function or callable object that takes a protein and a RotamerEnsemble object as input and
+            Python function or callable object that takes a protein or a RotamerEnsemble object as input and
             returns an energy value (kcal/mol) for each atom of each rotamer in the ensemble. See also
-            :mod:`Scoring <chiLife.scoring>` . Defaults to :mod:`chiLife.get_lj_rep <chiLife.get_lj_rep>` .
-        forgive : float
-           Softening factor to be passed to ``energy_func``. Only used if ``energy_func`` uses a softening factor.
-           Defaults to 1.0. See :mod:`Scoring <chiLife.scoring>` .
+            :mod:`Scoring <chiLife.scoring>` . Defaults to a capped lennard-jones repulsive energy function.
         temp : float
            Temperature to use when running ``energy_func``. Only used if ``energy_func`` accepts a temperature
            argument  Defaults to 298 K.

diff --git a/src/chilife/dRotamerEnsemble.py b/src/chilife/dRotamerEnsemble.py
@@ -59,12 +59,9 @@ class dRotamerEnsemble:
                 Name of the forcefield you wish to use to parameterize atoms for the energy function. Currently,
                 supports `charmm` and `uff`
             energy_func : callable
-               Python function or callable object that takes a protein and a RotamerEnsemble object as input and
-               returns an energy value (kcal/mol) for each atom of each rotamer in the ensemble. See also
-               :mod:`Scoring <chiLife.scoring>` . Defaults to :mod:`chiLife.get_lj_energy <chiLife.get_lj_energy>` .
-            forgive : float
-               Softening factor to be passed to ``energy_func``. Only used if ``energy_func`` uses a softening factor.
-               Defaults to 0.95. See :mod:`Scoring <chiLife.scoring>` .
+               Python function or callable object that takes a protein or a RotamerEnsemble object as input and
+               returns an energy value (kcal/mol) for each rotamer in the ensemble. See also
+               :mod:`Scoring <chiLife.scoring>`. Defaults to a capped lennard-jones potentail.
             temp : float
                Temperature to use when running ``energy_func``. Only used if ``energy_func`` accepts a temperature
                argument  Defaults to 298 K.