From c2f989befbe7d5d9fba102b0f4199d8fb27971d0 Mon Sep 17 00:00:00 2001
From: Alejandro Martinez Leon <ale94mleon@gmail.com>
Date: Wed, 10 Jan 2024 20:50:56 +0100
Subject: [PATCH] Update doc

---
 README.rst                    |  4 ++--
 src/moldrug/constraintconf.py | 10 +++++++---
 src/moldrug/utils.py          |  5 +++++
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index ae7a4bd..00a0b6e 100644
--- a/README.rst
+++ b/README.rst
@@ -107,8 +107,8 @@ with the pharmaceutical company `Boehringer Ingelheim <https://www.boehringer-in
 ..  |crem| image:: https://img.shields.io/static/v1?label=Powered%20by&message=CReM&color=9438ff&style=flat
     :target: https://crem.readthedocs.io/en/latest/
     :alt: crem
-..  |license| image:: https://badgen.net/pypi/license/moldrug/
-    :target: https://pypi.python.org/pypi/moldrug/
+..  |license| image:: https://img.shields.io/badge/License-Apache_2.0-blue.svg
+    :target: https://github.com/ale94mleon/moldrug/?tab=Apache-2.0-1-ov-file#readme
     :alt: license
 ..  |downloads| image:: https://static.pepy.tech/personalized-badge/moldrug?period=total&units=international_system&left_color=grey&right_color=brightgreen&left_text=Downloads
     :target: https://pepy.tech/project/moldrug
diff --git a/src/moldrug/constraintconf.py b/src/moldrug/constraintconf.py
index 12d0401..982ca58 100644
--- a/src/moldrug/constraintconf.py
+++ b/src/moldrug/constraintconf.py
@@ -9,9 +9,13 @@
     https://github.com/JoshuaMeyers/Snippets/blob/master/200405_constrained_conformers.ipynb
     and that code was adapted from Tim Dudgeon
     https://github.com/InformaticsMatters/pipelines/blob/master/src/python/pipelines/rdkit/constrained_conf_gen.py
-    All I've done is change the command line wrapper, modify how to remove conformers
-    that clash with the protein, add documentation and
-    handle some possible run time exceptions.
+    All I've done is:
+    * Change command line
+    * Fix get_mcs function for cases rdkit.Chem.rdFMCS.FindMCS fails.
+    * Add the function gen_aligned_conf to fix possible failures of generate_conformers
+    * Change how to remove conformers that clash with the protein
+    * Add documentation
+    * Fix handling of some possible exceptions.
 """
 from copy import deepcopy
 from rdkit import Chem
diff --git a/src/moldrug/utils.py b/src/moldrug/utils.py
index 63aa94f..f46bc52 100644
--- a/src/moldrug/utils.py
+++ b/src/moldrug/utils.py
@@ -1080,6 +1080,8 @@ def __init__(self, seed_mol: Chem.rdchem.Mol, crem_db_path: str, costfunc: objec
             If True the explicit hyrgones will be added, by default False
         randomseed : Union[None, int], optional
            Set a random seed for reproducibility, by default None
+        deffnm : str
+            Just a place holder for compatibility with the CLI.
 
         Raises
         ------
@@ -1353,6 +1355,9 @@ def __init__(self, seed_mol: Union[Chem.rdchem.Mol, Iterable[Chem.rdchem.Mol]],
 
         self.nc = round(pc * popsize)
         self.get_similar = get_similar
+        # Internally update with default values, TODO, maybe I should remove this
+        # and the user should handled CReM parameters byt itself.
+        # I think that this will avoid confusion.
         self.mutate_crem_kwargs = {
             'radius': 3,
             'min_size': 1,