improve docs

docs/notebooks/how_to.ipynb

@@ -164,7 +164,8 @@
     }
    ],
    "source": [
-    "inspect.getfullargspec(utils.Local.__init__).args"
+    "inspect.getfullargspec(utils.Local.__init__).args\n",
+    "# The sam can be done for GA: inspect.getfullargspec(utils.Local.__init__).args"
    ]
   },
   {
@@ -195,7 +196,7 @@
     "  costfunc: Cost\n",
     "  costfunc_kwargs:\n",
     "    vina_executable: vina\n",
-    "    receptor_path: /tmp/your_tmp_dir/x0161.pdbqt\n",
+    "    receptor_pdbqt_path: /tmp/your_tmp_dir/x0161.pdbqt\n",
     "    boxcenter:\n",
     "      - 12.11\n",
     "      - 1.84\n",
@@ -236,7 +237,7 @@
     "```yaml\n",
     "  costfunc_kwargs:\n",
     "    vina_executable: vina\n",
-    "    receptor_path: /tmp/your_tmp_dir/x0161.pdbqt\n",
+    "    receptor_pdbqt_path: /tmp/your_tmp_dir/x0161.pdbqt\n",
     "    boxcenter:\n",
     "      - 12.11\n",
     "      - 1.84\n",
@@ -576,7 +577,7 @@
     "try:\n",
     "    whole_result = utils.decompress_pickle(os.path.join(tmp_path.name, 'custom_fitness', 'local_result.pbz2'))\n",
     "except Exception as e:\n",
-    "    print(f\"This was the problem: {e}. So we have to add to the system path the directory where CustomMolDrugFitness.py is located.\")   \n",
+    "    print(f\"This was the problem: {e}. So we have to add to the system path the directory where CustomMolDrugFitness.py is located.\")\n",
     "    sys.path.append(os.path.join(tmp_path.name, 'custom_fitness'))\n",
     "    whole_result = utils.decompress_pickle(os.path.join(tmp_path.name, 'custom_fitness', 'local_result.pbz2'))\n",
     "\n",

docs/source/api.rst

@@ -4,8 +4,8 @@ Summary
 Input data
 ----------
 
-Currently, **MolDrug** only accepts valid RDKit molecules and valid pdbqt files that
-will be processed by Vina.
+Currently, **MolDrug** only accepts valid RDKit molecules and a valid pdbqt file that
+will be processed in case AutoDock-Vina is used.
 
 The idea
 --------

docs/source/installation.rst

@@ -36,11 +36,14 @@ or:
     pip install -U git+https://github.com/ale94mleon/MolDrug.git@main
 
 There are multiple methods to obtain `AutoDock-Vina <https://vina.scripps.edu/>`_. You can use `conda <https://anaconda.org/conda-forge/vina>`_ or download the latest release from the `Vina Repository <https://github.com/ccsb-scripps/AutoDock-Vina/releases>`_.
-We highly recommend using the ast release posted on method `Vina Repository <https://github.com/ccsb-scripps/AutoDock-Vina/releases>`_, which we will demonstrate here.
+We highly recommend using the last release posted on `Vina Repository <https://github.com/ccsb-scripps/AutoDock-Vina/releases>`_.
+
+.. note::
+
 
 
-Getting last Vina
-~~~~~~~~~~~~~~~~~
+Getting last AutoDock-Vina
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 AutoDock-Vina is an ongoing project, and it is advisable to stay up-to-date by regularly checking for the latest `release <https://github.com/ccsb-scripps/AutoDock-Vina/releases/>`_.
 As of the creation of this documentation, the most recent version is `v1.2.5 <https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.5>`_.
@@ -71,10 +74,10 @@ MacOS
 Windows
 ^^^^^^^
 
-Please, download form `release <https://github.com/ccsb-scripps/AutoDock-Vina/releases/>`_. Conda installation may not work.
+Please, download from `release <https://github.com/ccsb-scripps/AutoDock-Vina/releases/>`_. Conda installation may not work.
 
 Via conda
----------
+^^^^^^^^^
 
 MolDrug is also available through conda. However, the pip installation is the recommended one.
 
@@ -87,17 +90,32 @@ MolDrug is also available through conda. However, the pip installation is the re
 .. note::
     MacOS users may face some problems trying to install because of the AutoDock-Vina dependency. If that is so, please follow the pip instructions.
 
-If some dependencies are missing, please installed through pip. Some of them could be:
+If some dependencies are missing, please install them through pip. Some of them could be:
 
 .. code-block:: bash
 
     pip install meeko crem pyyaml scipy tqdm
 
+Converting pdb to pdbqt
+~~~~~~~~~~~~~~~~~~~~~~~
+
+This step can be archived through `OpenBabel <https://github.com/openbabel/openbabel>`__ or through `ADFR <https://ccsb.scripps.edu/adfr/downloads/>`_. We recommend ADFR. Depending on the platform you should be able to access the program `prepare_receptor``. In my case, it lays on `/Users/klimt/ADFRsuite-1.0/bin/prepare_receptor`. Then you can convert your pdb with:
+
+.. code-block:: bash
+
+    /Users/klimt/ADFRsuite-1.0/bin/prepare_receptor -r your_protein.pdb -o your_protein.pdbqt
+
+Check `here <https://ccsb.scripps.edu/adfr/how-to-create-a-pdbqt-for-my-receptor/>`_ for more information.
+
+Getting box information
+~~~~~~~~~~~~~~~~~~~~~~~
+
+To perform the docking you must provide ``boxcenter`` and ``boxsize`` to the cost functions defined in :mod:`moldrug.fitness` For that two PyMol plugins are useful: `GetBox <https://github.com/MengwuXiao/GetBox-PyMOL-Plugin/blob/master/GetBox%20Plugin.py>`_ and/or `autodock <https://github.com/ADplugin/ADplugin/blob/master/autodock.py>`_. Details of their installation and use are not discussed here, please visit their corresponding repositories for more information.
 
 Work with a docker container
 ----------------------------
 
 #. Use the `Docker configuration file on GitHub <https://github.com/ale94mleon/MolDrug/blob/main/Dockerfile>`__.
-#. Vist the `MolDrug <https://hub.docker.com/r/ale94mleon/4moldrug>`__ docker container.
+#. Visit the `MolDrug <https://hub.docker.com/r/ale94mleon/4moldrug>`__ docker container.
 
 Finally ``pip install moldrug`` inside it.

src/moldrug/utils.py

@@ -1225,8 +1225,8 @@ class GA:
         The list of average cost for each generations.
     """
     def __init__(self, seed_mol: Union[Chem.rdchem.Mol, Iterable[Chem.rdchem.Mol]],
-                 costfunc: object, costfunc_kwargs: Dict, crem_db_path: str, maxiter: int, popsize: int,
-                 beta: float = 0.001, pc: float = 1, get_similar: bool = False, mutate_crem_kwargs: Dict = None,
+                 costfunc: object, costfunc_kwargs: Dict, crem_db_path: str, maxiter: int = 10, popsize: int = 20,
+                 beta: float = 0.001, pc: float = 1, get_similar: bool = False, mutate_crem_kwargs: Union[None, Dict] = None,
                  save_pop_every_gen: int = 0, checkpoint: bool = False, deffnm: str = 'ga',
                  AddHs: bool = False, randomseed: Union[None, int] = None) -> None:
         """Constructor
@@ -1242,17 +1242,17 @@ def __init__(self, seed_mol: Union[Chem.rdchem.Mol, Iterable[Chem.rdchem.Mol]],
             The keyword arguments of the selected cost function
         crem_db_path : str
             Path to the CReM data base.
-        maxiter : int
-            Maximum number of iteration (or generation).
-        popsize : int
-            Population size.
+        maxiter : int, optional
+            Maximum number of iteration (or generation), by default 10.
+        popsize : int, optional
+            Population size, by default 20.
         beta : float, optional
             Selection pressure, by default 0.001
         pc : float, optional
             Proportion of children, by default 1
         get_similar : bool, optional
             If True the searching will be bias to similar molecules, by default False
-        mutate_crem_kwargs : Dict, optional
+        mutate_crem_kwargs : Union[None, Dict], optional
             Parameters for mutate_mol of CReM, by default {}
         save_pop_every_gen : int, optional
             Frequency to save the population, by default 0