diff --git a/docs/notebooks/how_to.ipynb b/docs/notebooks/how_to.ipynb
index 61378f3..fa31190 100644
--- a/docs/notebooks/how_to.ipynb
+++ b/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",
diff --git a/docs/source/api.rst b/docs/source/api.rst
index 1988eda..fea97b0 100644
--- a/docs/source/api.rst
+++ b/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
--------
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 668e2e5..4dd3762 100644
--- a/docs/source/installation.rst
+++ b/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 `_. You can use `conda `_ or download the latest release from the `Vina Repository `_.
-We highly recommend using the ast release posted on method `Vina Repository `_, which we will demonstrate here.
+We highly recommend using the last release posted on `Vina Repository `_.
+
+.. 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 `_.
As of the creation of this documentation, the most recent version is `v1.2.5 `_.
@@ -71,10 +74,10 @@ MacOS
Windows
^^^^^^^
-Please, download form `release `_. Conda installation may not work.
+Please, download from `release `_. 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 `__ or through `ADFR `_. 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 `_ 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 `_ and/or `autodock `_. 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 `__.
-#. Vist the `MolDrug `__ docker container.
+#. Visit the `MolDrug `__ docker container.
Finally ``pip install moldrug`` inside it.
diff --git a/src/moldrug/utils.py b/src/moldrug/utils.py
index 3793855..ec42cc5 100644
--- a/src/moldrug/utils.py
+++ b/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