change READMEs

README.md

@@ -4,6 +4,7 @@ The Molecular Docking Tool (`moldocker`) is a software designed to create confor
  - Sampling of the space using Voronoi diagrams
  - Geometrical fitness functions
  - Batched docking using tensorial operations
+ - Monte Carlo docking
 
 ## Installation
 
@@ -32,12 +33,12 @@ pip install .
 
 ### Zeo++ dependency
 
-Zeo++ and its interface to pymatgen are required to use the Voronoi sampler. Please follow the instructions in the [pymatgen documentation](https://pymatgen.org/pymatgen.io.zeopp.html#zeo-installation-steps) to install both accordingly.
+Zeo++ and its interface to pymatgen are required to use the Voronoi sampler. Please follow the instructions at the [pymatgen documentation](https://pymatgen.org/pymatgen.io.zeopp.html#zeo-installation-steps) to install both accordingly.
 
 ## Usage
 
 ### Command line
-The simplest way to use the `moldocker` package is to use the premade scripts (in the `scripts`) folder. As an example, we provide a molecule and a zeolite in [moldocker/tests/files](moldocker/tests/files). With `moldocker` installed, you can dock the molecule to the zeolite using the following command:
+The simplest way to use the `moldocker` package is to use the premade script `dock.py` (in the `scripts`) folder. As an example, we provide a molecule and a zeolite in [moldocker/tests/files](moldocker/tests/files). With `moldocker` installed, you can dock the molecule to the zeolite using the following command:
 
 ```bash
 dock.py moldocker/tests/files/{AFI.cif,molecule.xyz} -o ~/Desktop/dock -d batch -s voronoi_cluster -f min_distance
@@ -47,6 +48,10 @@ This will dock the molecule contained in `molecule.xyz` to the zeolite in `AFI.c
 
 For more information on the dockers, samplers and fitness functions available, run `dock.py --help`. Help on further commands are available once the choice of dockers, samplers and fitness functions are made, e.g. `dock.py -d batch -s voronoi_cluster -f min_distance --help`.
 
+## Examples
+
+Further examples can be seen in the [examples](examples/README.md) folder.
+
 ## Nomenclature
 
 The nomenclature of the variables in this software follows (mostly) the [traditional molecular docking terminology](https://en.wikipedia.org/wiki/Docking_(molecular))

examples/README.md

@@ -0,0 +1,8 @@
+# Examples and usage tutorial
+
+The following examples are currently available in this repository:
+
+1. [Docking TMAda+ to CHA zeolite](CHA_TMada): one molecule is docked to CHA with Voronoi (sequential) and Monte Carlo dockers.
+2. [Docking triethylamine to MOR zeolite](MOR_loading): several triethylamine molecules are docked to MOR zeolite with Voronoi batch docker.
+3. [Docking benzene to MOF-5](MOF-5): several benzene molecules are docked to MOF-5 using the Voronoi batched docker. The MOF-5 structure was retrieved from the Cambridge Structural Database (ID [SAHYIK](https://www.ccdc.cam.ac.uk/structures/search?identifier=SAHYIK))
+4. [Docking water to a Ni(111) surface](Ni111): one water molecule is docked to a Ni(111) surface using the Gaussian target fitness function. The Ni(111) surface structure was retrieved from the [Materials Project](https://materialsproject.org) (ID [mp-23](https://materialsproject.org/materials/mp-23/surfaces/[1,%201,%201]/cif))