From 6de5761e2675221614097a685c7280966a141803 Mon Sep 17 00:00:00 2001 From: Daniel Schwalbe-Koda Date: Wed, 15 Jul 2020 09:15:08 -0400 Subject: [PATCH] change READMEs --- README.md | 9 +++++++-- examples/README.md | 8 ++++++++ 2 files changed, 15 insertions(+), 2 deletions(-) create mode 100644 examples/README.md diff --git a/README.md b/README.md index e5cffd4..afba0d1 100644 --- a/README.md +++ b/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)) diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000..fd55063 --- /dev/null +++ b/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))