Updated to openmmforcefields 0.13 and espaloma 0.3.2

forlilab · May 14, 2024 · 6bc8a15 · 6bc8a15
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![License: LGPL v2.1](https://img.shields.io/badge/License-LGPL_v2.1-green.svg)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) [![PyPI - Version](https://img.shields.io/pypi/v/cosolvkit)](https://pypi.org/project/cosolvkit/0.4.3/) [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
+[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![License: LGPL v2.1](https://img.shields.io/badge/License-LGPL_v2.1-green.svg)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) [![PyPI - Version](https://img.shields.io/pypi/v/cosolvkit)](https://pypi.org/project/cosolvkit/0.4.4/) [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![Documentation Status](https://readthedocs.org/projects/cosolvkit/badge/?version=latest)](https://cosolvkit.readthedocs.io/en/latest/?badge=latest)
 
 
@@ -14,7 +14,7 @@ The installation instructions, documentation and tutorials can be found on http:
 ## Installation
 I highly recommend you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed. To install everything properly, you just have to do this:
 ```bash
-$ conda create -n cosolvkit -c conda-forge -f cosolvkit_env.yml
+$ conda create -n cosolvkit -c conda-forge -f environment.yml
 ```
 For faster installation, use `mamba` or `micromamba` instead of `conda`.
 

diff --git a/cosolvkit/data/config.json b/cosolvkit/data/config.json
@@ -1,9 +1,9 @@
 {
-  "cosolvents": "data/cosolvents.json",
-  "forcefields": "data/forcefields.json",
+  "cosolvents": "cosolvkit/data/cosolvents.json",
+  "forcefields": "cosolvkit/data/forcefields.json",
   "md_format": "openmm",
   "receptor": true,
-  "protein_path": "/path/to/protein/structure",
+  "protein_path": "example/protein.pdb",
   "clean_protein": true,
   "keep_heterogens": false,
   "variants_d": {},
@@ -19,7 +19,7 @@
   "cosolvent_placement": 0,
   "waters_to_keep": [],
   "radius": null,
-  "output": "/path/to/where/to/save/results",
+  "output": "results",
   "run_cosolvent_system": true,
   "run_md": false
 }
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -17,7 +17,7 @@ To install cosolvkit dependencies:
 
 .. code-block:: bash
 
-    $ conda create -n cosolvkit --file cosolvkit_env.yml && conda activate cosolvkit
+    $ conda create -n cosolvkit --file environment.yml && conda activate cosolvkit
 
 
 Installation from source code
@@ -27,7 +27,7 @@ Installation from source code
 
     $ git clone git@github.com:forlilab/cosolvkit.git
     $ cd cosolvkit
-    $ conda create -n cosolvkit --file cosolvkit_env.yml
+    $ conda create -n cosolvkit --file environment.yml
     $ pip install .