diff --git a/README.md b/README.md index 56a2d206..97234704 100644 --- a/README.md +++ b/README.md @@ -23,10 +23,10 @@ We show that this approach is not only sufficiently expressive to reproduce lega # Installation ```bash -$ conda install -c conda-forge -c dglteam "espaloma=0.3.1" "dgl<1" +$ conda install -c conda-forge "espaloma=0.3.2" ``` -# Example: Deploy espaloma 0.3.1 pretrained force field to arbitrary MM system +# Example: Deploy espaloma 0.3.2 pretrained force field to arbitrary MM system ```python # imports @@ -51,7 +51,7 @@ espaloma_model(molecule_graph.heterograph) openmm_system = esp.graphs.deploy.openmm_system_from_graph(molecule_graph) ``` -If using espaloma from a local `.pt` file, say for example `espaloma-0.3.1.pt`, +If using espaloma from a local `.pt` file, say for example `espaloma-0.3.2.pt`, then you would need to run the `eval` method of the model to get the correct inference/predictions, as follows: @@ -59,13 +59,26 @@ inference/predictions, as follows: import torch ... # load local pretrained model -espaloma_model = torch.load("espaloma-0.3.1.pt") +espaloma_model = torch.load("espaloma-0.3.2.pt") espaloma_model.eval() ... ``` The rest of the code should be the same as in the previous code block example. +# Compatible models + +Below is a compatibility matrix for different versions of `espaloma` code and `espaloma` models (the `.pt` file). + +| Model πŸ§ͺ | DOI πŸ“ | Supported Espaloma version πŸ’» | Release Date πŸ—“οΈ | Espaloma architecture change πŸ“? | +|---------------------|-------|------------------------------|----------------|---------------------------------| +| `espaloma-0.3.2.pt` | | 0.3.1, 0.3.2 | Sep 22, 2023 | βœ… No | +| `espaloma-0.3.1.pt` | | 0.3.1, 0.3.2 | Jul 17, 2023 | ⚠️ Yes | +| `espaloma-0.3.0.pt` | | 0.3.0 | Apr 26, 2023 | ⚠️Yes | + +> [!NOTE] +> `espaloma-0.3.1.pt` and `espaloma-0.3.2.pt` are the same model. + # Using espaloma to parameterize small molecules in relative free energy calculations An example of using espaloma to parameterize small molecules in relative alchemical free energy calculations is provided in the `scripts/perses-benchmark/` directory. diff --git a/docs/deploy.rst b/docs/deploy.rst index 06f0ac3a..414ca0a5 100644 --- a/docs/deploy.rst +++ b/docs/deploy.rst @@ -1,4 +1,4 @@ -Deploy espaloma 0.3.1 force field to parametrize your MM system +Deploy espaloma 0.3.2 force field to parametrize your MM system =============================================================== Pretrained espaloma force field could be deployed on arbitrary small molecule systems in a few lines:: @@ -24,12 +24,12 @@ systems in a few lines:: # create an OpenMM System for the specified molecule openmm_system = esp.graphs.deploy.openmm_system_from_graph(molecule_graph) -If using espaloma from a local ``.pt`` file, say for example ``espaloma-0.3.1.pt``, +If using espaloma from a local ``.pt`` file, say for example ``espaloma-0.3.2.pt``, then you would need to run the ``eval`` method of the model to get the correct inference/predictions, as follows:: # load local pretrained model - espaloma_model = torch.load("espaloma-0.3.1.pt") + espaloma_model = torch.load("espaloma-0.3.2.pt") espaloma_model.eval() The rest of the code should be the same as in the previous example. diff --git a/docs/install.rst b/docs/install.rst index 01638b01..cdf7ed15 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -4,9 +4,7 @@ Installation conda ----- -While we are working to put `dgl` on conda-forge, please follow the instructions below to install `espaloma` from `conda-forge` and the package `dgl` package from `dglteam`. - Install espaloma:: - conda install -c conda-forge -c dglteam "espaloma=0.3.1" "dgl<1" + conda install -c conda-forge "espaloma=0.3.2"