add devcontainer configuration

.devcontainer/Dockerfile

@@ -0,0 +1,12 @@
+FROM FROM mcr.microsoft.com/devcontainers/universal:2
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -0,0 +1,40 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
+{
+	"name": "Anaconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	},
+
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.python",
+				"ms-toolsai.jupyter"
+			],
+
+			"settings": {
+					"python.defaultInterpreterPath": "/opt/conda/bin/python",
+					"python.languageServer": "Pylance"
+				}
+		}
+	}
+
+
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "python --version",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file copied into the container along with environment.yml* from the parent
+folder. This file is included to prevents the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

environment.yml

@@ -1,15 +1,23 @@
-name: sermacs-workshop
+name: sermacs-2024
 channels:
   - conda-forge
   - defaults
 dependencies:
   - python=3.11
+  - pip
   - pandas
-  - plotly
   - matplotlib
   - numpy
-  - scipy
   - jupyterlab
+  - plotly
+  - nglview
   - rdkit
-  - scikit-learn
-  - pip
+  - openbabel
+  - mdanalysis
+  - vina
+  - ipywidgets>8
+  - prolif
+  - pip:
+    - pdb2pqr
+    - meeko
+    - py3Dmol