Merge pull request #37 from janash/rdkit-postgres

Add recipe and documentation for RDKit Postgres image

docs/compchem/index.rst

@@ -24,4 +24,6 @@ construct and run containerized computational chemistry software.
     psi4v180-mamba141-ase322-jupyter
     psi4-ase_example
     pyscf221-mamba141
-    pyscf_example
+    pyscf_example
+    rdkit-postgres162
+    rdkitpostgres-example

docs/compchem/rdkit-postgres162.rst

@@ -0,0 +1,76 @@
+.. _rdkit_postgres162:
+
+*********************************************************
+{{ rdkit_postgres162.hub_specifications[0]["Source"].split("/")[-1] }}
+*********************************************************
+
+{% set title = rdkit_postgres162.get("name") %}
+
+{{title}}
+=========================================================
+
+{% block content %}
+    {{ rdkit_postgres162.description }}
+{% endblock content %}
+
+Source Specifications
+=====================
+
+{% block specifications %}
+    {% for dc in rdkit_postgres162.source_specifications %}
+        {% for key, value in dc.items() %}
+            * **{{ key }}**: {{ value }}
+        {% endfor %}
+    {% endfor %}
+{% endblock specifications %}
+
+MolSSI Container Hub Specifications
+===================================
+
+{% block hub_specifications %}
+    {% for dc in rdkit_postgres162.hub_specifications %}
+        {% for key, value in dc.items() %}
+            * **{{ key }}**: {{ value }}
+        {% endfor %}
+    {% endfor %}
+{% endblock hub_specifications %}
+
+* **Image pull command**:
+
+    .. code-block:: bash
+
+        {{ rdkit_postgres162.docker_pull_command }}
+
+* **Container run command**:
+
+    .. code-block:: bash
+
+        {{ rdkit_postgres162.docker_run_command }}
+
+{% block note %}
+{% if rdkit_postgres162.note != "" %}
+.. note::
+
+        {{ rdkit_postgres162.note }}
+{% endif %}
+{% endblock note %}
+
+Image Specifications
+====================
+
+{% block image_specifications %}
+    {% for dc in rdkit_postgres162.image_specifications %}
+        {% for key, value in dc.items() %}
+            {% if dc[key] is string or dc[key] == "" %}
+                * **{{ key }}**: {{ value }}
+            {% else %}
+                * **{{ key }}**:
+                {% for key2 in dc[key] %}
+                    {% for key3, val3 in key2.items() %}
+                        + *{{ key3 }}*: {{ val3 }}
+                    {% endfor %}
+                {% endfor %}
+            {% endif %}
+        {% endfor %}
+    {% endfor %}
+{% endblock image_specifications %}

docs/compchem/rdkitpostgres-example.rst

@@ -0,0 +1,82 @@
+.. _rdkitpostgres_example:
+
+********************************
+RDKit Postgres Cartridge Example
+********************************
+
+This example demonstrates how to use the RDKit cartridge with a PostgreSQL database.
+When using the RDKit Postgres container, you can launch the container then access the database server using the `psql` command line tool 
+from the host machine or from within the container.
+
+Launching the RDKit Postgres Container
+--------------------------------------  
+
+You can launch the server using the following command. 
+Note that you should replace `mysecretpassword` with a password of your choice.
+
+.. code-block:: bash
+
+    docker run --name rdkitpostgres -e POSTGRES_PASSWORD=mysecretpassword -p 5432:5432 -d molssi/rdkitpostgres-postgres162:latest
+
+
+This will start the server. 
+You can access it from within the container using the following command.
+
+.. code-block:: bash
+
+    docker exec -it rdkitpostgres psql -U postgres
+
+Because the command set up port mapping (`-p 5432:5432`), you can also access the server from the host machine using the following command.
+Note that you will need to have the `psql` command line tool installed on your host machine and enter the password you specified when launching the container.
+
+.. code-block:: bash
+
+    psql -h localhost -U postgres -d postgres
+
+
+Loading Data
+------------
+
+For a more detailed tutorial, please refer to the `RDKit PostgreSQL cartridge documentation <https://www.rdkit.org/docs/Cartridge.html>`_
+
+The following example demonstrates how to load data into the database.
+
+First, make sure the RDKit extension is loaded:
+
+.. code-block:: sql 
+
+    CREATE EXTENSION IF NOT EXISTS rdkit;
+
+
+Next, create a table called `mols` with a `mol` column.
+
+.. code-block:: sql 
+
+    CREATE TABLE mols (id serial primary key, mol mol);
+
+
+Next, load a few molecules into the database using SMILES strings:
+
+.. code-block:: sql 
+
+    INSERT INTO mols (mol) VALUES ('c1ccccc1');
+    INSERT INTO mols (mol) VALUES ('CCO');
+    INSERT INTO mols (mol) VALUES ('CC(=O)O');
+    INSERT INTO mols (mol) VALUES ('C(=O)CC');
+
+
+Querying Data
+--------------
+
+You can now perform queries like substring searches, similarity searches, and other analysis associated with RDKit.
+For example, to find all molecules that contain a carbonyl group, you can use the following query.
+
+.. code-block:: sql 
+    
+    SELECT * FROM mols WHERE mol @> 'C(=O)';
+  
+
+
+
+
+

molssi_hub/compchem/rdkit-postgres162/Dockerfile

@@ -0,0 +1,8 @@
+FROM postgres:16.2
+
+LABEL maintainer="Jessica A. Nash, \
+                  Molecular Sciences Software Institute"
+
+RUN apt update && \
+    apt install -y --no-install-recommends postgresql-16-rdkit && \
+    rm -rf /var/lib/apt/lists/*

molssi_hub/compchem/rdkit-postgres162/metadata.json

@@ -0,0 +1,46 @@
+{
+    "name": "RDKit Postgres Cartridge",
+    "description": "RDKit PostgreSQL cartridge is a PostgreSQL extension that provides chemical structure handling functionality to the PostgreSQL database. It is based on the RDKit cheminformatics library.",
+    "source_specifications": [
+        {
+            "Developers": "https://github.com/rdkit/rdkit/graphs/contributors",
+            "Source": "https://github.com/rdkit/rdkit",
+            "Documentation": "https://www.rdkit.org/docs/Cartridge.html"
+        }
+    ],
+    "hub_specifications": [
+        {
+            "Repository": "https://hub.docker.com/r/molssi/rdkit-postgres162",
+            "Tags": "https://hub.docker.com/r/molssi/rdkit-postgres162/tags",
+            "Source":"https://github.com/MolSSI/molssi-hub/tree/main/molssi_hub/compchem/rdkit-postgres162",
+            "Recipe":"https://github.com/MolSSI/molssi-hub/blob/main/molssi_hub/compchem/rdkit-postgres162/Dockerfile"
+        }
+    ],
+    "docker_pull_command": "docker pull molssi/rdkitpostgres-postgres162:latest",
+    "docker_run_command": "docker run --name rdkitpostgres -e POSTGRES_PASSWORD=mysecretpassword -p 5432:5432 -d molssi/rdkitpostgres-postgres162:latest",
+    "note": "See the full documentation for the base PostgreSQL image for alternative environment variables and run commands - https://hub.docker.com/_/postgres",
+    "tip": "See the full documentation for the base PostgreSQL image for alternative environment variables and run commands - https://hub.docker.com/_/postgres",
+    "image_specifications":[
+        {
+            "OS/Arch": "debian:bookworm-slim",
+            "Users (UID)": "root (0)",
+            "Groups (GID)": "root (0)",
+            "Environment variables": [
+                {
+                    "POSTGRES_PASSWORD": "",
+                    "POSTGRES_USER": "postgres",
+                    "POSTGRES_DB": "postgres"
+
+                }
+            ],
+            "Volumes": "None",
+            "Network": "None",
+            "Extras": [
+                {
+                    "Added directories": "None",
+                    "Important packages installed": ""
+                }
+            ]
+        }
+    ]
+}