CLaM Database Management

For a detailed description, please see the documentation website

# Install clamr using devtools (clamdb dependency)
devtools::install_github("https://github.com/calico/clamr.git")

# Install clamdb using devtools
devtools::install_github("https://github.com/calico/clamdb.git")

clamdb has functionality to import and build .msp libraries, however, this requires some additional installation. Specifically, some python code that comes bundled with this package must also be installed.

All of the python code clamdb requires is located in the inst/python folder.

To install this code, you must first install the following python packages:

pandas
rdkit

You must also have configured a conda environment, which is necessary for using the R package reticulate.

Once your conda environment has been configured, you can install the python code here by cloning this repository, navigating to the inst/python subfolder, and executing python setup_mschem.py sdist bdist_wheel, e.g.

git clone <this-repo> <your-system-path>
cd <your-system-path>/clamdb/inst/python
python setup_mschem.py sdist bdist_wheel

Where your-system-path would be specific to where you would like to clone this repository.