A collection of tiny scripts to help automate the process of downloading and extracting coordinates, sequences, and secondary-structure information from (a representative subset of) structures from the entire PDB library.
These scripts were originally used to estimate distances distances and angles
between specific atoms in proteins and DNA.
The distribution of these distances and angles can be used to estimate force-field parameters for coarse grained models for these biomolecules. (Such as the DNA example shown above.)
The dlpdb tools requires the Bourne-shell, and a recent version of python (2.7, 3.0 or higher), and can run on OS X, linux, or windows. (...if a suitable shell environment has been installed. See below.)
There are two ways to install dlpdb:
Installation using pip
If you are familiar with pip, then run the following command from within the directory where this README file is located:
pip install .
Make sure that your default pip install bin directory is in your PATH. (This is usually something like ~/.local/bin/ or ~/anaconda3/bin/. If you have installed anaconda, this will be done for you automatically.) Later, you can uninstall dlpdb using:
pip uninstall dlpdb
Instructions for editing your PATH are included below.
Manual Installation method:
Alternatively, you can edit your PATH variable manually to include the subdirectory where the dlpdb.sh script is located, as well as the subdirectory where most of the python scripts are located. Suppose the directory with this README file is named ``dlpdb'' and is located in your home directory:
If you use the bash shell, typically you would edit your
to contain the following lines:
export PATH="$PATH:$HOME/dlpdb/dlpdb" export PATH="$PATH:$HOME/dlpdb/dlpdb/scripts"
This directory should contain 3 folders:
dlpdb/ <-- source code doc/ <-- README files examples/ <-- examples of usage
dlpdb is not a single program or module, but a collection of many short python and bash scripts that work together. Documentation can be found within the "doc" and "examples" directories.
dlpdb is available under the terms of the open-source 3-clause BSD