https://github.com/jewettaij/dlpdb

collect statistics from the entire PDB library
https://github.com/jewettaij/dlpdb

pdb-files structural-bioinformatics

Last synced: 5 months ago
JSON representation

collect statistics from the entire PDB library

• Host: GitHub
• URL: https://github.com/jewettaij/dlpdb
• Owner: jewettaij
• License: mit
• Created: 2017-04-21T16:53:14.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2022-02-18T03:03:29.000Z (over 4 years ago)
• Last Synced: 2025-09-30T14:19:37.004Z (8 months ago)
• Topics: pdb-files, structural-bioinformatics
• Language: Python
• Homepage: http://www.moltemplate.org
• Size: 2.02 MB
• Stars: 5
• Watchers: 1
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

Awesome Lists containing this project

README

          
[![GitHub](https://img.shields.io/github/license/jewettaij/dlpdb)](./LICENSE.md)

[![PyPI - Downloads](https://img.shields.io/pypi/dm/dlpdb)](https://pypistats.org/packages/dlpdb)

[![PyPI - Version](https://img.shields.io/pypi/v/dlpdb)](https://pypi.org/project/dlpdb/)

[![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/jewettaij/dlpdb)]()

dlpdb

===========

##  Description

![distances_and_angles_from_DNA](./examples/dna_example/statistics_keeping_every_3rd_base_pair/dsDNA_3to1_C3p.png)

A collection of tiny scripts to help automate the process of downloading and

extracting sequences, coordinates, distances, angles, 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.)

## Requirements

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.)

## Installation Instructions

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 

`~/.profile`, `~/.bash_profile` or `~/.bashrc` files 

to contain the following lines:

    export PATH="$PATH:$HOME/dlpdb/dlpdb"

    export PATH="$PATH:$HOME/dlpdb/dlpdb/scripts"

##  Documentation

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.

## License

dlpdb is available under the terms of the [MIT license](LICENSE.md).