protCAD official development tree

protCAD is an implementation of the protein design software library that originated in the Bill Degrado Lab and is currently maintained by The Vikas Nanda Lab.

-Computational Methods and their Applications for de novo Functional Protein Design and Memebrane Protein Solubilization Summa CM 2002

 Installation
===========================

-Install dependencies

sudo apt-get install g++ git 

-Add protcad to your bash file and link in path as follows (in ubuntu edit .bashrc and add this to the end of file with directory of choosing)

export PROTCADDIR=/home/username/protcad
export PATH=$PATH:$PROTCADDIR:$PROTCADDIR/bin

-protCAD can be installed from the root directory of protcad (protcad/) by entering this statement into the terminal: make lib


 Usage
===========================

-New programs are written in C++ and added to the projects directory for compilation and usage

-In protcad/projects is an example program (example.cc) that can be compiled by typing this into the terminal in the protcad root directory: make example 

-New programs need to be added to the makefile called 'Makefile' in protcad/ for compilation, like example has been. 

-Additional examples are in the protcad/src/examples folder for reference and can be added to the projects directory and MakeFile for compilation.

-New programs written are intended to follow the same directory structure and usage as 'example' does.


 Development process
===========================

Developers work in their own trees, then submit pull requests when
they think their feature or bug fix is ready.

The patch will be accepted if there is broad consensus that it is a
good thing. 

The master branch is regularly built and tested.  Tags are regularly created to indicate new
official, stable release versions of protCAD.

Feature branches are created when there are major new features being
worked on by one or several people.

From time to time a pull request will become outdated. If this occurs, and
the pull is no longer automatically mergeable; a comment on the pull will
be used to issue a warning of closure. The pull will be closed 15 days
after the warning if action is not taken by the author. Pull requests closed
in this manner will have their corresponding issue labeled 'stagnant'.

Issues with no commits will be given a similar warning, and closed after
15 days from their last activity. Issues closed in this manner will be 
labeled 'stale'.