Mosaist

Mosaist is a C++ library for working with and designing protein structures and sequences. It is publicly available under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License.

Installation

Running make (after appropriately modifying makefile, as necessary) will compile all library components, tests, and programs. Running programs without command line arguments will display usage statements. Programs search and design may be of particular interest to users:

• search demonstrates the use of our efficient protein sub-structure search algorithm FASST. See programs/search.cpp for how to use FASST, with the relevant library code found in srs/mstfasst.cpp and include/mstfasst.h. Use program fasstDB to build a searchable database out of an arbitrary set of structures.
• design uses our newest efficient implementation of the dTERMen design method (see Zhou et al.) to enable a variety of structure-based design and optimization tasks.

Python interface

A minimal python interface to Mosaist, which relies on the Boost.Python library, is implemented in src/mstpython.cpp. At this time, this is not the primary means by which we (in the Grigoryan lab) use Mosaist ourselves, so the interface is provided mainly as a starting point for folks who might find such an interface useful. Running make libs python (after installing Boost.Python for your version of python) should produce a python library under libs/mstpython.so, which can then be accessed in python (e.g., impost mstpython as mst), provided the .so file is placed in the library path. However, we have found that compiling Boost.Python interfaces tends to be very brittle and compilation details often need to be adjusted based on machine and operating system. At the very least, you will likely need to modify the pythonExec variable within makefile to point to your python interpreter.