Copyright © 2008-2024, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester

Quick Links

Clone LOOS from GitHub
Online tutorials and documentation
Download a tutorial (pdf) on using LOOS
YouTube video describing LOOS
Ask the developers a question at loos..nosp@m.main.nosp@m.taine.nosp@m.r@gm.nosp@m.ail.c.nosp@m.om or by opening an issue on GitHub.
Building LOOS
Tools included with LOOS
Selection Language
Common Options for Tools
Supported File Formats
Citing LOOS in published work
Exceptions in LOOS and PyLOOS
Changes
FAQ
- FAQ for PyLOOS
Posters and presentations on LOOS
2020 Biophysical Society Poster

Introduction

Welcome to LOOS, a product of the Grossfield Lab at the University of Rochester Medical School and the Department of Biochemistry and Biophysics. Our goal in developing LOOS is to make it easier to analyze molecular dynamics simulations. LOOS is a code library for developing new analysis applications, designed to simplify the common tasks (reading structure and trajectory files, selecting atoms, computing geometric quantities) found in almost every application. Moreover, it is distributed with a number of useful standalone tools, ranging from simple things like radial distribution functions and radii of gyration to principal component analysis to sophisticated methods for analyzing statistical errors.

LOOS has several major features:

It transparently reads the native file formats for most major biomolecular simulation pacakges, including CHARMM, NAMD, gromacs, AMBER, and Tinker.
It uses an expressive syntax to allow selection of atoms using all available metadata (e.g. atom number, residue name, etc). For more information see Selection Language.
It allows novel analysis applications to be developed rapidly, with minimal programming skill required. For example, atoms are referred to using reference-counted shared pointers, which retain the benefits of using pointers (e.g. rapid, lightweight copying) without requiring the developer to do manual memory management.
It should run on any unix-like environment, and is tested under multiple linux versions and Mac OSX.

For assistance using LOOS, to suggest a patch, to request a feature, or simply to offer positive feedback, email loos.maintainer [AT] gmail.com. The latest version of LOOS can be found at our GitHub page.

We strongly suggest that you also follow LOOS on Github.

Applications

Although we primarily view LOOS as a development platform – a tool for making tools – it is distributed with a number of prebuilt applications. The included tools were developed in the course of research in the Grossfield lab, but we believe them to be generally useful enough to merit their inclusion. Some of the code for these programs is found in the Tools/ directories, while other related programs are grouped together as Packages (e.g. Packages/Convergence/).

For more information, see the Tools page

In addition to providing valuable functionality (principal component analysis, structure alignment, etc), these applications can also be useful as templates for developing new applications using LOOS. We have taken a general design approach of developing relatively simple, single-purpose tools, as we believe that makes it easier to quickly add functionality and experiment with analysis methods, without the overhead of integrating with a larger package. Many (if not most) analysis involve the same sequence of steps: read a description of the system (e.g. a PDB, PSF, parmtop, or gro file), select which atoms will be examined, and then, for each frame in a trajectory, compute some geometric quantity using the coodinates (e.g. their centroid or moments of inertia).

Bugs

There are none...only features. So don't worry about them! Either mail us directly (loos.maintainer [AT] gmail.com) or raise an issue on GitHub.

Future Plans

More extensive manual, including developer's tutorial
More applications

License

LOOS (Lightweight Object-Oriented Structure library)
Copyright © 2008-2024, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester
This package (LOOS) is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation under version 3 of the License.

This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.