LOOS  v2.1.2
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Lightweight Object-Oriented Structure library (LOOS)

Copyright © 2008-2013, Tod D. Romo, Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine & Dentistry, University of Rochester

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Important News

Our email address has changed. Please use loos..nosp@m.main.nosp@m.taine.nosp@m.r@gm.nosp@m.ail.c.nosp@m.om to contact us regarding LOOS. We now have two mailing lists available,


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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, Mac OSX, and cygwin.

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 http://loos.sourceforge.net.

We strongly suggest that you also subscribe to the loos-announce mailing list; it's a low-volume list used primarily to announce new releases. Since most releases contain bug-fixes, we always recommend using the most recent version of LOOS.

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! Email us directly (loos.maintainer [AT] gmail.com) if you find a bug^H^H^H unintended feature.

Future Plans

  • More extensive manual, including developer's tutorial
  • More applications

License

LOOS (Lightweight Object-Oriented Structure library)
Copyright © 2008-2012, 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/.

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