LOOS: a lightweight object-oriented structure analysis library
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README.md

The Lightweight Object Oriented Structure analysis library

Build Status

Getting Help

You can also contact us directly at loos.maintainer@gmail.com

Documentation

Documentation is currently available online at http://loos.sourceforge.net and bundled with the official release downloads. If you are cloning from GitHub, then local documentation will need to be built using Doxygen. See the INSTALL file for more details.

IMPORTANT NOTE FOR MACOS 10.11 "EL CAPITAN" USERS

There is a problem with using PyLOOS with the new System Integrity Protection (SIP) enabled (see https://support.apple.com/en-us/HT204899 for more information about SIP). We are aware of this and working on a decent solution. See the Mac section of the INSTALL file for more details.

Using LOOS from GitHub

Welcome to the GitHub version of LOOS. This repository was created by converting our old SVN repository. The SVN feature branches exist as refs/tags, and appear in GitHub as releases, but they should not be confused with the actual LOOS releases. Those can be found using semantic versioning (e.g. release-2.3.1, release-2.3.0, ...)

We recommend that, unless you want to develop with LOOS, you stick to downloading releases either by using tags, the releases tab in GitHub, or downloading a release tarball from sourceforge.

For help with installing LOOS, please see the INSTALL file. For more details about what has changed in LOOS, see the ChangeLog file.

Release 2.3.3 (beta)

Note: Checking out a beta release means you are checking out a version of LOOS that is under active development. This may include build issues, tools not working, and undocumented "features."

Major changes in LOOS include better DCD handling, support for multiple trajectories in some tools (and at the API level), as well as a new parser for specifying frame ranges for tools.

LOOS now has the ability to handle DCD trajectories with a 0 frame count in the header (fixdcd is no longer required for this case). The count will be estimated based on the model-size and trajectory file size.

A new subclass of Trajectory has been added called MultiTrajectory. A MultiTrajectory object may contain multiple pTraj's and treats them as one giant trajectory. Each sub-trajectory can have its own skip and stride. In addition, there is a MultiTrajOptions class for handling multiple trajectories in a tool.

The parse for specifying ranges has been upgraded to use Boost Spirit. This should make it more robust. In addition, you now no longer need to know the length of a trajectory to use a range. An empty "field" will be filled in with the appropriate value. For example, to skip the first 10 frames, then take every other frame until the end of the trajectory, use: toolname -r 10:2: model.psf trajectory.dcd

NOTE: The short options to subsetter have been changed to be consistent with the new MultiTrajOptions set of options: "-i" is used for stride and "-k" for skip. The long options have not changed.

Additional changes to LOOS include the addition of a new lipid_survival tool and a multi-rmsds tool. Proper (full) support for atom inequalities in Python has been addressed. A new reimaging mode has been added to subsetter (--reimage=zealous) that fixes some issues coming from Gromacs. The output of dibmops has been changed to have a "0" in bins with no data rather than "-1". Finally, a number of bugs have been fixed. See the ChangeLog for more details.

RELEASE 2.3.2

This release includes a number of changes to support our migration to GitHub as well as some important bug fixes and additions.

We have reorganized the LOOS source code so that the core library now resides in the "src" directory. The shared library that's built (along with the python code) is still copied to the top-level LOOS directory.

The Doxygen-based documentation is now handled a little bit differently. When cloning from GitHub, the documentation will be automatically built by SCons. This means doxygen and graphviz are now required to build LOOS. If you download a release from GitHub, then you can also download the pre-built tar file containing the documentation. If this is in the top LOOS source directory, then SCons will see it and unpack it for you. Finally, if you download a release from SourceForge, the the pre-built documentation is bundled with the release. In all cases, you can always find the docs for the current release online at http://grossfieldlab.github.io/loos/ or http://loos.sourceforge.net

Bugs fixed in this release include some important fixes to the OMG, a bug affecting aligner and membrane_map when aligning to a reference structure, making XTCWriter available to PyLOOS, and a few more minor fixes. See the INSTALL file for more details.

New tools in this release include verap, a quick vertical area profile tool, cylindrical-thickness, and inside_helices. New features include providing support for manually mapping molecule names to segids in the gmxdump2pdb tool and support for writing GRO files.

RELEASE 2.3.1

This release of LOOS is a bug-fix release. A bug was discovered in membrane_map that caused the z-axis of all coordinates to be set to 0. This affects height and vector calculations, but not density.

The build system has been changed slightly. Some compilers require multiple environment variables to work correctly. In order to handle these cases, the LOOS build will import all environment variables into SCons before building. This is not the SCons way to do things, however it makes handling these edge cases much easier. In the event that these extra environment variables cause problems, you can revert to a mostly "clean" build environment by editing the SConstruct file. Starting at line 72 with "env = Environment(...)", uncomment the first invocation and comment out the second one.

In addition, improvements were made to the documentation.

RELEASE 2.3.0

This release of LOOS comes with a number of major changes, most related to PyLOOS. A detailed description of these changes is available in the new "what's new in PyLOOS" section of the documentation, and is listed in the "Quick Links" off the main page.

NUMPY IS NOW REQUIRED FOR BUILDING PYLOOS. For Linux users, this will just be a package install. For Mac users, the system numpy will be used. See the INSTALL file for more information.

PyLOOS has been reorganized and new trajectory handling classes have been added. All Python-based components of PyLOOS are now in the loos.pyloos module. The new trajectory classes are easier to use than the old PyTraj classes (they no longer require you to explicitly wrap a loos.Trajectory object). In addition, you can combine multiple trajectories into a large "virtual" trajectory. The frames of the composite trajectory can be iteratively aligned (a la aligner) or aligned to a reference structure. See the documentation for pyloos under the Namespace tab or search for Trajectory.

Additional PyLOOS changes include bug fixes for the iterativeAlignment function. The splitting functions in AtomicGroup now return a Python list rather than an AtomicGroupVector. Coordinates can be extracted from an AtomicGroup or a Trajectory as a NumPy matrix. An SVD/PCA function has also been added to PyLOOS. All old PyLOOS functions that begin or end with Py are now deprecated and will be removed in the next release. These include PyTraj, PyAlignedTraj, and iterativeAlignmentPy. Finally, a k-means clustering program (using PyLOOS) has been added. Also, we've added a new package (Voronoi), which will help users analyze membrane/membrane protein simulations.

There are a number of significant non-PyLOOS changes as well. An "index" keyword has been added to pick atoms based on their position in a model (rather than atom id). The rmsds tool (all-to-all RMSD) has been significantly optimized and can now be run multithreaded. The default is to use only a single thread. If you built LOOS with a multithreaded math library, be aware of possible conflicts (though that shouldn't happen with rmsds). Last, but not least, a number of minor bug fixes are included. See the ChangeLog file or the change log in the documentation for more details.