LOOS Files

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Our email address has changed.  Please use <loos.maintainer@gmail.com>
to contact us regarding LOOS.


   * RELEASE 2.0.5 *

This release consists of some minor internal changes, a few bug fixes,
and a few added or changed tools.  There is one major change, however,
in the setup scripts (setup.sh and setup.csh).  Previously, LOOS
directories were *appended* to the appropriate environment variables
(e.g. PATH, LD_LIBRARY_PATH, etc).  Now, these directories are
*prepended*.

New tools include the transition_contacts tool (time series of
transition between two structures) and serialize-selection tool
(transforms a trajectory containing multiple molecules into a longer
trajectory with a single molecule).  We have also added fcontacts
an an alternative to contact-time.  Bug fixes include gmxdump2pdb,
native_contacts, and renum-pdb.  We have added LOOS exceptions to
PyLOOS, so functions such as selectAtoms() can throw without crashing
python.

The principal internal change involves the iterative alignment and
averaging functions so that the versions that take a pTraj no longer
cache trajectory frames.  This change also affects the aligner and
rmsd2ref tools.  In addition, the API for both trajectory and
structure classes has changed slightly, taking an istream object
rather than an ifstream object.

For more details, see the ChangeLog file included with LOOS.




   * RELEASE 2.0.4 *

This release includes a number of bug fixes and important changes.  An
issue with building LOOS when using Boost 1.52+ has been addressed.
MacOS is now supported by the beta version of PyLOOS.  PyLOOS may also
be installed now.  Note, however, that how you build PyLOOS has
changed: use "scons pyloos=1".  We have also added a "chainid" keyword
to the selection language.

For more details, please refer to the ChangeLog file or the "Changes"
section in the documentation.



   * RELEASE 2.0.3b *

! IMPORTANT NOTICE ! ! IMPORTANT NOTICE ! ! IMPORTANT NOTICE ! ! IMPORTANT NOTICE !

The previously posted 2.0.3 release was a binary version that was
inadvertently released.  The current 2.0.3b release is the official
source code release.  We sincerely apologize for any
inconvenience/confusion this may have caused, and strongly recommend
downloading and installing this version.


This release includes a number of bug fixes and new features,
including support for the AMOEBA variant of Amber prmtop files as well
as NetCDF formatted Amber trajectories (if a suitable NetCDF library
is installed prior to building LOOS).  The gridgauss tool has been
changed to allow more control over the smoothing kernel.  The command
line arguments have therefore changed and the old way of running it
will no longer work.

For more details, see the ChangeLog or the "Changes" section in the
Doxygen-generated documentation.


   * RELEASE 2.0.2 *

This is a maintenance release of loos that addresses issues with
reading and writing PDB files that contain CONECT records for bonds.
Previously, if the PDB held a bond from A to B, the bond from B to A
was not implicitly made.  When writing a PDB, both the A to B and B to
A bonds would be written out.  Now, the implicit bonds are made when
reading in a PDB and only the unique bonds are written out.

There was also a side-effect in the PDB writing code where the
underlying PDB object could end up being sorted when writing out a PDB
that contained bonds.  This has been fixed.

Finally, the model-select tool now uses command-line options, so a
selection requires the "-s" or "--selection" option.  The tool also
supports a "--splitby" option that can be used to diagnose
connectivity and group-splitting disorders.

   * RELEASE 2.0.1 *
   
This release of LOOS introduces support for Mac OS X 10.8 (Mountain
Lion) and Fedora 17.  Note that the Python interface is still
unsupported with MacOS.  A new tool, gmxdump2pdb.pl, has also been
added.  This program creates a PDB and a minimal PSF for
Gromacs/MARTINI systems by parsing the output of gmxdump.  Several
minor bugs have also been addressed along with minor improvements in
the python interface and the addition of two new hydrogen bonds
analysis tools.

An internal change has been made in how the Atom::bondsbit is
handled.  Previously, it reflected whether or not an atom had any
bonds to any other atoms.  Calling Atom::getBonds() on an atom that
had no bonds would throw an exception.  Now, the bondsbit is set if
the atom has valid connectivity, even if that includes not having any
bonds to it.  Additionally, getBonds() will no longer throw an
exception if the bonds list is empty and there is valid connectivity.
Instead, it will return an empty vector.  Reading in a PSF or a PDB
with CONECT records will result in atoms that have valid connectivity,
for example.

For more complete details, refer to the ChangeLog or the LOOS
documentation.


   * RELEASE 2.0.0 *

This is a new major release of LOOS that includes the beta-release of
PyLOOS--the Python bindings for LOOS.  PyLOOS is currently only
supported under Linux and requires a recent version of SWIG.
Additionally, the interface and subsequent functionality may change in
future releases.  See the INSTALL file and/or the Doxygen
documentation for LOOS to build PyLOOS and get started using it.
PyLOOS support is not turned on by default and must be explicitly
built by typing "scons pyloos".  There are also a few examples of
using the Python interface in the Packages/PyLOOS.

LOOS is now built using shared libraries.  The shell environment must
be configured for the location of the shared LOOS library.  Upon
building LOOS, setup scripts (setup.csh and setup.sh) will be
created.  These must be sourced (i.e. "source setup.sh") prior to
executing any LOOS tool.

There are also a number of minor bugs addressed by this release,
including bugs in subsetter, averager, blurrogram.pl, aligner, and
potential bugs in the GROMACS trr file support and in PDB output
files.  See the release notes in either ChangeLog or in the LOOS
documentation for more details.

Improvements to LOOS include a "--fullhelp" option added to most
tools, describing in more detail the tool, the algorithms used, and
typical use-cases.  The performance of AtomicGroup::within() has been
improved and support for periodic boundaries added.  In addition, the
density-dist tool's original behavior (the first selection is always
"all") has been restored.  New tools include potential_profile.py to
compute the electrostatic potential profile and a cross-dist tool to
compute the distribution of crossing angles and torsions for chains.
For more complete details, see either the ChangeLog or the LOOS
documentation.