What's new in LOOS 2.2.5
Apr 25, 2015
- Fixed handling of non-netCDF Amber files when buildind LOOS with netCDF support
- Fixed reading of Amber prmtop files with mixed case format specifiers
- Fixed bug in merge-traj that required downsampled dcd filename
- Fixed bug in fcontacts resulting in NaN's in output if there are no target atoms near the probe.
- Fixed fullhelp in subsetter
- (PyLOOS ONLY) Fixed bug in GCoord operator overloads
New in LOOS 2.2.4 (Feb 7, 2015)
- Just in time for the Biophysical Society meeting, we are releasing another maintenance release of LOOS. This release addresses two issues with reading Amber files. The first involves reading prmtop files where the format specification was not in caps. The second
- issue fixed involves the detection of NetCDF vs plain ASCII trajectory files (mdcrd) when LOOS is built with NetCDF support. For versions 2.2.0 through 2.2.3, only NetCDF trajectories could be read if LOOS had been built with NetCDF support. As of version 2.2.4, LOOS will correctly read either type of Amber trajectory.
New in LOOS 2.2.3 (Jan 27, 2015)
- This is another maintenance release of LOOS. It addresses a PyLOOS bug that caused some values to be wrapped by SWIG that should not have been (e.g. coord.x() would return a wrapped float rather than the float value). This bug likely affects most PyLOOS programs and tools (including the OptimalMembraneGenerator Package). In addition, the error handling in the build system has been improved. We strongly encourage all users to update to this release.
New in LOOS 2.2.2 (Jan 19, 2015)
- This is a maintenance release of LOOS. There was a bug affecting version 2.2.0 and 2.2.1 that prevented LOOS from reading Amber parmtop files. There was also a bug preventing building in MacOS with the latest version of XCode and LOOS 2.2.1. We strongly encourage everyone to update to this release.
New in LOOS 2.2.1 (Jan 15, 2015)
- This is a maintenance release of LOOS. It primarily involves a revamped build system that addresses some changes in how Atlas is installed in recent Linux releases (such as Fedora 21 and OpenSUSE 13). It also corrects some linkage inconsistencies that were found such as using a system lapack rather than the ATLAS provided version (mixing the two libraries). While the build system should be more intelligent about finding and correctly linking in the numeric libraries, there are many permutations what we've seen in our testing and it may choose incorrectly. You can override which libraries are used and what the search path will be by creating a custom.py file and setting ATLAS_LIBS and/or ATLAS_LIBPATH. See the INSTALL file or the "Building LOOS" section of the documentation.
- Other changes to LOOS include the addition of -upper-only and --lower-only flags to membrane_map and how dibmops and mops split the selection has been changed. Additionally, mops can now write out the average molecular order parameter as a time-series. A new tool in version 2.2.0 was also not noted: model-meta-stats. This tool gives you an overview of the metadata in your model.
New in LOOS 2.2.0 (Dec 29, 2014)
- Fixed bug in smooth-traj where a half-window's worth of frames at the end of the trajectory would be excluded.
- Added --clip flag to smooth-traj to control whether output trajectory has clipped ends, or is the same size as the input trajectory.
New in LOOS 2.0.6 (Sep 14, 2013)
- This release addresses a number of bugs and includes a few improvements and new tools.
- The bugs include ones in gmxdump2pdb.pl where hybrid-36 encoding was used where it shouldn't have been, and problems handling cases with more topology segments than molecular segments (as can happen with bilayer systems).
- A bug in serial-selection was addressed that caused the output to be interleaved by molecule rather than contiguous.
- We have seen some cases where DCD trajectories could have 0 frames listed in the DCD header, yet the trajectory has many frames. Instantiating the DCD (or pTraj) for these trajectories would cause LOOS to throw an exception.
- This behavior has been fixed. However, these trajectories will not be read correctly, i.e. LOOS will think they have no frames in them.
- We have included a special fixdcd tool that will update the header (in-place) with the correct number of frames found by manually scanning the trajectory.
- Finally, a bug in the setup.csh script causing the user package directory to not be inserted into the $PATH has been fixed. Improvements we have made include a change to cross-dist to disambiguate the sign of PCA vectors (courtesy of Jerome Henin), better handling of file I/O errors, a change of the default exponential spring constant in the ENM suite (to -0.5), and transition_contacts can now smooth the contacts matrix when the contact is near the cutoff (this is the default behavior now). When installing with the PyLOOS option (pyloos=1 on the command line), the PyLOOS-based tools are now installed as well as everything else. And finally, a new tool, protein_tilt.py, is available for PyLOOS.
New in LOOS 2.0.5 (Jun 20, 2013)
- 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.
New in LOOS 2.0.4 (Apr 4, 2013)
- 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.
New in LOOS 2.0.3b (Feb 12, 2013)
- Added Simplex::maximumIterations() for returning the max [Dejun]
- Added Simplex::numberOfIterations() to return internal count of function evaluations. [Dejun]
- Fixed incomplete help messages
- Changed ramachandran to not use tabs in output
- Fixed warnings in builds under Fedora
- Fixed bug in AtomicGroup::AtomicGroup
New in LOOS 2.0.3 (Feb 2, 2013)
- Added Simplex::maximumIterations() for returning the max [Dejun]
- Added Simplex::numberOfIterations() to return internal count of
- function evaluations. [Dejun]
- Fixed incomplete help messages
- Changed ramachandran to not use tabs in output
- Fixed warnings in builds under Fedora
- Fixed bug in AtomicGroup::AtomicGroup(const int n) found by H. Elgabarty.
New in LOOS 2.0.2 (Aug 27, 2012)
- 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.
New in LOOS 2.0.1 (Aug 14, 2012)
- 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.
New in LOOS 1.5.2 (Jan 21, 2010)
- Two bugs affecting Amber restart files have been fixed: the readFrame() iterator indicated an end-of-file on the first read, and a variant of the restart file format was incorrectly read.
- In addition, the "segname" property in the atom selection parser (a synonym for "segid") was not correctly recognized and flagged as a parse error. Finally, the eigenvalues returned by AtomicGroup::principalAxes() are now scaled by the number
- of atoms used in the calculation.
New in LOOS 1.3.4 (Feb 18, 2009)
- This is a maintenance release. It addresses a bug in the aligner tool when centering the output trajectory and using different selections to align on versus transform over. The bug causes the transformation to be incorrect, depending on how different the centroids of the two selections are. A minor bug in the svd tool's command line arguments (two short options had the same name) has been fixed as well as a potential bug in how the histograms are built for the rdf tools (causing an overflow/underflow).
New in LOOS 1.3.3 (Feb 12, 2009)
- This release is both a maintenance update and introduces new functionality.
- Bug fixes include correcting a typo in the default selection for the rmsd2ref tool and correcting the default unit cell angles written to DCD trajectories when using periodic boundary conditions.
- A potential bug in several tools that could manifest itself when using PSF files rather than PDBs to describe the system/model has also been addressed.
- In addition, better error-handling when using malformed DCD files is included.
- New functionality includes support for non-native endian DCD files, better handling of specifying command line ranges (for trajectory frames, for example), and new tools for reporting trajectory information, centering trajectories, and creating "blurrogram" figures from trajectories.
- The subsetter tool is now considerably improved and can extract arbitrary frames as well as combined trajectories, adjust periodic box information, and center the subsetted trajectory.
New in LOOS 1.3.2 (Jan 21, 2009)
- This maintenance release addresses a potentially serious bug in how LOOS reads in Amber prmtop files. This bug causes LOOS to mangle the connectivity information, causing serious problems when "splitting by molecule" or reimaging a trajectory that has periodic box information.
New in LOOS 1.3.1 (Jan 15, 2009)
- This maintenance release addresses a problem with building LOOS using MacOS 10.5 along with a few bugs in the aligner, averager, and svd tools.