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ChangeLog
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2020-02-28 Alan Grossfield <alan>
* added new tool set_segids.py
2020-02-13 Alan Grossfield <alan>
* Merged in new radius of gyration tool rad-gyr from Louis Smith
2019-12-24 Alan Grossfield <alan>
* Added experimental tSNE feature to cluster-structures.py
2019-12-19 Alan Grossfield <alan>
* Release 3.1 New build system
* New Clustering package
* Bug fix to omg.py and it's handling of internal waters
* Added rotation options to solvate.py
* Fixed bug in omg and solvate where salt missed atom names
* fullhelper.py tool to simplify writing fullhelp messages
* New tool: packing_score_per_res.py
* Precision option to RMSD computing tools
* make_library.py: new tool to make a lipid library
* add_molecules.py: packmol-like tool to scatter small molecules in a box
* updates to cluster-structures.py: more output information
2019-02-27 Alan Grossfield <alan>
* Release of LOOS 3.0. This is a major change, in that LOOS now
requires Python 3.x.
2019-01-21 Alan Grossfield <alan>
* Merged in a new reweighting framework. Added a new options class to
support it, and implemented it in rdf and xy_rdf as examples.
2018-11-01 Alan Grossfield <alan>
* Added --postcenter-xy and postcenter-z to merge-traj. Updated fullhelp
to include a better explanation of when you might need these methods.
2018-10-26 Alan Grossfield <alan>
* Added new option --postcenter to merge_traj, to improve reimaging in
challenging cases.
2018-10-23 Alan Grossfield <alan>
* Further change to order_params -- I decided the previous version could
produce odd answers if there are a small number of chains selected.
2018-10-18 Alan Grossfield <alan>
* Major change in order_params. A previous change to take the absolute value
of the Legendre polynomial resulted in incorrect values. I still think
the absolute value is physically correct, but we've moved it to after
averaging within a given snapshot. The results are now more consistent
with what other packages generate.
2018-10-15 Tod Romo <tromo>
* Changed src/timers.hpp to be src/loos_timers.hpp in order to avoid filename conflicts
2018-05-17 <tromo>
* Changed PSF code to accept hybrid-36 encoding for atomid's and resid's
2018-05-08 <tromo>
* Fixed potential bug in gmxdump2pdb.pl when using newer PERLs (missing an escaped
closing brace that did not appear to affect the program...)
* Fixed bug in subsetter that allowed zealous reimaging mode without a centering selection.
2018-02-02 <alan>
* Bugfix in order_params to allow selecting chain 1
2018-01-10 <alan>
* Added new tool (distance_prob)
2017-11-02 <tromo>
* Changed SConsctruct and support scripts to make print a function (required by scons-3.0.0)
2017-09-21 <alan>
* added new tool all_contacts.py to PyLOOS, to compute probabilities
for residue-residue contacts
2017-09-07 <alan>
* added option to ignore neighboring residues to native_contacts
2017-08-31 <alan>
* Added --per-residue option to native_contacts
2017-08-09 <alan>
* Added kineticEnergy() method to AtomicGroup
2017-08-09 <alan>
* Added NAMDBin.py, to read NAMD binary format.
2017-08-02 <alan>
* Added the ability to manually select the water to crossing-waters tool.
Based on a bug report from Violeta Casamayor.
2017-07-18 <tromo>
* Added support for indexing relative to the end of the trajectory in
frame2pdb (using negative frame numbers)
2017-05-29 <tromo>
* Fixed bug in rmsd_to_average.py
2017-04-28 <tromo>
* Fixed bug in PDB reader affecting parsing of CONECT records and hybrid36 atomids
* Changed extreme reimaging mode in subsetter to use middle-residue for repositioning
rather than the first atom.
2017-04-02 <tromo>
* Fixed bug in backbone selection causing terminal nucleic acids to be skipped
2017-03-21 <tromo>
* Added support for gro files that are missing velocities.
2017-01-23 <alan@membrane>
* Added new tool all_contacts.py to PyLOOS package
2016-12-16 <alan@membrane>
* Added new program helix_axes.py to PyLOOS package
2016-12-05 <alan@membrane>
* Add 4 skeleton programs to PyLOOS
2016-11-30 <alan@membrane>
* order_params averages the absolute value of the 2nd Legendre polynomial,
instead of the actual value.
2016-11-17 <tromo@hill>
* Fixed bug in rmsds and multi-rmsds that caused the memory usage warning to not happen.
2016-11-14 <tromo>
* Fixed bug in bug in AmberNetcdf where the reader would always try to read velocities
and fail if not present.
* Changed AtomicGroup::findBonds() to be optionally PBC aware (with Alan's help)
2016-11-12 <tromo@hill>
* Fixed bug in AmberNetcdf where the Trajectory iterator would show one more
frame than actual.
2016-11-11 <[email protected]>
* Added support for velocities in Atom.
* Added support for velocities in Trajectory. Formats that natively store velocities will use those,
otherwise LOOS will assume that the coords are actually velocities.
* Changed Trajectory::coords() to be const
2016-10-28 <tromo@hill>
* Added MultiTrajectory class: a Trajectory that can contain other
Trajectory objects. Each sub-trajectory can have its own skip and
stride.
* Added MultiTrajOptions for handling multi-trajectories on the command
line. This must be the last option included.
* Changed Trajectory to be copyable. Now saves iterator state internally.
* Added Trajectory::filename()
* Removed StreamWrapper from Trajectory. StreamWrapper will likely go away
in a future release.
* Changed the frame range parser to use BOOST::Spirit. This includes support
for using an empty range end to specify the end of a file, e.g. 10:2: means
take every other frame, starting at frame 10, until the end of the file.
* Changed subsetter and svd to use the new MultiTrajectory
* Added multi-rmsds tool to compute a pair-wise RMSD matrix for an arbitrary
number of trajectories.
2016-10-13 <alan@membrane>
* Added option to native_contacts to supply a reference structure
2016-10-05 <tromo@hill>
* Added --reimage=zealous to subsetter
* Added proper support for atom inequality in PyLOOS (uses metadata only)
2016-09-13 <tromo@hill>
* Added --verify option to trajinfo to suppress frame count verification when using
the brief output.
2016-09-08 <tromo@hill>
* Fixed bug affecting water density tools and the radius filter. Too few waters
were actually being selected.
2016-09-02 <tromo@hill>
* Changed DCD to handle trajectories with 0 frame count in the header (no longer
requires running fixdcd first)
2016-08-26 <tromo@hill>
* Added option to remove bonds with model-select
* Changed dibmops to use 0 for avg in bins with no data rather than -1
2016-08-17 <tromo@hill>
* Added support for using ranges of frames and skip in rdf, atomic-rdf, and xy_rdf
* Fixed bug in water-autocorrel
2016-08-03 <tromo@hill>
* Fixed bug in effsize.pl affecting some Unix distros
* Fixed bug affecting python alignment results (when converting the vector of xforms to
a Python list).
* Fixed bug in rmsd_to_average.py causing it to break at the end when showing overall average
2016-07-21 <alan@membrane>
* Added new tool lipid_survival to compute lifetime of lipids at surface
of protein
2016-07-11 <alan@membrane>
* Added periodicity support to native_contacts
* Fixed (tromo) bug in doxygen handling that cause docs to be rebuilt excessively
2016-07-08 <tromo@hill>
* Released loos-2.3.2
* Added support for unpacking prebuilt docs tarball
2016-07-01 <tromo@hill>
* Added support for manually setting molecule name to segid mapping in gmxdump2pdb tool
2016-06-28 <tromo@hill>
* Changed documentation so it will be automatically built in github clones
* Fixed bug in amber parmtop reader that affected Ubuntu 16
* Added functions in utils_structural.cpp to PyLOOS
2016-06-24 Tod Romo <tromo@hill>
* Fixed bug in density-dist that prevented the number calculation from working
2016-06-22 Tod Romo <tromo@hill>
* Fixed bug in PyLOOS that made XTCWriter unavailable
2016-06-15 Tod Romo <tromo@hill>
* Fixed bug in aligner where xyonly was ignored if using a reference structure to align to
* Fixed bug in membrane_map where specifying a reference structure would not actually align with it
2016-06-13 Tod Romo <tromo@hill>
* Added verap tool for quick vertical area profiles
2016-06-07 Tod Romo <tromo@hill>
* Changed how LOOS is organized (slightly). The core library code
now resides in the "src" directory. The built shared library is
still stored at the top-level LOOS directory.
2016-06-03 Tod Romo <tromo@hill>
* Added HSD, HSE, and HSP to recognized residues for backbone selector
2016-06-03 Alan Grossfield <[email protected]>
* Added new tool cylindrical-thickness
2016-06-02 Alan Grossfield <[email protected]>
* Fixed bug in cylindrical-density -- accidentally left options
hardwired.
2016-04-19 Alan Grossfield <[email protected]>
* Added ability to write GRO files. Added Gromacs class to pyloos
2016-04-15 Tod Romo <[email protected]>
* Fixed bug in fullhelp for serialize-selection and default output
when using pdbout
2016-03-24 <[email protected]>
* Added --positive and --negative flags to enmovie controlling which direction
motion is depicted
2016-03-11 <[email protected]>
* Added new tool inside_helices.py to Packages/PyLOOS
2016-01-11 <tromo@hill>
* Released loos-2.3.1
2016-01-08 <[email protected]>
* Fixed bug in center-molecule affecting --center_xy
2016-01-07 <[email protected]>
* Fixed bug in membrane_map causing alignments to be incorrect (affected height calculation)
2015-11-20 <[email protected]>
* Released loos-2.3.0
2015-11-11 <[email protected]>
* Added lipid_lifetime.py tool to the Voronoi package
2015-10-23 <[email protected]>
* Fixed bug affecting reading Charmm CRD files
2015-10-12 <[email protected]>
* Reorganized superposition and iterative alignment code into
alignment module. AtomicGroup methods call these functions now.
* Reorganized pyloos iterative alignment routines:
iterativeAlignment() will align anything that iterates over
AtomicGroups (e.g. pyloos.Trajectory()), while
iterativeAlignTrajectory() is a front-end to the standard LOOS functions.
* Added new tool cylindrical-density.py to PyLOOS package (Alan)
2015-09-30 <[email protected]>
* Change RMSD to optionally use multiple threads
* Added boost threads as a build requirement
2015-09-28 <[email protected]>
* Changed AtomicGroup::superposition() to use the faster dgesvj().
Note: this is an iterative method that may not converge. In
practice, the residual will be small if it does not. LOOS will
print out a warning in such cases. If you find many warnings
being issued, contact the LOOS developers.
* Changed the rmsds tool to use a much faster algorithm (up to an
order of magnitude faster). There is no option to disable caching
now--if the cached subsets do not fit in memory, you will want to
subsample the trajectories.
2015-09-14 <[email protected]>
* Changed pyloos organization
* Added numpy support in PyLOOS
* Added ensembles and SVD support in PyLOOS
2015-08-27 <[email protected]>
* Added k-means clustering PyLOOS program (cluster-structures.py)
* Added AtomicGroup::getCoords() and AtomicGroup::setCoords() for numpy
2015-07-23 <[email protected]>
* Changed trajinfo to handle read errors and only use first set of valid frames
* Changed trajinfo to ALWAYS scan trajectory frames
* Added [PYLOOS] iterativeAlignment functions that will return a
Python tuple (list of transforms, final rmsd, # of iterations)
* Deprecated [PYLOOS] iterativeAlignmentPy() functions
* Changed [PYLOOS] AtomicGroup::splitByMolecule() to return a
Python list of AtomicGroups rather than an AtomicGroupVector
* Changed [PYLOOS] AtomicGroup::splitByUniqueSegid() to return a
Python list of AtomicGroups rather than an AtomicGroupVector
* Changed [PYLOOS] AtomicGroup::splitByResidue() to return a
Python list of AtomicGroups rather than an AtomicGroupVector
2015-07-21 <[email protected]>
* Fixed bug in handling of extended format charmm coordinates, including
actually parsing the "EXT" flag
2015-06-30 <[email protected]>
* Fixed bug in xy_rdf where --sel1-spans, --sel2-spans, and --reselect were ignored
2015-06-22 <[email protected]>
* Added IndexSelector to pick atoms based on their index within the model
file (not the same as atom id)
* Added "index" keyword to selection language
* Changed integers in selection language to long ints (to avoid overflow problems)
2015-05-28 <[email protected]>
* Fixed handling of DEBUG in setup scripts
* Changed order_params tool to support ranges for what frames to use
2015-04-22 <[email protected]>
* Released 2.2.5
2015-04-10 <[email protected]>
* Fixed bug in operator overloadings for GCoords in PyLOOS
* Changed options and behavior of porcupine and enmovie. See their
fullhelp for more information.
* Changed default selection for ENM tools to alpha-carbons rather than all.
* Changed default selection for SVD to alpha-carbons
* Added -S as a spring function option shortcut for ENM tools
2015-03-30 <[email protected]>
* Added ".netcdf" as a recognized file suffix for Amber NetCDF
Trajectories.
* Fixed help and fullhelp in subsetter
2015-03-02 <[email protected]>
* Added --sort option to merge-traj
* Changed the default sort regex for subsetter and merge-traj to
sort on the *LAST* number in the filename
2015-02-25 <[email protected]>
* Fixed bug in fcontacts resulting in NaN's in output if there
are no target atoms near the probe.
* Added NAMD tag (optional) to PSF files created by gmxdump2pdb
2015-02-19 <[email protected]>
* Fixed bug in merge-traj that required downsampled dcd filename to operate
* Added support for sorting trajectory files numerically (as subsetter does)
2015-02-13 <[email protected]>
* Added new option --ref-structure to membrane_map, to facilitate combining
results from multiple trajectories
2015-02-06 <[email protected]
* released 2.2.4
2015-01-27 <[email protected]>
* Fixed reading of Amber prmtop files that use mixed case for
format specs
* Fixed handling of non-netCDF Amber files when built with NetCDF support
2015-01-26 <[email protected]>
* Released 2.2.3
2015-01-23 <[email protected]>
* Fixed bugs affecting functins in atoms, coords, and matrix44 that return
a ref in PyLOOS. These are now const refs and should no longer be wrapped
by swig (instead, the value will be returned)
* Added improved error handling in the build system
2015-01-17 <[email protected]>
* Released 2.2.2
2015-01-16 Tod Romo <tromo@Gorgoneion>
* Fixed bug in reading amber parmtop files
* Fixed bug when building with latest MacOS and XCode
2015-01-13 <[email protected]>
* Released loos 2.2.1
2015-01-12 <[email protected]>
* Changed mops and dibmops to split using connectivity (if available)
or force splitting by residue (--residue=1)
2015-01-09 <[email protected]>
* Changed the build system
* Changed mops to optionally write out a time-series of molecular order parameters
2015-01-07 <[email protected]>
* Removed dcd_utils.cpp and gridify()
2015-01-06 <[email protected]>
* Added --upper-only and --lower-only options to membrane_map to
easily allow the user to specify one leaflet to look at
2014-12-24 <[email protected]>
* Released loos 2.2.0
2014-12-22 <[email protected]>
* 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.
2014-12-18 <[email protected]>
* Added AtomicGroup::contactWith() which returns true or false if
two groups have a pair of atoms within a threshold distance
2014-12-16 <[email protected]>
* Changed aligner, smooth-traj, reimage-by-molecule, and
serialize-selection to allow selecting the output trajectory
format.
2014-12-10 <[email protected]>
* Added solvate.py to OptimalMembraneGenerator, to build
protein in water systems without lipids
* Added model-meta-stats to give on overview of metadata in a model
2014-12-09 <[email protected]>
* Fixed bug in aligner that caused incorrect output when using subset of
the trajectory (i.e. giving a stride, a skip, or some ranges on the
command line)
* Changed entire exception framework. Almost all exceptions thrown
by LOOS now derive from LOOSError. Most exceptions are now global
as well.
* Changed how Swig interface is generated (from the LOOS header
files directly)
* Removed char* based constructors in favor of const string&
* Added filename tracking within I/O classes for better error messages
* Changed DCD::readHeader() to be private
* Changed selectAtoms() to ONLY throw in the event of an error in parsing
the selection string. If no atoms are selected, then an empty AtomicGroup
is returned.
* Changed AtomicGroup::groupFromID() so that missing atoms are ignored
rather than cause an exception to be thrown
2014-11-20 <[email protected]>
* Deprecated gridify() in dcd_utils.cpp
2014-10-21 <[email protected]>
* Changed PDB reader so missing fields (to the right of
coordinates) will be tolerated and default values used.
See new functions to test for presence of missing data.
A one-time warning will be printed if missing fields are
found.
2014-10-15 <[email protected]>
* Add OptimalMembraneGenerator to Packages
2014-08-26 <[email protected]>
* Changed BackboneSelector to now include backbone hydrogens
2014-08-22 <[email protected]>
* Changed BackboneSelector to select backbone atoms for protein
and nucleic acids. Will only work for known residue names and
atom names (see Selector.cpp for the list)
* Changed backbone keyword action to be a wrapper around the
BackboneSelector
2014-08-17 <[email protected]>
* Added backbone keyword to selection language (selects protein backbone)
2014-08-11 Tod Romo <tromo@gorgoneion>
* Changed DCDWriter::framesWritten() to return an unsigned int
* Added TrajectoryWriter base class to provide a simple interface
to writing trajectories
* Added XTCWriter class for writing GROMACS XTC files (single
precision only...based heavily on the xdrfile library provided by
GROMACS)
* Changed DCDWriter to derive from TrajectoryWriter
* Added createOutputTrajectory() factory function to determine
output trajectory format and return a pTrajectoryWriter (boost
shared pointer to a TrajectoryWriter object).
* Added a static class function to all trajectories and systems
(e.g. pPDB PDB::create(const string &fname)).
* Changed how all of the createXXXX() factory functions work...
They use a table binding filename extension to the appropriate
object create() function.
* Added Trajectory::description() to return a string describing
the trajectory format.
* Changed trajinfo to report the trajectory file's format
* Changed subsetter and mergetraj to use TrajectoryWriter.
* Added splitFilename() utility function to break a filename into
the basename and a dotted suffix.
* Added OutputTrajectoryOptions class.
2014-07-31 <[email protected]>
* Added support for periodic boxes in Tinker XYZ and arc files
2014-07-30 <[email protected]>
* Added support for getting the step and time for the currently
read XTC frame.
* Added support for calculating the timestep (time per step) from
an XTC trajectory
2014-07-18 <[email protected]>
* Released 2.1.3
2014-07-17 <[email protected]>
* Fixed bug in rebond that created bonds from subset atoms to themselves
2014-07-16 <[email protected]>
* Changed chist tool to operate in either cumulative or windowed
mode...
2014-06-18 <[email protected]>
* in merge-traj, added support for separate selections to recenter
in xy and z
2014-06-16 <[email protected]>
* Removed center-model (this had been deprecated back in 2011)
2014-06-11 <[email protected]>
* Fixed bug in rmsds when using 2 trajectories causing progress
updates to have absurdly long run-time estimates
2014-06-05 <[email protected]>
* Added note about testing with Manjaro and Slackware
2014-06-03 <[email protected]>
* Fixed bug in in TRR/XDR affecting double precision data (found by Pin-Kuang Lai)
2014-06-02 <[email protected]>
* Added number density option to density-dist
2014-05-06 <[email protected]>
* Added new package Voronoi. Requires numpy and scipy in addition
to LOOS.
2014-04-18 <[email protected]>
* Added "core" water filter for DensityTools. An alternative
method for finding the protein axis. See protein_tilt.py or the
Doxygen docs for WaterFilterCore for more details.
2014-04-14 <[email protected]>
* Fixed build issue when specifying ATLAS_LIBS
2014-04-10 <[email protected]>
* Added --threshold=f to interdist that will segment the output
based on the given cutoff/threshold
2014-03-13 <[email protected]>
* Fixed help info for dcdinfo
* Added cumulative histogram tool (chist) in Convergence package
* Changed XForm::rotate(const GCoord&, const greal)
to throw an invalid_argument exception if the
rotation axis does not have some minimal length.
2014-03-06 <[email protected]>
* Fixed bad HTML tag in dox
2014-03-05 <[email protected]>
* Fixed crash in phasepdb caused by default chunk size setting
2014-02-25 <[email protected]>
* Added mops and dibmops for molecular order parameters and
distance-based molecular order parameters respectively
2014-02-14 <[email protected]>
* Released version 2.1.2
2014-02-13 <[email protected]>
* Fixed bug where PyTraj was not installed
* Fixed bug affecting AmberTraj::updateGroupCoords() [mdcrd files]
resulting in a segfault.
2014-02-07 <[email protected]>
* Added new feature to xy_rdf (--reselect) to handle the case where
molecules move back and forth between leaflets
2014-01-31 <[email protected]>
* Released version 2.1.1
2014-01-29 <[email protected]>
* Added support for OpenSUSE 13 and Fedora 20
2014-01-23 <[email protected]>
* Fixed bug in drifter that prevented it from running
* Fixed bug in parseStringAs<> that can affect shortened fields
at the end of a line causing it to return a default value.
2014-01-21 <[email protected]>
* Fixed a bug in protein_tilt.py, where the average vector wasn't reset
upon successive frames in the trajectory.
* Fixed bug in rmsds tool where the average RMSD reported
was incorrect (sligthly under when using one trajectory,
with large error when using two trajectories) [Tod]
2014-01-10 Tod Romo <tromo@gorgoneion>
* Changed [PyLOOS] GCoord, AtomicGroup, TimeSeries, and Matrix44
to be iterable
* Added [PyLOOS] PyTraj and PyAlignedTraj for Python iteration through a
Trajectory
2014-01-08 Alan Grossfield <[email protected]>
* Added new tool packing_score, to quantify the packing between
to selections over the course of a trajectory
2013-11-04 Tod Romo <tromo@ubuntu-mac-12>
* Added MacOS 10.9 (Mavericks) compatibility
* Added support for writing truncated SVD in big-svd
* Changed rmsds to optionally cache the trajectory for improved
performance
* Changed build system (refactoring and various improvements, see
INSTALL or Doxygen docs for more information)
* Deprecated tests build target
2013-10-18 <[email protected]>
* Added new tool membrane_map, which computes the 2D distribution of
a variety of physical properties around a membrane protein
* Fixed bug in svd tool where basic options (such as -v1) would
fail with an options error.
2013-10-17 <[email protected]>
* Changed Matrix operator[] to only check for out of bounds index
when debugging (i.e. -DDEBUG)
2013-10-15 <[email protected]>
* Added BasicSplitBy option to the options framework. Use the
BasicSplitBy::split() member function to split an AtomicGroup
based on a user-specified method.
2013-10-11 <[email protected]>
* Added Math::eigenDecomp() that calculates the eigenpairs for
the passed DoubleMatrix (using DSYEV).
* Added gnm-traj and anmo-traj tools for analyzing trajectories
using elastic network models.
2013-10-08 <[email protected]>
* Changed how atomid's are handled in LOOS. Previously in LOOS,
atomid's had special meaning. Not only should they be unique, but
they also identify which "slot" in a trajectory frame that a
specific atom was located. This meant that if a model's atomid's
didn't begin at 1 were not contiguous, then bad things could
happen. Now, LOOS assigns and atom "index" to every atom as it is
being read in by the appropriate model format class (e.g. PDB,
Amber, etc). This index tells LOOS which slot to use with a
trajectory, rather than the atomid. In general, this should just
work. For more information, see the Doxygen documentation for
Trajectory or the LOOS FAQ.
* Changed all Trajectory-derived updateGroupCoords() to honor the
atom index information. This affects primarily the PDB-based
trajectory classes which used to ignore atom metadata if the
passed AtomicGroup was the same size as the trajectory frame.
* Changed updateGroupCoords() to use NVI idiom. Now calls
updateGroupCoordsImpl() in the derived classes.
2013-10-01 <[email protected]>
* Added smooth-traj tool for smoothing trajectories
2013-09-13 Tod Romo <[email protected]>
* Released 2.0.6
2013-08-26 <[email protected]>
* Changed default exponential spring constant to -0.5
2013-08-22 <[email protected]>
* Added new flag to rdf to allow the two selections to be split using
different methods.
2013-08-20 <[email protected]>
* Fixed bug with XTC trajectories when the system contains too
few atoms (<= 9). Gromacs does not compress the coordinates, but
LOOS expected all system sizes to have compression.
* Changed transition_contacts to add a --smoothed-transition
option to use a tanh() function to effectively smooth the contacts
matrix when a contact is near the cutoff. This is now the default
behavior. (Nick)
2013-08-15 <[email protected]>
* Changed installation to now include python scripts if pyloos is
being built.
* Added .nc and .crd as Amber trajectory extensions. Note that
.crd for a structure is still interpreted as a CHARMM coordinate
file.
2013-08-12 <[email protected]>
* Fixed bug in serialize-selection where the output molecules were
interleaved rather than each chunk of T-frames consisting of a
single molecule (e.g. it would have been mol 1, mol 2, mol 1, mol
2 instead of mol 1, mol 1, mol 2, mol 2)
* Added --fullhelp output to phase-pdb
* Fixed bug in phase-pdb where a duplicate (and incorrect) set of
bonds could be added when using --chunk and --rows options
2013-08-01 <[email protected]>
* Added a new tool to Packages/PyLOOS: protein_tilt.py computes the time
series of the tilt angle for a transmembrane protein by averaging the
tilt vectors of individual selects (e.g. individual helices)
2013-07-26 <[email protected]>
* Fixed hierarchy so that it now catches bad input and generates a
useful error message rather than segfaulting...
* Fixed multiple tools to more gracefully handle problems when
opening files.
2013-07-23 <[email protected]>
* Changed coverlap tool to internally use double-precision for
eigenpair matrices. This resolves a fringe-case where coverlap
would fail with a conversion error when using eigenpairs from the
ENM suite.
2013-07-23 Tod Romo <[email protected]>
* Fixed gmxdump2pdb.pl so that it can handle cases where there are
more topology segments than molecular segments (as can happen with
bilayer systems)
2013-07-19 <[email protected]>
* Added link to tutorial on LOOS in documentation
2013-07-03 <[email protected]>
* Added change to cross-dist. Disambiguate sign of PCA vectors
by checking against end-to-end vector. Code (and idea) courtesy of
Jerome Henin.
* Fixed bug in setup.csh (user package directory was mispelled).
2013-07-01 <[email protected]>
* Fixed gmxdump2pdb.pl to NOT use hybrid-36 encoding for the
PSF file.
2013-06-25 <[email protected]>
* Fixed potential bug in DCD reader nstep was used internally in
place of nfile.
* Fixed bug when instantiating DCD files with nfile==0 so it
doesn't immediately throw an error.
* Added fixdcd tool to update a DCD header (in-place) with the
correct # of frames.
2013-06-19 <[email protected]>
* Released 2.0.5
2013-06-18 <[email protected]>
* Changed rmsd2ref so that it no longer caches trajectory frames
2013-05-29 <[email protected]>
* Added --xyonly option to aligner so that alignment (rotations)
only occur in the x,y plane. Note that all systems are translated
so their centroids are coincident, so there may be a
Z-translation.
* Changed AtomicGroup::superposition() to not throw if the
alignment matrix is singular. Instead, aligner will warn if too few
atoms are selected instead.
* Changed setup scripts to prepend paths rather than append
* Added transition_contacts tool from N. Leioatts
2013-05-22 Tod Romo <[email protected]>
* Changed renum-pdb so that connectivity is preserved
2013-05-17 Tod Romo <tromo@gorgoneion>
* Changed timeAsString() to accept an optional precision parameter
for the seconds field.
2013-05-07 <[email protected]>
* Updated native_contacts tool. Fixed an off-by-one bug that
caused the last residue in the selection to be handled wrong. Switched
to using the standard program options, so now the selection defaults to
name == "CA", and is prefixed by --sel. Added new option to output the
timeseries of individual contacts to a separate file. Added new option to
exclude the backbone atoms.
2013-05-01 <[email protected]>
* Added serialize-selection tool. Given a trajectory with T
frames and a selection consisting of N molecules (by connectivity
of segid), this tool will create a new trajectory that consists of
only one molecule but is N*T frames long. Each chunk of T-frames
consists of one of the molecules.
2013-04-25 <[email protected]>
* Changed how some versions of averageStructure() and
iterativeAlignment() work. The versions that take an AtomicGroup
and a pTraj as arguments no longer cache the trajectory in
memory. Instead, they will read through the trajectory as
necessary, only operating on a frame at a time. In the case of
aligning, this may involve multiple reads through the trajectory.
2013-04-18 <[email protected]>
* Fixed bug in gmxdump2pdb.pl that affected systems with 100,000
atoms or more.
2013-04-14 Tod Romo <[email protected]>
* Added fcontacts tool that should, in most cases, supercede the
contact-time tool. It calculates the contacts made
between a probe and a set of target selections as a fraction of
all contacts with the probe.
* Added LOOS exceptions to PyLOOS
* Fixed selectAtoms() in PyLOOS to throw LOOS exceptions (i.e. it
will no longer crash python)
2013-04-12 <[email protected]>
* Added HBondDetector class: given a triple of atoms, will
efficiently apply angle and distance criteria (Alan)
* Changed StreamWrapper to use an istream internally rather than
iostream.
* Changed Trajectory (& derived classes) to take an istream in
constructor rather than an ifstream
* Changed all structure classes (i.e. pdb, amber, tinkerxyz, etc)
to take an istream in the constructor rather than an ifstream
* Changed XDR class, refactoring it into XDRReader (which takes an
istream) and XDRWriter (which takes an ostream)
2013-04-03 <[email protected]>
* Released 2.0.4
2013-04-01 <[email protected]>
* Changed build procedure(s). To build pyloos, use "scons
pyloos=1". PyLOOS can now be installed with "scons pyloos=1
install". Only PyLOOS can be built by using "scons pyloos_only".
2013-03-28 <[email protected]>
* Changed PSF reader to NOT try to use hybrid-36 encoding. This
affected large systems that should have been readable but
weren't.
* Added --bonds option to frame2pdb and convert2pdb that controls
whether CONECT records are written.
2013-03-27 <[email protected]>
* Fixed performance issue with writing PDB files containing bonds
and lots of atoms
2013-03-22 <[email protected]>
* Added --assign option to ramachandran for printing out a rough
secondary structure assignment
2013-03-21 <[email protected]>
* Fixed error in fullhelp for subsetter tool (cannot use multiple
--range options, must use a comma-separated list instead)
2013-03-14 Tod Romo <[email protected]>
* Fixed bug in OptionsFramework with MacOS and Boost 1.52+.
2013-03-12 <[email protected]>
* Added a --brief option to area_per_lipid
* Fixed bug in area_per_lipid where the --skip option was ignored
when generating the area timeseries
2013-02-16 Tod Romo <tromo@isteno>