Adaptivepele

New features:

- Add possibility to generate cylinder box from pdb
- Add coordinate wrapping to XTC reporter

Bug fixes:

- Fix bug restarting MD simulation with constraints
- Fix bug that crashed when constraining HIS
- Fix colorbar range for plotAdaptive script
- Fix bug in HIS protonation

Behaviour changes from previous version:

- Allow PELE equilibration to run without a box
- Read PELE and MD reports seemingly
- Add postprocessing option to simulationRunner
- Add proper topology support to selectOnPlot and backtrackAdaptiveTrajectory
- Write topologies.pkl at the start of the first epoch

New features:

- Add cylindrical box for MD
- Add script to generate cylindrical box for visualization
- Introduce new postprocessing function for MD

Bug fixes:

- Fix bug selecting topolgies for odd number of initial conditions
- Fix bug extracting indexes from topology in MSMClustering
- Fix bug in atomset writing PDBs with gaps, now if there are residues with
a difference in more than one in the residue number a TER is written

Behaviour changes from previous version:

- Now the MSMClustering with PELE simulation repeats the rejected steps

New features:

- Add the possibility of running MD simulations using OpenMM
- Add new script analysis/identifyClusterSnapshot.py, to identify to which
cluster belongs a given conformation within a simulation
- Add support for formats trr, dcd and dtr, mdcrd, nc
- Add the null clustering method
- Add independentMetric spawning
- Add MSM-based spawning methods
- Add reportName template for PELE control file

Bug fixes:

- Fix bug in PELE equilibration when number of initial structures selected
exceeded number of processors
- Fix bug in atomset that wrote MODEL lines in PDBs non-compliant with the
standard
- Fix minor bug in in select equilibration structure with trajectories with
no accepted steps

Behaviour changes from previous version:

- Restructured a good part of the code in the adaptiveSampling main
referring to simulation, moved into SimulationRunner class
- Change how AdaptivePELE deals with topologies, now it supports several
different topologies in a single simulation
- Change how the spawning parameters are used, now are an attribute of the
spawning calculator
- Update how the srun command is called when running PELE, also added
srunParameters to customize the call to srun
- AdaptivePELE now runs with replicas synchronized via files, needed for
running MD in GPU clusters

New features:

- AdaptivePELE can now be installed through pip

Bug fixes:

- Fix bug in setup.py in environments without cython

New features:

- The extractCoords script now works seemesly with pdb or xtc trajectories

Behaviour changes from previous version:

- Improve the speed of handling xtc trajectories by switching to the
low-level API of mdtraj
- Optimize and parallelize extractCoords script from the freeEnergies
subpackage, change the multiprocess module to multiprocessing

Bug fixes:

- Fix several bugs in extractCoords script

New features:

- Make code compatible with python2 and python3
- Add posibility of using a third column as color in plotAdaptive
- Add __version__ attribute to package
- Add possibility of skipping first structure of each trajectory in
clustering when calling cluster function
- Add compatibility with non-pdb trajectories

Behaviour changes from previous version:

- Change rmsd and be otions of plotAdaptive to lines and points
- Change name of writePrecisePathToSnapshots to
bactrackAdaptiveTrajectory, added name parameter to select the name of the
output file and automatic detection of said name, so that if a file exists
with the same name, a number is added at the end to differentiate them
- Optimize and parallelize extractCoords script from the freeEnergies
subpackage

Bug fixes:

- Fix bug in alternative structure when a cluster had no other structure
than the representative
- Fix several bugs related to unicode and string handling