Adaptivepele

New features:

- Added null spawning calculator
- Added possibility of max metric in epsilon

Behaviour changes from previous version:

- Improvements in REAP spawning
- Metric columns in control file now start by 1
- Changed symbolic links in rawData in freeEnergies calculation to
relative paths

Bug fixes:

- Various bug fixes

New features:

- Added scripts plot3DNetwork, plotSpawningClusters for better
visualization of simulations
- Added exitContinuous density for exit path simulations
- Added possibility to change the simulation box at each epoch
- Added equilibration procedure
- Added possibility to test metric greater than in metric exit condition
- Added metricMultipleTrajectories exit condition

Behaviour changes from previous version:

- Moved buildRevTransitionMatrixFunction to Cython code (speed-up of up to
500x)

Bug fixes:

- Fixed minor bug in controlFileValidator
- Fixed bug in writePrecisePathToSnapshot, where backtracking was not
carried out until the initial structure

New features:

- Added script to reconstruct precise path to a given snapshot
(writePrecisePathToSnapshot.py)
- Added possibility of chain and resnum selection in PDB
- Added scripts to calculate free energies in pyemma_scripts
- Added new parameter to control the number of clusters considered in
epsilon scoring

Behaviour changes from previous version:

- Change names of clustering in control file

Bug fixes:

- Minor bug fixes in scripts to calculate free energies
- Fixed bug of incorrect trajectory selection in estimateDG
- Fixed bug of multiple its plot not visible (bug due to pyemma)

New features:

- Added conformation network and first discovery tree to improve
simulation analysis
- Added scripts to plot RMSF for each residue over a trajectory
- Added scripts to calculate contact map histogram for each residue over a
trajectory or a complete simulation
- Added scripts to create a network of residues over a trajectory or a
complete simulation
- Added more robust pickling interface so old simulation can be used with
newer version (to some extent)
- Added script to reconstruct approximate path to a given snapshot
(writeTrajToSnapshot.py)

Behaviour changes from previous version:

- Alternative structures are stored in a priority queue with the priority
set to the population of the subclusters spawn inversely proportinal way
according to this population

Bug fixes:

- Fix bug in spawning of alternative structures, was not calling the new
code for randomly spawn from cluster center of alternative structure
- Fix bug in pickling (serializing) coordinates of Atom objects
- Fix bug in pickling AltStructures objects

New features:

- Follow proper packaging conventions for Python packaging
- Added alternative structure to each cluster that will spawn 50% of the
time
- Implemented UCB algorithm for spawning

Behaviour changes from previous version:

- Atomset package implemented in Cython (faster)
- Jaccard index is calcualed using only the cells of the matrix that are 1

New features:

- Added support for symmetry with contactMap
- Added lastSnapshot clustering for easy restart of sequential runs
- Added independent spawning to perform classical PELE simulations
- Added exitCondition on metric
- Added support for changing clustering when clustering method parameter changes, and be able to handle
metric column change in spawning
- Added suport for wildcard in control file input structures
- Added several scripts for analysis

Behaviour changes from previous version:

- Changed quadratic function for continuous
- Changed symmetry dictionary for list of dictionaries, with symmetry groups

Bug fixes:

- Fixed bug of incorrect atom consideration in symmetries
- Fixed bug of NaN correlation similarity evaluator in contactMap