Changelog¶
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog.
1.7.2 - Unreleased¶
New features:¶
Add script to run RMSD clustering from scratch
Add filters for plotAdaptive script
Bug fixes:¶
Fix bug in pdb processing for MD simulation when no protein was present
Fix bug extracting the ligand for MD in some weird edge cases
1.7.1 - 2021-05-14¶
New features:¶
Add equilibrationRotationRange, equilibrationTranslationRange and equilibrationBoxRadius parameters to tune equilibration performance
Add support to correctly run simulations with PELE interstep reports and trajectories
Bug fixes:¶
Fix bug reading the ligand information in the adaptiveSampling main, which caused to set the equilibration box in the center of mass of the whole system
1.7 - 2021-02-11¶
New features:¶
Use residue numbers and chain names in clustering, which makes possible to run protein-protein simulations
The plotAdaptive script now accepts a path to the simulation folder and has an option to skip the first step, or a number of steps when plotting
Bug fixes:¶
Fix bugs running MD simulations without ligand after the changes in previous version
1.6.3 - 2020-09-28¶
New features:¶
Add annotations to plotAdaptive, which show the origin (epoch, trajectory and snapshot) of the plot points
Parametrize more than one ligand in MD simulations
Include confactors in MD simulations
MD simulations can now be extended in time
Bug fixes:¶
Fix bug ignoring ligandName parameter in the simulation block
Behaviour changes from previous version:¶
Modify plotAdaptive to generate the plots using matplotlib and not rely on gnuplot
Raise separate and more informative errors for the cases of input file not existing, resname selection incorrect, input file in text file but not pdb and topology mismatching for binary files
Constrain the heavy atoms in the minimization run at the begging of the epochs in MD simulation, to preserve similiraty with the original cluster
1.6.2 - 2019-07-24¶
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
1.6.1 - 2019-04-26¶
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
1.6 - 2019-02-19¶
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
1.5.2 - 2018-08-13¶
New features:¶
AdaptivePELE can now be installed through pip
Bug fixes:¶
Fix bug in setup.py in environments without cython
1.5.1 - 2018-06-07¶
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
1.5 - 2018-05-11¶
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
1.4.2 - 2018-03-02¶
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
1.4 - 2018-01-30¶
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
1.3 - 2017-06-01¶
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)
1.2 - 2017-05-09¶
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
1.1 - 2017-02-17¶
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
1.0 - 2017-01-19¶
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