OpenMichroM 1.1.0

Major changes:

• Change the format of variable names to camelCase for the entire code.
• Rewrite the output display into a classical OpenMM Reporter
• Include the reader for Chromosome Types via bed files
• Create Reporters for statistics and trajectory in CNDB, SWB, PDB, GRO, NDB
• Create the Homopolymer function that adds all homopolymer potentials to the system
• Create the Classic Michrom Simulation function to run Classic Michrom

What's Changed

• Fix various bugs and improve code readability by @junioreif in #103

Full Changelog: v1.0.9...v1.1.0

OpenMichroM 1.0.9

Major changes:

• added "addCustomMultiChainIC potential."
• Adam optimization class can switch between QH Adam and Classical Adam.

Minor changes:

• CustomMiChroMTraining - when starting the IC training, there is no need to insert the TypeTables.
• Includes proper citation and references to Polychrom.
• Added the option to save the velocity, moment, and iteration parameters in Full Inversion Optimization

OpenMichroM 1.0.8

Minor changes:

• Long outputs in tutorials removed
• bugfix in cndbtools reading types due to an update in HDF5 format
• fix: warning message when including new forces.

OpenMichroM 1.0.7

Main changes:
ChromDynamics.py:

• addAdditionalForces() : one can add force objects after the system and context has been initialized
• addCylindricalConfinement(): method to add confining external potential that is cylindrical
• addCorrelatedNoise(): active noise can be added to the simulation object
• addHarmonicBonds(): Harmonic bonds for nearest neighbors
• addSelfAvoidance(): repulsive softcore without diverging LJ

Optimization.py:

• modified cutoff into cutoff_low and cutoff_high in getPars
• added norm in getPars -- normalization of input hic is now optional
• get_lambdas_IC() def now computes and returns the new lambdas
• Ideal Chromosome list of beads to be trained now should be informed in the initialization of CustomMiChroMTraining class by the new variable IClist.
• get_lambdas_IC() and get_lambdas_types() def's now has the boolean variable write_error that computes the tolerance and Pearson correlation of the inversion and write in the output file tolerance_and_pearson.

Integrators.py:

• added integrator object CustomBrownianIntegrator that uses active noise

Minor changes:

• added Active Chromosome Dynamics tutorial to run correlated noise simulations
• CustomMiChroMTraining() had its variable and def names standardized, mainly for the Types and Ideal Chromosome training procedure
• added a tutorial for the Ideal Chromosome potential term
• New scripts were included in the tutorial folder for the MiChroM training procedure on GPU-based clusters.

OpenMichroM 1.0.6

Main changes:

• CustomMiChroMTraining class now allows using any letter to labeling the parameters
• getLamb_types() returns a DataFrame using the labels assigned in CustomMiChroMTraining class

Minor changes:

• bugfix on cndbTools() label reading

OpenMichroM 1.0.5

Main changes:

• getForceIndex() function was added to allow deletion of the correct force
• fixed ForceGroup assignment for MultiChainIC
• addAdditionalForce() function was added to allow the addition of forces in the system after the initialization
  Minor changes:
• bug fix on printStats() and saveStructure()
• implemented changes on setFibPosition

OpenMichroM 1.0.4

v1.0.4

Add new tutorials

OpenMiChroM-1.0.2

Fix a bug when saving CNDB files

OpenMiChroM-1.0.1

Fix a typo/bug in AddCustomIC

OpenMiChroM-1.0.0

Open-MiChroM is a Python library for performing chromatin dynamics simulations and analyses. Open-MiChroM uses the OpenMM Python API employing the MiChroM (Minimal Chromatin Model) energy function.