polychrom

polychrom copied to clipboard

## Description move the initialization of `Simulation.masses` to the constructor, such that it can be edited before the actual `openmm.System` and `openmm.Context` are created. Necessary for particles with different masses....

SGrosse-Holz

Problem: we want to calculate scalings, compartment score, and insulation o the maps generated from simulations. Should we include these functions into polychrom, or rely on and support them in...

agalitsyna

Probably would help with docs, which are probably broken... ## Description _Describe what this PR is for_ ## PR Checklist - [] apply "black" to the whole codebase (`black .`)...

Phlya

cuda incompatibility

2

I tried running a 3D loop extrusion example with CUDA platform but encountered an "error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)". This error happens when the cudatoolkit is incompatible with the...

hrahmanin

loop extrusion example

1

I've tried to get the examples/loopExtrusion/extrusion_3D.ipynb example going, but I've run into an error. The jupyter notebook tries to read in LEF positions from a "trajectory" directory that doesn't seem...

SorenKyhl

[question] Timestep unit in Simulation

2

According to Polychrom documentation, the timestep of simulation is always fs scale (`integrator="langevin"`). But I need simulation in ms scale to fit experiment data, just setting timestep=1e12 fs will lead...

undulating-moon

Forcekit for simulations preserving topology

3

@golobor @gfudenberg - have you done topological simulations recently? What parameters did you use? I was thinking that it would be nice to have a forcekit that would be guaranteed...

mimakaev

0.1.2 roadmap

2

- [ ] rename branch `master` → `main` - [x] add get_requirements to setup.py, move install instructions to readme - [ ] change functions with camelCase → snake_case (note: seems...

gfudenberg

SMC translocator: do we need a more general code?

4

**Problem** After discussing with Hugo, we were thinking that current SMCTranslocator is outdated. First, it is written in Cython, which is not necessary unless you want to create SMC-only contact...

mimakaev

implement a cosine-based repulsive force

9

I found a nice cosine-based repulsive force which may be worth testing:  Not urgent, but I just wanted to document it somewhere.

golobor