config_auto.ini

####################
#   LoopSage Model   #
####################

# This is automatically generated config file.
# Generated at: 2025-06-03T15:11:48.412827

# Notes:
# Some fields require units. Units are represented as objects from mm.units module.
# Simple units are parsed directly. For example: 
# HR_R0_PARAM = 0.2 nanometer
# But more complex units does not have any more sophisticated parser written, and will fail.'
# In such cases the unit is fixed (and noted in comment), so please convert complex units manually if needed.
# <float> and <int> types does not require any unit. Quantity require unit.

# Default values does not mean valid value. In many places it's only a empty field that need to be filled.

[Main]; Name of the platform. Available choices: Reference CPU CUDA OpenCL, type: str, default: CPU
PLATFORM = CUDA

; Device index for CUDA or OpenCL (count from 0), type: str, default: 
DEVICE = 

; Number of Simulation Beads., type: int, default: 
N_BEADS = 2000

; A .bedpe file path with loops. It is required., type: str, default: 
BEDPE_PATH = /home/skorsak/Data/method_paper_data/ENCSR184YZV_CTCF_ChIAPET/LHG0052H_loops_cleaned_th10_2.bedpe

; An optional track file for cohesin or condensin in bw format. If this file is specified LEF preferentially binds were the signal is enriched., type: str, default: 
LEF_TRACK_FILE = 

; List of bigWig file paths for feature extraction., type: list, default: []
BW_FILES = []

; Output folder name., type: str, default: ../results
OUT_PATH = /home/skorsak/Data/Simulations/LE_test

; Starting region coordinate., type: int, default: 
REGION_START = 15550000

; Ending region coordinate., type: int, default: 
REGION_END = 16850000

; Chromosome that corresponds the the modelling region of interest (in case that you do not want to model the whole genome)., type: str, default: 
CHROM = chr6

; List of floating-point numbers., type: list, default: []
FLOAT_LIST = []

; List of strings., type: list, default: []
STRING_LIST = []

; True in case that you would like to make cohesins slide as random walk, instead of sliding only in one direction., type: bool, default: True
LEF_RW = True

; True in case that LEFs are pushed back when they encounter other LEFs., type: bool, default: False
LEF_DRIFT = False

; Number of Monte Carlo steps., type: int, default: 40000
N_STEPS = 80000

; Number of loop extrusion factors (condensins and cohesins). If you leave it empty it would add for LEFs twice the number of CTCFs., type: int, default: 
N_LEF = 200

; Number of second family loop extrusion factors, in case that you would like to simulate a second group with different speed., type: int, default: 0
N_LEF2 = 0

; Monte Carlo frequency. It should be hundreds of steps so as to avoid autocorrelated ensembles., type: int, default: 200
MC_STEP = 400

; Burnin-period (steps that are considered before equillibrium)., type: int, default: 1000
BURNIN = 1000

; Initial Temperature of the Stochastic Model., type: float, default: 2.0
T_INIT = 1.8

; Final Temperature of the Stochastic Model., type: float, default: 1.0
T_FINAL = 0.01

; Stochastic modelling method. It can be Metropolis or Simulated Annealing., type: str, default: Annealing
METHOD = Metropolis

; Folding coefficient., type: float, default: 1.0
FOLDING_COEFF = 1.0

; Folding coefficient for the second family of LEFs., type: float, default: 0.0
FOLDING_COEFF2 = 0.0

; LEF crossing coefficient., type: float, default: 1.0
CROSS_COEFF = 1.0

; List of strengths of the energy (floats) corresponding to each BW file. This equivalent to the `r` parameter in the LoopSage paper., type: list, default: []
BW_STRENGTHS = []

; It true if the penalty is applied for situations mi<mj<ni<nj and mi=nj, and false if it is applied only for mi=nj., type: bool, default: True
CROSS_LOOP = True

; Penalty for LEF2s that are crossing LEFs., type: bool, default: True
BETWEEN_FAMILIES_PENALTY = True

; CTCF binding coefficient., type: float, default: 1.0
BIND_COEFF = 1.0

; It should be true in case that you would like to save diagnostic plots. In case that you use small MC_STEP or large N_STEPS is better to mark it as False., type: bool, default: True
SAVE_PLOTS = True

; In case that you would liketo save metadata of the stochastic simulation., type: bool, default: True
SAVE_MDT = True

; In case that you would like to find out if there are knots in the structure., type: bool, default: False
DETECT_KNOTS = True

; you can choose between: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere., type: str, default: rw
INITIAL_STRUCTURE_TYPE = rw

; It can be either EM (multiple energy minimizations) or MD (one energy minimization and then run molecular dynamics)., type: str, default: 
SIMULATION_TYPE = MD

; The step of the integrator., type: Quantity, default: 100 femtosecond
INTEGRATOR_STEP = 100.0 femtosecond

; Path to XML file with forcefield., type: str, default: /home/skorsak/.pyenv/versions/openmm/lib/python3.10/site-packages/loopsage/forcefields/classic_sm_ff.xml
FORCEFIELD_PATH = /home/skorsak/.pyenv/versions/openmm/lib/python3.10/site-packages/loopsage/forcefields/classic_sm_ff.xml

; Angle force strength., type: float, default: 200.0
ANGLE_FF_STRENGTH = 200.0

; Equillibrium distance of loop forces., type: float, default: 0.1
LE_FF_LENGTH = 0.1

; Interaction Strength of loop forces., type: float, default: 50000.0
LE_FF_STRENGTH = 50000.0

; True if topoisomerase disables EV in a continuous region rather than a discrete set of points., type: bool, default: False
CONTINUOUS_TOP = True

; Probability that randomly excluded volume may be disabled., type: float, default: 0.0
EV_P = 0.01

; Excluded-volume strength., type: float, default: 100.0
EV_FF_STRENGTH = 100.0

; Excluded-volume power., type: float, default: 3.0
EV_FF_POWER = 3.0

; Friction coefficient of the Langevin integrator., type: float, default: 0.1
FRICTION = 0.1

; Tolerance that works as stopping condition for energy minimization., type: float, default: 0.001
TOLERANCE = 1.0

; Visualize the output average heatmap., type: bool, default: True
VIZ_HEATS = True

; The temperature of the 3D simulation (EM or MD)., type: Quantity, default: 310 kelvin
SIM_TEMP = 310.0 kelvin

; This is the amount of simulation steps that are perform each time that we change the loop forces. If this number is too high, the simulation is slow, if is too low it may not have enough time to adapt the structure to the new constraints., type: int, default: 1000
SIM_STEP = 1000