Index

A

ActiveBrownianIntegrator (class in OpenMiChroM.Integrators) AdamTraining (class in OpenMiChroM.Optimization) addAdditionalForce() (OpenMiChroM.ChromDynamics.MiChroM method) addAngles() (OpenMiChroM.ChromDynamics.MiChroM method) addCorrelatedNoise() (OpenMiChroM.ChromDynamics.MiChroM method) addCustomIC() (OpenMiChroM.ChromDynamics.MiChroM method) addCustomMultiChainIC() (OpenMiChroM.ChromDynamics.MiChroM method) addCustomTypes() (OpenMiChroM.ChromDynamics.MiChroM method) addCylindricalConfinement() (OpenMiChroM.ChromDynamics.MiChroM method) addFENEBonds() (OpenMiChroM.ChromDynamics.MiChroM method)

addFlatBottomHarmonic() (OpenMiChroM.ChromDynamics.MiChroM method) addHarmonicBonds() (OpenMiChroM.ChromDynamics.MiChroM method) addHomoPolymerForces() (OpenMiChroM.ChromDynamics.MiChroM method) addIdealChromosome() (OpenMiChroM.ChromDynamics.MiChroM method) addLoops() (OpenMiChroM.ChromDynamics.MiChroM method) addMultiChainIC() (OpenMiChroM.ChromDynamics.MiChroM method) addRepulsiveSoftCore() (OpenMiChroM.ChromDynamics.MiChroM method) addSelfAvoidance() (OpenMiChroM.ChromDynamics.MiChroM method) addSphericalConfinementLJ() (OpenMiChroM.ChromDynamics.MiChroM method) addTypetoType() (OpenMiChroM.ChromDynamics.MiChroM method) appCutoff() (OpenMiChroM.Optimization.FullTraining method)

B

buildClassicMichrom() (OpenMiChroM.ChromDynamics.MiChroM method)

C

calc_phi_exp_IC() (OpenMiChroM.Optimization.CustomMiChroMTraining method) calc_phi_exp_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method) calc_phi_sim_IC() (OpenMiChroM.Optimization.CustomMiChroMTraining method) calc_phi_sim_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method) cndbTools (class in OpenMiChroM.CndbTools) compute_Chirality() (OpenMiChroM.CndbTools.cndbTools method) compute_FFT_from_Oij() (OpenMiChroM.CndbTools.cndbTools method) compute_GyrTensorEigs() (OpenMiChroM.CndbTools.cndbTools method) compute_MSD() (OpenMiChroM.CndbTools.cndbTools method) compute_Orientation_OP() (OpenMiChroM.CndbTools.cndbTools method)

compute_RadNumDens() (OpenMiChroM.CndbTools.cndbTools method) compute_RDP() (OpenMiChroM.CndbTools.cndbTools method) compute_RG() (OpenMiChroM.CndbTools.cndbTools method) createInitialLambda() (OpenMiChroM.Optimization.FullTraining method) createLine() (OpenMiChroM.ChromDynamics.MiChroM method) createRandomWalk() (OpenMiChroM.ChromDynamics.MiChroM method) createReporters() (OpenMiChroM.ChromDynamics.MiChroM method) createSimulation() (OpenMiChroM.ChromDynamics.MiChroM method) createSpringSpiral() (OpenMiChroM.ChromDynamics.MiChroM method) CustomMiChroMTraining (class in OpenMiChroM.Optimization)

F

FullTraining (class in OpenMiChroM.Optimization)

G

get_chrom_seq() (OpenMiChroM.Optimization.CustomMiChroMTraining method) get_HiC_exp() (OpenMiChroM.Optimization.CustomMiChroMTraining method) get_HiC_sim() (OpenMiChroM.Optimization.CustomMiChroMTraining method) get_indices() (OpenMiChroM.Optimization.FullTraining method) get_lambdas_IC() (OpenMiChroM.Optimization.CustomMiChroMTraining method) get_lambdas_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method) get_Pearson() (OpenMiChroM.Optimization.CustomMiChroMTraining method) get_PiPj_sim_IC() (OpenMiChroM.Optimization.CustomMiChroMTraining method)

get_PiPj_sim_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method) getForces() (OpenMiChroM.ChromDynamics.MiChroM method) getHiCexp() (OpenMiChroM.Optimization.AdamTraining method) getLamb() (OpenMiChroM.Optimization.AdamTraining method) getLambdas() (OpenMiChroM.Optimization.FullTraining method) getLoops() (OpenMiChroM.ChromDynamics.MiChroM method) getPars() (OpenMiChroM.Optimization.AdamTraining method) getPearson() (OpenMiChroM.Optimization.FullTraining method) getPositions() (OpenMiChroM.ChromDynamics.MiChroM method)

I

initPositions() (OpenMiChroM.ChromDynamics.MiChroM method)

initStructure() (OpenMiChroM.ChromDynamics.MiChroM method) initVelocities() (OpenMiChroM.ChromDynamics.MiChroM method)

K

knight_ruiz_balance() (OpenMiChroM.Optimization.AdamTraining method)

L

load() (OpenMiChroM.CndbTools.cndbTools method) loadBed() (OpenMiChroM.ChromDynamics.MiChroM method) loadGRO() (OpenMiChroM.ChromDynamics.MiChroM method)

loadNDB() (OpenMiChroM.ChromDynamics.MiChroM method) loadPDB() (OpenMiChroM.ChromDynamics.MiChroM method) loadStructure() (OpenMiChroM.ChromDynamics.MiChroM method)

M

MiChroM (class in OpenMiChroM.ChromDynamics) module OpenMiChroM.ChromDynamics OpenMiChroM.CndbTools OpenMiChroM.Integrators OpenMiChroM.Optimization

N

ndb2cndb() (OpenMiChroM.CndbTools.cndbTools method)

normalize_matrix() (OpenMiChroM.Optimization.AdamTraining method) (OpenMiChroM.Optimization.CustomMiChroMTraining method)

O

OpenMiChroM.ChromDynamics module OpenMiChroM.CndbTools module

OpenMiChroM.Integrators module OpenMiChroM.Optimization module

P

printForces() (OpenMiChroM.ChromDynamics.MiChroM method) printHeader() (OpenMiChroM.ChromDynamics.MiChroM method) prob_calculation_IC() (OpenMiChroM.Optimization.CustomMiChroMTraining method)

prob_calculation_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method) probCalc() (OpenMiChroM.Optimization.AdamTraining method) (OpenMiChroM.Optimization.FullTraining method)

R

random_ChromSeq() (OpenMiChroM.ChromDynamics.MiChroM method) removeFlatBottomHarmonic() (OpenMiChroM.ChromDynamics.MiChroM method)

removeForce() (OpenMiChroM.ChromDynamics.MiChroM method) reset_Pi() (OpenMiChroM.Optimization.AdamTraining method) run() (OpenMiChroM.ChromDynamics.MiChroM method)

S

saveFolder() (OpenMiChroM.ChromDynamics.MiChroM method) saveLambdas() (OpenMiChroM.Optimization.FullTraining method) saveStructure() (OpenMiChroM.ChromDynamics.MiChroM method)

setChains() (OpenMiChroM.ChromDynamics.MiChroM method) setFibPosition() (OpenMiChroM.ChromDynamics.MiChroM method) setPositions() (OpenMiChroM.ChromDynamics.MiChroM method) setup() (OpenMiChroM.ChromDynamics.MiChroM method)

T

traj2HiC() (OpenMiChroM.CndbTools.cndbTools method)

X

xyz() (OpenMiChroM.CndbTools.cndbTools method)