OpenMiChroM
latest
Getting Started
Installation
Introduction
Open-MiChroM Modules
OpenMiChroM
Tutorials
Single Chromosome Simulation
Multiple Chromosome Simulation
Tutorial: Single chromosome optimization using OpenMiChroM
Full Inversion Method for a single chromosome using OpenMiChroM
Pulling Simulations
Temporally Correlated Active Noise Simulation Tutorial
Reference
How to cite
OpenMiChroM
References
License
OpenMiChroM
»
Index
Edit on GitHub
Index
A
|
C
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
X
A
AdamTraining (class in OpenMiChroM.Optimization)
addAdditionalForce() (OpenMiChroM.ChromDynamics.MiChroM method)
addAngles() (OpenMiChroM.ChromDynamics.MiChroM method)
addBond() (OpenMiChroM.ChromDynamics.MiChroM method)
addCorrelatedNoise() (OpenMiChroM.ChromDynamics.MiChroM method)
addCustomIC() (OpenMiChroM.ChromDynamics.MiChroM method)
addCustomTypes() (OpenMiChroM.ChromDynamics.MiChroM method)
addCylindricalConfinement() (OpenMiChroM.ChromDynamics.MiChroM method)
addFENEBonds() (OpenMiChroM.ChromDynamics.MiChroM method)
addFlatBottomHarmonic() (OpenMiChroM.ChromDynamics.MiChroM method)
addHarmonicBond_ij() (OpenMiChroM.ChromDynamics.MiChroM method)
addHarmonicBonds() (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)
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)
chromRG() (OpenMiChroM.ChromDynamics.MiChroM 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)
createSpringSpiral() (OpenMiChroM.ChromDynamics.MiChroM method)
CustomMiChroMTraining (class in OpenMiChroM.Optimization)
F
FullTraining (class in OpenMiChroM.Optimization)
G
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)
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)
getScaledData() (OpenMiChroM.ChromDynamics.MiChroM method)
getVelocities() (OpenMiChroM.ChromDynamics.MiChroM method)
I
initPositions() (OpenMiChroM.ChromDynamics.MiChroM method)
initStorage() (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)
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.Optimization
N
ndb2cndb() (OpenMiChroM.CndbTools.cndbTools method)
normalize_matrix() (OpenMiChroM.Optimization.AdamTraining method)
O
OpenMiChroM.ChromDynamics
module
OpenMiChroM.CndbTools
module
OpenMiChroM.Optimization
module
P
printForces() (OpenMiChroM.ChromDynamics.MiChroM method)
printHeader() (OpenMiChroM.ChromDynamics.MiChroM method)
printStats() (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)
randomizePositions() (OpenMiChroM.ChromDynamics.MiChroM method)
removeFlatBottomHarmonic() (OpenMiChroM.ChromDynamics.MiChroM method)
removeForce() (OpenMiChroM.ChromDynamics.MiChroM method)
reset_Pi() (OpenMiChroM.Optimization.AdamTraining method)
runSimBlock() (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)
Read the Docs
v: latest
Versions
latest
stable
v1.0.7
v1.0.6
v1.0.5
v1.0.4
main
Downloads
On Read the Docs
Project Home
Builds