OpenMiChroM
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Getting Started
Installation
Introduction
Open-MiChroM Modules
OpenMiChroM
Tutorials
Single Chain: Chromatin Dynamics Simulations on Chromosome 10 of GM12878 Cell Line
Multiple Chains: Chromatin Dynamics Simulations on Chromosome 10 and Chromosome 11 of GM12878 Cell Line
Reference
How to cite
OpenMiChroM
References
License
OpenMiChroM
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Index
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Index
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C
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F
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G
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I
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L
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M
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N
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O
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P
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A
AdamTraining (class in OpenMiChroM.Optimization)
addAdditionalForce() (OpenMiChroM.ChromDynamics.MiChroM method)
addAngles() (OpenMiChroM.ChromDynamics.MiChroM method)
addBond() (OpenMiChroM.ChromDynamics.MiChroM method)
addCustomIC() (OpenMiChroM.ChromDynamics.MiChroM method)
addCustomTypes() (OpenMiChroM.ChromDynamics.MiChroM method)
addFENEBonds() (OpenMiChroM.ChromDynamics.MiChroM method)
addFlatBottomHarmonic() (OpenMiChroM.ChromDynamics.MiChroM method)
addIdealChromosome() (OpenMiChroM.ChromDynamics.MiChroM method)
addLoops() (OpenMiChroM.ChromDynamics.MiChroM method)
addMultiChainIC() (OpenMiChroM.ChromDynamics.MiChroM method)
addRepulsiveSoftCore() (OpenMiChroM.ChromDynamics.MiChroM method)
addSphericalConfinementLJ() (OpenMiChroM.ChromDynamics.MiChroM method)
addTypetoType() (OpenMiChroM.ChromDynamics.MiChroM method)
appCutoff() (OpenMiChroM.Optimization.FullTraining method)
C
calc_exp_phi() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
calc_exp_phi_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
calc_sim_phi() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
calc_sim_phi_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_indices() (OpenMiChroM.Optimization.FullTraining method)
getBijsim() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
getChromSeq() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
getHiCexp() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
(OpenMiChroM.Optimization.FullTraining method)
getHiCSim() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
getLamb() (OpenMiChroM.Optimization.AdamTraining method)
(OpenMiChroM.Optimization.CustomMiChroMTraining method)
getLamb_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
getLambdas() (OpenMiChroM.Optimization.FullTraining method)
getlambfromfile() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
getLoops() (OpenMiChroM.ChromDynamics.MiChroM method)
getPars() (OpenMiChroM.Optimization.AdamTraining method)
getPearson() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
(OpenMiChroM.Optimization.FullTraining method)
getPiPjsim_types() (OpenMiChroM.Optimization.CustomMiChroMTraining 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)
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)
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)
probCalc() (OpenMiChroM.Optimization.AdamTraining method)
(OpenMiChroM.Optimization.FullTraining method)
probCalculation_IC() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
probCalculation_types() (OpenMiChroM.Optimization.CustomMiChroMTraining method)
R
random_ChromSeq() (OpenMiChroM.ChromDynamics.MiChroM method)
randomizePositions() (OpenMiChroM.ChromDynamics.MiChroM method)
removeFlatBottomHarmonic() (OpenMiChroM.ChromDynamics.MiChroM method)
removeForce() (OpenMiChroM.ChromDynamics.MiChroM 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)
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v1.0.5
v1.0.4
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