Index

A

add_angle_force() (Chromosome method) add_chr_lam() (Lamina method) add_chr_nuc() (Nucleolus method) add_chr_spec() (Speckle method) add_chromosome_potential() (OpenNucleome method) add_class2_bond() (Chromosome method) add_fene_bond() (Chromosome method) add_hardwall() (Lamina method) add_ideal_potential() (Chromosome method) add_inter_potential() (Chromosome method)

add_lam_lam() (Lamina method) add_lamina_potential() (OpenNucleome method) add_nuc_nuc() (Nucleolus method) add_nuc_spec() (Nucleolus method) add_nucleolus_potential() (OpenNucleome method) add_softcore() (Chromosome method) add_spec_spec() (Speckle method) add_speckle_potential() (OpenNucleome method) add_squeeze_nucleus() (Lamina method) add_type_type_potential() (Chromosome method)

C

Chromosome (class in openNucleome.chromosome) construct_topology() (OpenNucleome method)

coor_transformation() (in module openNucleome.utils.coor_transformation) create_simulation() (OpenNucleome method) create_system() (OpenNucleome method)

D

DamID_TSASeq_calculation() (in module openNucleome.utils.DamID_TSASeq_calculation)

F

final_frame() (in module openNucleome.utils.final_frame)

G

generate_element() (OpenNucleome method)

L

Lamina (class in openNucleome.lamina)

load_customized_settings() (OpenNucleome method) load_default_settings() (OpenNucleome method)

M

module openNucleome.chromosome openNucleome.lamina openNucleome.nucleolus openNucleome.speckle openNucleome.utils.coor_transformation openNucleome.utils.DamID_TSASeq_calculation openNucleome.utils.final_frame openNucleome.whole_nucleus_model

N

Nucleolus (class in openNucleome.nucleolus)

O

OpenNucleome (class in openNucleome.whole_nucleus_model) openNucleome.chromosome module openNucleome.lamina module openNucleome.nucleolus module openNucleome.speckle module

openNucleome.utils.coor_transformation module openNucleome.utils.DamID_TSASeq_calculation module openNucleome.utils.final_frame module openNucleome.whole_nucleus_model module

S

save_system() (OpenNucleome method)

Speckle (class in openNucleome.speckle)