wlcsim
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wlcsim Python Module
wlcsim Fortran Codebase Structure
Fortran Simulation Features
Fortran Simulation Output
About Parallel Tempering
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Meiotic Homolog Pairing
Example plots for Frank Elastic Constants
wlcsim
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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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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R
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S
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T
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U
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V
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W
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Y
_
_get_bead_msd (in module wlcsim.bd.runge_kutta)
_get_scalar_corr (in module wlcsim.bd.runge_kutta)
_get_vector_corr (in module wlcsim.bd.runge_kutta)
_jit_rouse_homologs (in module wlcsim.bd.homolog)
_jit_sswlc_clean() (in module wlcsim.bd.tsswlc)
_jit_sswlc_lena() (in module wlcsim.bd.tsswlc)
A
accept_all_energies() (fortran subroutine in module energies)
apply_energy_ison() (fortran subroutine in module energies)
B
basepairsperturn (fortran variable in module nucleosome)
bend_ (fortran variable in module energies)
bind_ (fortran variable in module energies)
C
calc_all_de_from_dx() (fortran subroutine in module energies)
calc_dphi() (fortran subroutine)
chi_ (fortran variable in module energies)
confine_ (fortran variable in module energies)
correct_param_name() (in module wlcsim.input)
correct_param_value() (in module wlcsim.input)
couple_ (fortran variable in module energies)
D
decide_input_format() (wlcsim.input.ParsedInput method)
E
end2end_distance() (in module wlcsim.analytical.rouse)
end2end_distance_gauss() (in module wlcsim.analytical.rouse)
end_to_end_corr() (in module wlcsim.analytical.rouse)
energies (module)
energyof (fortran variable in module energies)
explicitbinding_ (fortran variable in module energies)
external_ (fortran variable in module energies)
F
f_conf_ellipse (in module wlcsim.bd.forces)
f_elas_homolog_rouse (in module wlcsim.bd.forces)
f_elas_linear_rouse (in module wlcsim.bd.forces)
f_elas_linear_sswlc (in module wlcsim.bd.forces)
f_tether_ellipse (in module wlcsim.bd.forces)
field_ (fortran variable in module energies)
find_gamma() (in module wlcsim.FrankElastic.plot_frank)
frac_cv() (in module wlcsim.analytical.fractional)
frac_discrete_cv() (in module wlcsim.analytical.fractional)
frac_discrete_cv_normalized() (in module wlcsim.analytical.fractional)
frac_msd() (in module wlcsim.analytical.fractional)
frac_rouse_cvv() (in module wlcsim.analytical.fractional)
frac_rouse_mid_msd() (in module wlcsim.analytical.fractional)
frac_rouse_mode_corr() (in module wlcsim.analytical.fractional)
G
gaussian_G (in module wlcsim.analytical.rouse)
gaussian_Ploop (in module wlcsim.analytical.rouse)
get_a() (in module wlcsim.FrankElastic.frank)
get_data_for_Splot() (in module wlcsim.FrankElastic.plot_frank)
get_first_pole() (in module wlcsim.FrankElastic.frank)
get_Frank_values() (in module wlcsim.FrankElastic.frank)
get_Multi_frank_data() (in module wlcsim.FrankElastic.plot_frank)
get_Nsweep_data() (in module wlcsim.FrankElastic.plot_frank)
get_params() (fortran subroutine in module nucleosome)
global_twistliner_ (fortran variable in module energies)
global_twistquadratic_ (fortran variable in module energies)
Gmll_matrix (in module wlcsim.FrankElastic.stonefence)
H
hamiltonian() (fortran subroutine)
head_node() (fortran subroutine)
I
ind_sphere() (in module wlcsim.FrankElastic.yyyreal)
InputFormat (class in wlcsim.input)
internucleosome_ (fortran variable in module energies)
internucleosome_energy() (fortran function in module nucleosome)
interp() (fortran subroutine)
intYYYnum() (in module wlcsim.FrankElastic.yyyreal)
invLaplace() (in module wlcsim.FrankElastic.invlaplace)
invLaplace_path() (in module wlcsim.FrankElastic.invlaplace)
J
jit_confined_srk1 (in module wlcsim.bd.rouse)
jit_confinement_clean (in module wlcsim.bd.rouse)
jit_srk1 (in module wlcsim.bd.rouse)
K
kap_ (fortran variable in module energies)
kp_over_kbt (in module wlcsim.analytical.rouse)
L
linear_mid_msd (in module wlcsim.analytical.rouse)
linear_mscd() (in module wlcsim.analytical.rouse)
load_nucleosome_positions() (fortran subroutine in module nucleosome)
M
maiersaupe_ (fortran variable in module energies)
main (fortran program)
make_path() (in module wlcsim.FrankElastic.invlaplace)
mc_adapt() (fortran subroutine)
mc_energy (fortran type in module energies)
mc_int_chem() (fortran subroutine)
mc_int_intitialize() (fortran subroutine)
mc_int_rep() (fortran subroutine)
mc_int_super_rep() (fortran subroutine)
mc_int_swap() (fortran subroutine)
mc_int_update() (fortran subroutine)
mcsim() (fortran subroutine)
measured_D_to_rouse() (in module wlcsim.bd.rouse)
mu_ (fortran variable in module energies)
Multi_frank_plot() (in module wlcsim.FrankElastic.plot_frank)
multi_process_fun() (in module wlcsim.FrankElastic.plot_frank)
multiparams (fortran variable in module nucleosome)
N
nucleosome (module)
nucleosome_energy() (fortran function in module nucleosome)
nucleosome_prop() (fortran subroutine in module nucleosome)
nucleosomerot (fortran variable in module nucleosome)
nucleosometran (fortran variable in module nucleosome)
number_of_energy_types (fortran variable in module energies)
O
ou() (in module wlcsim.bd.runge_kutta)
P
parse_defines_params_file() (wlcsim.input.ParsedInput method)
parse_lena_params_file() (wlcsim.input.ParsedInput method)
parse_original_params_file() (wlcsim.input.ParsedInput method)
parse_params_file() (wlcsim.input.ParsedInput method)
ParsedInput (class in wlcsim.input)
PgammaB_vec (in module wlcsim.FrankElastic.stonefence)
plot_Frank() (in module wlcsim.FrankElastic.plot_frank)
plot_S() (in module wlcsim.FrankElastic.plot_frank)
plotNsweep() (in module wlcsim.FrankElastic.plot_frank)
points_to_loops_list() (in module wlcsim.bd.homolog)
precalculate_data() (in module wlcsim.FrankElastic.stonefence)
print_all_denergies() (fortran subroutine in module energies)
R
recommended_dt() (in module wlcsim.bd.rouse)
replicaexchange() (fortran subroutine)
ring_mscd() (in module wlcsim.analytical.rouse)
rk4_thermal_bruno() (in module wlcsim.bd.runge_kutta)
rk4_thermal_lena() (in module wlcsim.bd.runge_kutta)
rouse() (in module wlcsim.bd.homolog)
rouse_cv_mid() (in module wlcsim.analytical.fractional)
rouse_cvv_ep() (in module wlcsim.analytical.fractional)
rouse_large_cvv_g() (in module wlcsim.analytical.rouse)
rouse_mode (in module wlcsim.analytical.rouse)
rouse_mode_coef (in module wlcsim.analytical.rouse)
rouse_nondim_() (in module wlcsim.analytical.fractional)
S
self_ (fortran variable in module energies)
seperate_bend_twist_splay() (in module wlcsim.FrankElastic.plot_frank)
set_all_denergy_to_zero() (fortran subroutine in module energies)
set_all_energy_to_zero() (fortran subroutine in module energies)
set_up_energyof() (fortran subroutine in module energies)
setup_nucleosome_constants() (fortran subroutine in module nucleosome)
shear_ (fortran variable in module energies)
sim_loc() (in module wlcsim.bd.homolog)
split_homolog_x() (in module wlcsim.bd.homolog)
split_homologs_X() (in module wlcsim.bd.homolog)
srk1_roberts() (in module wlcsim.bd.runge_kutta)
sswlc() (in module wlcsim.bd.tsswlc)
startworker() (fortran subroutine)
sterics_ (fortran variable in module energies)
stretch_ (fortran variable in module energies)
sum_all_denergies() (fortran subroutine in module energies)
T
tDeltaN() (in module wlcsim.analytical.fractional)
test_Frank_accuracy() (in module wlcsim.FrankElastic.frank)
test_rouse_msd_line_approx() (in module wlcsim.analytical.rouse)
tR() (in module wlcsim.analytical.fractional)
twist_ (fortran variable in module energies)
twobody_ (fortran variable in module energies)
U
umbrella_ (fortran variable in module energies)
umbrellaquadratic_ (fortran variable in module energies)
un_rouse_nondim() (in module wlcsim.analytical.fractional)
V
vc() (in module wlcsim.analytical.fractional)
vvc_rescaled_theory() (in module wlcsim.analytical.fractional)
vvc_unscaled_theory() (in module wlcsim.analytical.fractional)
W
with_integrator() (in module wlcsim.bd.rouse)
wlcsim (fortran program)
(module)
wlcsim.analytical (module)
wlcsim.analytical.fractional (module)
wlcsim.analytical.rouse (module)
wlcsim.bd (module)
wlcsim.bd.forces (module)
wlcsim.bd.homolog (module)
wlcsim.bd.rouse (module)
wlcsim.bd.runge_kutta (module)
wlcsim.bd.tsswlc (module)
wlcsim.FrankElastic.frank (module)
wlcsim.FrankElastic.invlaplace (module)
wlcsim.FrankElastic.plot_frank (module)
wlcsim.FrankElastic.stonefence (module)
wlcsim.FrankElastic.yyyreal (module)
wlcsim.input (module)
wlcsim_bruno() (fortran subroutine)
wlcsim_quinn() (fortran subroutine)
worker_node() (fortran subroutine)
write() (wlcsim.input.ParsedInput method)
Y
YR() (in module wlcsim.FrankElastic.yyyreal)
YYY() (in module wlcsim.FrankElastic.yyyreal)
YYY_0mm() (in module wlcsim.FrankElastic.yyyreal)
YYY_l1() (in module wlcsim.FrankElastic.yyyreal)
YYYreal() (in module wlcsim.FrankElastic.yyyreal)
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