v0.0.6.0
Table of Contents
Installation
Usage
Core package
Scripts
Developer’s guide
References
mdtools
Index
Edit on GitHub
Index
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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L
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M
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N
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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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X
A
acf() (in module mdtools.statistics)
acf_confint() (in module mdtools.statistics)
acf_np() (in module mdtools.statistics)
acf_se() (in module mdtools.statistics)
ag_info_str() (in module mdtools.run_time_info)
annotate_heatmap() (in module mdtools.plot)
argmax_last() (in module mdtools.numpy_helper_functions)
argmin_last() (in module mdtools.numpy_helper_functions)
array() (in module mdtools.check)
assign_atoms_to_grid() (in module mdtools.structure)
atoms() (in module mdtools.select)
atoms_around_point() (in module mdtools.select)
attribute_hist
module
B
backup() (in module mdtools.file_handler)
bin_edges() (in module mdtools.check)
bins() (in module mdtools.check)
block_average() (in module mdtools.statistics)
block_averaging() (in module mdtools.check)
box() (in module mdtools.check)
box2cart() (in module mdtools.box)
box_mat() (in module mdtools.check)
box_volume() (in module mdtools.box)
C
cart2box() (in module mdtools.box)
cd_up() (in module mdtools.file_handler)
ceil_divide() (in module mdtools.numpy_helper_functions)
center() (in module mdtools.statistics)
(in module mdtools.structure)
close() (mdtools.parallel.ProcessPool method)
cm_fill_missing_cmp_ix() (in module mdtools.structure)
cm_selix_stats() (in module mdtools.structure)
cmp_attr() (in module mdtools.structure)
cmp_contact_count_matrices() (in module contact_hist)
cmp_contact_count_matrix() (in module mdtools.structure)
cmp_contact_matrix() (in module mdtools.structure)
cms_n_common_contacts() (in module mdtools.structure)
cms_n_contacts() (in module mdtools.structure)
coc() (in module mdtools.structure)
cog() (in module mdtools.structure)
com() (in module mdtools.structure)
contact_hist
module
contact_hist_refcmp_diff_selcmp() (in module mdtools.structure)
contact_hist_refcmp_same_selcmp() (in module mdtools.structure)
contact_hist_refcmp_selcmp_pair() (in module mdtools.structure)
contact_hist_refcmp_selcmp_tot() (in module mdtools.structure)
contact_hists() (in module mdtools.structure)
contact_matrices() (in module mdtools.structure)
contact_matrix() (in module mdtools.structure)
correct_intermittency() (in module mdtools.dynamics)
correct_intermittency_1d() (in module mdtools.dynamics)
correlogram() (in module mdtools.plot)
cross_section() (in module mdtools.numpy_helper_functions)
cross_section2d() (in module mdtools.numpy_helper_functions)
cumav() (in module mdtools.statistics)
D
diagonal() (in module mdtools.box)
diff_mic() (in module mdtools.numpy_helper_functions)
digitize_dd() (in module mdtools.numpy_helper_functions)
discrete_pos
module
discrete_pos_trj() (in module mdtools.structure)
distance_bins() (in module mdtools.check)
dtrj() (in module mdtools.check)
dtrj_trans_info() (in module mdtools.run_time_info)
dtrj_trans_info_str() (in module mdtools.run_time_info)
E
ekin_dist() (in module mdtools.statistics)
errorbar() (in module mdtools.plot)
excel_colname() (in module mdtools.numpy_helper_functions)
excel_colnum() (in module mdtools.numpy_helper_functions)
exp_dist() (in module mdtools.statistics)
exp_dist_log() (in module mdtools.statistics)
extend() (in module mdtools.numpy_helper_functions)
F
fill_between() (in module mdtools.plot)
fill_betweenx() (in module mdtools.plot)
find_const_seq_long() (in module mdtools.numpy_helper_functions)
find_const_seq_n() (in module mdtools.numpy_helper_functions)
find_linear_region() (in module mdtools.numpy_helper_functions)
find_nearest() (in module mdtools.numpy_helper_functions)
frame_lag() (in module mdtools.check)
frame_slicing() (in module mdtools.check)
G
gaussian() (in module mdtools.statistics)
get_const_seqs() (in module mdtools.numpy_helper_functions)
get_middle() (in module mdtools.numpy_helper_functions)
get_num_CPUs() (in module mdtools.run_time_info)
get_results() (mdtools.parallel.ProcessPool method)
group_by() (in module mdtools.numpy_helper_functions)
H
header_str() (in module mdtools.file_handler)
hist() (in module mdtools.plot)
hlines() (in module mdtools.plot)
I
imshow() (in module mdtools.plot)
imshow_new() (in module mdtools.plot)
indent() (in module mdtools.file_handler)
item_change_ix() (in module mdtools.numpy_helper_functions)
ix_along_axis_to_global_ix() (in module mdtools.numpy_helper_functions)
ix_of_item_change() (in module mdtools.numpy_helper_functions)
ix_of_item_change_1d() (in module mdtools.numpy_helper_functions)
J
join() (mdtools.parallel.ProcessPool method)
L
lig_change_at_pos_change_blocks
module
lig_change_at_pos_change_blocks_hist
module
list_of_cms() (in module mdtools.check)
load_dtrj() (in module mdtools.file_handler)
locate_item_change() (in module mdtools.numpy_helper_functions)
locate_trans() (in module mdtools.dtrj)
M
make_whole() (in module mdtools.box)
masses() (in module mdtools.check)
masses_new() (in module mdtools.check)
match_shape() (in module mdtools.numpy_helper_functions)
matshow() (in module mdtools.plot)
matshow_new() (in module mdtools.plot)
mb_dist() (in module mdtools.statistics)
mdtools.box
module
mdtools.check
module
mdtools.dtrj
module
mdtools.dynamics
module
mdtools.file_handler
module
mdtools.numpy_helper_functions
module
mdtools.parallel
module
mdtools.plot
module
mdtools.run_time_info
module
mdtools.scipy_helper_functions
module
mdtools.select
module
mdtools.statistics
module
mdtools.structure
module
mdtools.version
module
mem_usage() (in module mdtools.run_time_info)
MidpointNormalize (class in mdtools.plot)
module
attribute_hist
contact_hist
discrete_pos
lig_change_at_pos_change_blocks
lig_change_at_pos_change_blocks_hist
mdtools.box
mdtools.check
mdtools.dtrj
mdtools.dynamics
mdtools.file_handler
mdtools.numpy_helper_functions
mdtools.parallel
mdtools.plot
mdtools.run_time_info
mdtools.scipy_helper_functions
mdtools.select
mdtools.statistics
mdtools.structure
mdtools.version
numpy_archive
plot_discrete_hex_trj
plot_discrete_pos_trj
plot_energy_dist
plot_gmx_densmap
plot_msd_layer
plot_msd_layer_cross_section_at_constant_time
plot_msd_layer_cross_section_xyz_at_constant_msd
plot_msd_layer_cross_section_xyz_at_constant_time
plot_msd_layer_heatmap
plot_state_lifetime
plot_state_lifetime_discrete
plot_trans_per_state_vs_time
rmsd_trj_trj
rmsd_vs_time
script_template
script_template_dtrj
script_template_plot
state_lifetime
state_lifetime_discrete
subvolume_charge
unwrap_trj
movav() (in module mdtools.statistics)
msd() (in module mdtools.dynamics)
msd_non_diffusive() (in module mdtools.dynamics)
multiple_multiply() (in module mdtools.scipy_helper_functions)
N
n_restarts() (in module mdtools.dynamics)
n_tasks_done() (mdtools.parallel.ProcessPool method)
n_tasks_submitted() (mdtools.parallel.ProcessPool method)
natms_per_cmp() (in module mdtools.structure)
net_charge_of_cubes() (in module subvolume_charge)
ngp() (in module mdtools.statistics)
numpy_archive
module
P
pcolormesh() (in module mdtools.plot)
pcolormesh_new() (in module mdtools.plot)
plot() (in module mdtools.plot)
plot_2nd_xaxis() (in module mdtools.plot)
plot_2nd_yaxis() (in module mdtools.plot)
plot_discrete_hex_trj
module
plot_discrete_pos_trj
module
plot_energy_dist
module
plot_gmx_densmap
module
plot_msd_layer
module
plot_msd_layer_cross_section_at_constant_time
module
plot_msd_layer_cross_section_xyz_at_constant_msd
module
plot_msd_layer_cross_section_xyz_at_constant_time
module
plot_msd_layer_heatmap
module
plot_state_lifetime
module
plot_state_lifetime_discrete
module
plot_trans_per_state_vs_time
module
pos_array() (in module mdtools.check)
power_law() (in module plot_trans_per_state_vs_time)
ProcessPool (class in mdtools.parallel)
ProgressBar (class in mdtools.run_time_info)
Python Enhancement Proposals
PEP 20
,
[1]
PEP 257
,
[1]
PEP 440
,
[1]
PEP 8
,
[1]
R
read_matrix() (in module plot_gmx_densmap)
remain_prob() (in module mdtools.dtrj)
remain_prob_discrete() (in module mdtools.dtrj)
replace_short_sequences() (in module mdtools.dynamics)
replace_short_sequences_global() (in module mdtools.dynamics)
restarts() (in module mdtools.check)
rmsd() (in module mdtools.structure)
rmsd_trj_trj
module
rmsd_vs_time
module
run_time_info() (in module mdtools.run_time_info)
run_time_info_str() (in module mdtools.run_time_info)
S
save_dtrj() (in module mdtools.file_handler)
savetxt() (in module mdtools.file_handler)
savetxt_matrix() (in module mdtools.file_handler)
scatter() (in module mdtools.plot)
sci_notation_tex() (in module mdtools.plot)
script_template
module
script_template_dtrj
module
script_template_plot
module
sequenize() (in module mdtools.numpy_helper_functions)
split_into_contig_seqs() (in module mdtools.numpy_helper_functions)
standardize() (in module mdtools.statistics)
state_lifetime
module
state_lifetime_discrete
module
std_weighted() (in module mdtools.statistics)
str2bool() (in module mdtools.file_handler)
str2none_or_type() (in module mdtools.file_handler)
submit_task() (mdtools.parallel.ProcessPool method)
subtract_mic() (in module mdtools.numpy_helper_functions)
subvolume_charge
module
symmetrize() (in module mdtools.numpy_helper_functions)
T
tail() (in module mdtools.file_handler)
take() (in module mdtools.numpy_helper_functions)
terminate() (mdtools.parallel.ProcessPool method)
tilt_diagonals() (in module mdtools.numpy_helper_functions)
time_step() (in module mdtools.check)
trailing_digits() (in module mdtools.numpy_helper_functions)
trans_ix() (in module mdtools.dtrj)
trans_per_state() (in module mdtools.dtrj)
trans_per_state_vs_time() (in module mdtools.dtrj)
trapz2d() (in module mdtools.numpy_helper_functions)
triclinic_box() (in module mdtools.box)
triclinic_vectors() (in module mdtools.box)
U
universe() (in module mdtools.select)
unwrap_frame() (in module mdtools.box)
unwrap_trj
module
V
var_weighted() (in module mdtools.statistics)
vdist() (in module mdtools.box)
vlines() (in module mdtools.plot)
volume() (in module mdtools.box)
W
wcenter() (in module mdtools.structure)
wcenter_pos() (in module mdtools.structure)
wrap() (in module mdtools.box)
wrap_pos() (in module mdtools.box)
write_header() (in module mdtools.file_handler)
write_matrix_block() (in module mdtools.file_handler)
X
xopen() (in module mdtools.file_handler)
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