v0.0.0.dev1
Table of Contents
Installation
Usage
Core package
Scripts
Developer’s guide
References
mdtools
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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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W
A
ag_info_str() (in module mdtools.run_time_info)
argmax_last() (in module mdtools.numpy_helper_functions)
argmin_last() (in module mdtools.numpy_helper_functions)
array() (in module mdtools.check)
atoms() (in module mdtools.select)
atoms_around_point() (in module mdtools.select)
B
backup() (in module mdtools.file_handler)
bin_edges() (in module mdtools.check)
bins() (in module mdtools.check)
block_averaging() (in module mdtools.check)
box() (in module mdtools.check)
C
cd_up() (in module mdtools.file_handler)
ceil_divide() (in module mdtools.numpy_helper_functions)
close() (mdtools.parallel.ProcessPool method)
cm_fill_missing_cmp_ix() (in module mdtools.structure)
cm_selix_stats() (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)
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)
cross_section() (in module mdtools.numpy_helper_functions)
cross_section2d() (in module mdtools.numpy_helper_functions)
D
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
excel_colname() (in module mdtools.numpy_helper_functions)
excel_colnum() (in module mdtools.numpy_helper_functions)
extend() (in module mdtools.numpy_helper_functions)
F
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
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)
I
indent() (in module mdtools.file_handler)
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)
M
masses() (in module mdtools.check)
masses_new() (in module mdtools.check)
match_shape() (in module mdtools.numpy_helper_functions)
mdtools.check
module
mdtools.dtrj
module
mdtools.dynamics
module
mdtools.file_handler
module
mdtools.numpy_helper_functions
module
mdtools.parallel
module
mdtools.run_time_info
module
mdtools.scipy_helper_functions
module
mdtools.select
module
mdtools.structure
module
mdtools.version
module
mem_usage() (in module mdtools.run_time_info)
module
contact_hist
discrete_pos
lig_change_at_pos_change_blocks
lig_change_at_pos_change_blocks_hist
mdtools.check
mdtools.dtrj
mdtools.dynamics
mdtools.file_handler
mdtools.numpy_helper_functions
mdtools.parallel
mdtools.run_time_info
mdtools.scipy_helper_functions
mdtools.select
mdtools.structure
mdtools.version
scripts.script_template
scripts.script_template_dtrj
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)
P
pos_array() (in module mdtools.check)
ProcessPool (class in mdtools.parallel)
ProgressBar (class in mdtools.run_time_info)
Python Enhancement Proposals
PEP 20
PEP 257
PEP 440
,
[1]
,
[2]
,
[3]
PEP 8
,
[1]
,
[2]
R
replace_short_sequences() (in module mdtools.dynamics)
replace_short_sequences_global() (in module mdtools.dynamics)
restarts() (in module mdtools.check)
run_time_info() (in module mdtools.run_time_info)
run_time_info_str() (in module mdtools.run_time_info)
S
savetxt() (in module mdtools.file_handler)
savetxt_matrix() (in module mdtools.file_handler)
scripts.script_template
module
scripts.script_template_dtrj
module
sequenize() (in module mdtools.numpy_helper_functions)
split_into_consecutive_subarrays() (in module mdtools.numpy_helper_functions)
submit_task() (mdtools.parallel.ProcessPool method)
symmetrize() (in module mdtools.numpy_helper_functions)
T
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_per_state() (in module mdtools.dtrj)
trapz2d() (in module mdtools.numpy_helper_functions)
U
universe() (in module mdtools.select)
W
write_header() (in module mdtools.file_handler)
write_matrix_block() (in module mdtools.file_handler)
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