efmlrs
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A
add_boundary_names() (in module efmlrs.preprocessing.boundaries)
B
bounds_print() (in module efmlrs.util.data)
build_new_metas() (in module efmlrs.preprocessing.boundaries)
build_new_reas() (in module efmlrs.preprocessing.boundaries)
build_new_reversibilities() (in module efmlrs.preprocessing.boundaries)
build_new_smatrix() (in module efmlrs.preprocessing.boundaries)
build_reverse_mapping() (in module efmlrs.postprocessing.decompressing)
build_slack_metas_01() (in module efmlrs.preprocessing.boundaries)
build_slack_metas_02() (in module efmlrs.preprocessing.boundaries)
build_slack_metas_03() (in module efmlrs.preprocessing.boundaries)
building_slack_metabolites() (in module efmlrs.preprocessing.boundaries)
C
check_bounds() (in module efmlrs.preprocessing.get_data)
check_reactions() (in module efmlrs.preprocessing.compressions.deadend)
check_row() (in module efmlrs.preprocessing.compressions.deadend)
compartments_2_rm() (in module efmlrs.preprocessing.get_data)
convert_df2matrix() (in module efmlrs.util.data)
convert_float2fraction() (in module efmlrs.util.data)
convert_fraction2float() (in module efmlrs.util.data)
convert_matrix2df() (in module efmlrs.util.data)
D
decompressing() (in module efmlrs.postprocessing.decompressing)
decompressions() (in module efmlrs.postprocessing.decompressions.deadend)
E
efmlrs (module)
efmlrs.post (module)
efmlrs.postprocessing (module)
efmlrs.postprocessing.decompressing (module)
efmlrs.postprocessing.decompressions (module)
efmlrs.postprocessing.decompressions.deadend (module)
efmlrs.postprocessing.get_data (module)
efmlrs.pre (module)
efmlrs.preprocessing (module)
efmlrs.preprocessing.boundaries (module)
efmlrs.preprocessing.compressions (module)
efmlrs.preprocessing.compressions.deadend (module)
efmlrs.preprocessing.compressions.echelon (module)
efmlrs.preprocessing.get_data (module)
efmlrs.preprocessing.mplrs_output (module)
efmlrs.util (module)
efmlrs.util.convert_matrix (module)
efmlrs.util.data (module)
efmlrs.util.log (module)
efmlrs_finish_compressions() (in module efmlrs.util.data)
efmlrs_finish_decompressions() (in module efmlrs.util.data)
efmlrs_start_compressions() (in module efmlrs.util.data)
efmlrs_start_decompressions() (in module efmlrs.util.data)
extend_smatrix_1() (in module efmlrs.preprocessing.boundaries)
extend_smatrix_2() (in module efmlrs.preprocessing.boundaries)
F
find_counter() (in module efmlrs.postprocessing.decompressing)
find_deadends() (in module efmlrs.preprocessing.compressions.deadend)
find_redundant_metabolites() (in module efmlrs.preprocessing.compressions.echelon)
format_bounds() (in module efmlrs.preprocessing.boundaries)
G
get_bounds_index() (in module efmlrs.preprocessing.boundaries)
get_denominators() (in module efmlrs.util.convert_matrix)
get_efmtool_efms() (in module efmlrs.postprocessing.get_data)
get_int_smatrix() (in module efmlrs.util.convert_matrix)
get_min_smatrix() (in module efmlrs.util.convert_matrix)
get_mplrs_efms() (in module efmlrs.postprocessing.get_data)
get_rev_info() (in module efmlrs.postprocessing.get_data)
get_smatrix() (in module efmlrs.preprocessing.get_data)
L
log() (in module efmlrs.util.log)
log_add() (in module efmlrs.util.log)
log_close() (in module efmlrs.util.log)
log_del() (in module efmlrs.util.log)
log_delete() (in module efmlrs.util.log)
log_delete_meta() (in module efmlrs.util.log)
log_delete_rea() (in module efmlrs.util.log)
log_init() (in module efmlrs.util.log)
log_keep() (in module efmlrs.util.log)
log_merge() (in module efmlrs.util.log)
log_merge_many() (in module efmlrs.util.log)
log_merge_rea() (in module efmlrs.util.log)
log_module() (in module efmlrs.util.log)
log_strip() (in module efmlrs.util.log)
log_time() (in module efmlrs.util.log)
M
main() (in module efmlrs.post)
(in module efmlrs.pre)
merge_reaction_names() (in module efmlrs.util.log)
N
normalize_efms() (in module efmlrs.postprocessing.decompressing)
O
orphaned_metas_rm() (in module efmlrs.preprocessing.get_data)
P
parse_info() (in module efmlrs.postprocessing.decompressions.deadend)
parse_lrs() (in module efmlrs.postprocessing.get_data)
R
read_mfile() (in module efmlrs.util.data)
read_model() (in module efmlrs.preprocessing.get_data)
read_rfile() (in module efmlrs.util.data)
read_rvfile() (in module efmlrs.util.data)
read_sfile() (in module efmlrs.util.data)
read_sfile_int() (in module efmlrs.util.data)
remove_redundant_metabolites() (in module efmlrs.preprocessing.compressions.echelon)
remove_zeros() (in module efmlrs.postprocessing.get_data)
reversibilities4printing() (in module efmlrs.util.data)
rm_empty_reas() (in module efmlrs.preprocessing.get_data)
rm_metas_in_specified_compartment() (in module efmlrs.preprocessing.get_data)
rm_reactions() (in module efmlrs.preprocessing.get_data)
run() (in module efmlrs.postprocessing.decompressing)
(in module efmlrs.preprocessing.boundaries)
(in module efmlrs.preprocessing.compressions.deadend)
(in module efmlrs.preprocessing.compressions.echelon)
(in module efmlrs.preprocessing.get_data)
(in module efmlrs.util.convert_matrix)
run_cmp() (in module efmlrs.preprocessing.mplrs_output)
run_uncmp() (in module efmlrs.preprocessing.mplrs_output)
S
search_bounds() (in module efmlrs.preprocessing.boundaries)
split_reversible_reas() (in module efmlrs.preprocessing.mplrs_output)
start() (in module efmlrs.post)
(in module efmlrs.pre)
start_from_command_line() (in module efmlrs.post)
(in module efmlrs.pre)
W
write_all() (in module efmlrs.util.data)
write_bound_info() (in module efmlrs.preprocessing.get_data)
write_cmp_int_matrix() (in module efmlrs.util.data)
write_deadend_info() (in module efmlrs.preprocessing.compressions.deadend)
write_decompressed_efms() (in module efmlrs.postprocessing.decompressing)
write_efms() (in module efmlrs.util.data)
write_header() (in module efmlrs.preprocessing.mplrs_output)
write_info() (in module efmlrs.util.data)
write_init_mfile() (in module efmlrs.util.data)
write_init_rfile() (in module efmlrs.util.data)
write_initial_files_no_bounds() (in module efmlrs.util.data)
write_initial_files_with_bounds() (in module efmlrs.util.data)
write_lrs() (in module efmlrs.preprocessing.mplrs_output)
write_lrs_cmp() (in module efmlrs.preprocessing.mplrs_output)
write_mfile() (in module efmlrs.util.data)
write_rfile() (in module efmlrs.util.data)
write_rvfile() (in module efmlrs.util.data)
write_sfile() (in module efmlrs.util.data)
write_sfile_float() (in module efmlrs.util.data)
write_smatrix() (in module efmlrs.preprocessing.mplrs_output)
write_uncmp_int_matrix() (in module efmlrs.util.data)
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