Index

A

add() (in module mooonpy.molspace.doc_examples) add_type_labels() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) ADI_from_bonds() (in module mooonpy.molspace.distance) aggregate_fun() (in module mooonpy.tools.math_utils) angle_factory() (mooonpy.molspace.topology.Angles method)

Angles (class in mooonpy.molspace.topology) append() (mooonpy.tools.tables.ListListTable method) ArrayTable (class in mooonpy.tools.tables) atom_factory() (mooonpy.molspace.atom_styles.Styles method) atom_fill() (mooonpy.molspace.atom_styles.Styles method) atom_line() (mooonpy.molspace.atom_styles.Styles method) Atoms (class in mooonpy.molspace.atoms)

B

BADI_by_type() (in module mooonpy.molspace.distance) base (mooonpy.tools.loop_utils.DimensionInfo attribute) basename() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method) basic_read() (mooonpy.Thermospace class method) (mooonpy.thermospace.thermospace.Thermospace class method) best_guess() (mooonpy.fitting.fitting.CurveFit method)

bond_factory() (mooonpy.molspace.topology.Bonds method) Bonds (class in mooonpy.molspace.topology) bonds_from_distances() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) Box (class in mooonpy.molspace.box) butter() (in module mooonpy.molspace.doc_examples) butter_lowpass() (in module mooonpy.tools.signals)

C

cart_key (mooonpy.tools.loop_utils.DimensionEntry attribute) Cartesian (class in mooonpy.tools.loop_utils) CartesianResult (class in mooonpy.tools.loop_utils) Coefficients (class in mooonpy.molspace.force_field) coeffs_factory() (mooonpy.molspace.force_field.ForceField method) col() (mooonpy.tools.tables.ArrayTable method) (mooonpy.tools.tables.ColTable method) (mooonpy.tools.tables.ListListTable method) col_fun() (mooonpy.tools.tables.Table method) ColorMap (class in mooonpy.tools.misc_utils) ColTable (class in mooonpy.tools.tables) combined (mooonpy.tools.loop_utils.IndexInfo attribute) compute_ADI() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method)

compute_BADI_by_type() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) compute_bond_length() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) compute_derivative() (in module mooonpy.tools.math_utils) compute_fringe_slope() (in module mooonpy.tools.math_utils) compute_pairs() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) compute_PSD() (in module mooonpy.tools.signals) condition (mooonpy.tools.loop_utils.DimensionEntry attribute) conditionals (mooonpy.tools.loop_utils.DimensionInfo attribute) console() (mooonpy.tools.tables.Table method) copy() (mooonpy.tools.tables.Table method) csv() (mooonpy.tools.tables.Table method) CurveFit (class in mooonpy.fitting.fitting)

D

data_extension() (in module mooonpy.tools.signals) def_limit (mooonpy.fitting.fitting.CurveFit attribute) default_fit_kws (mooonpy.fitting.dihedral.DihedralDist attribute) (mooonpy.fitting.fitting.CurveFit attribute) determine_mirroring_locations() (in module mooonpy.tools.signals) dihedral_factory() (mooonpy.molspace.topology.Dihedrals method) DihedralDist (class in mooonpy.fitting.dihedral) Dihedrals (class in mooonpy.molspace.topology)

DimensionEntry (class in mooonpy.tools.loop_utils) DimensionInfo (class in mooonpy.tools.loop_utils) dimensions (mooonpy.tools.loop_utils.IndexInfo attribute) dir() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method) divide() (in module mooonpy.molspace.doc_examples) Domain (class in mooonpy.molspace.distance) domain_decomp_13() (in module mooonpy.molspace.distance)

E

edge_tan_intersect() (in module mooonpy.tools.math_utils) Element (class in mooonpy.molspace.periodic_table) element2mass() (mooonpy.molspace.periodic_table.Elements method)

element2radii() (mooonpy.molspace.periodic_table.Elements method) Elements (class in mooonpy.molspace.periodic_table) ext() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method)

F

filter_cutoff() (mooonpy.molspace.distance.Pairs method) find() (in module mooonpy.molspace.bonds_from_distances) find_cumulative_neighs() (in module mooonpy.molspace.graph_theory.interface) (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) find_peaks_and_valleys() (in module mooonpy.tools.math_utils) find_rings() (in module mooonpy.molspace.graph_theory.ring_analysis) (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method)

first_value_cross() (in module mooonpy.tools.math_utils) fit_model() (mooonpy.fitting.fitting.CurveFit method) ForceField (class in mooonpy.molspace.force_field) frac2pos() (mooonpy.molspace.box.Box method) function1() (mooonpy.molspace.doc_examples.MainClass1 method)

G

gaussian_quad_turn() (in module mooonpy.tools.math_utils) gaussian_turn() (in module mooonpy.tools.math_utils) GaussianTurnFit (class in mooonpy.fitting.hyperbolic) generate() (mooonpy.tools.loop_utils.Cartesian method) generate_graph() (in module mooonpy.molspace.graph_theory.interface) (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) generate_list() (mooonpy.tools.loop_utils.Cartesian method) get_combined_index() (mooonpy.tools.loop_utils.Cartesian method) get_fit_params() (mooonpy.fitting.fitting.CurveFit method) get_lengths() (mooonpy.molspace.box.Box method) get_per_line_styles() (mooonpy.molspace.force_field.ForceField method)

get_transformation_matrix() (mooonpy.molspace.box.Box method) global_idx (mooonpy.tools.loop_utils.IndexInfo attribute) greeter_msg() (in module mooonpy.guis.hw) (in module mooonpy.xrdspace.hw) guess_ic() (mooonpy.fitting.dihedral.DihedralDist method) (mooonpy.fitting.fitting.CurveFit method) (mooonpy.fitting.hyperbolic.GaussianTurnFit method) (mooonpy.fitting.hyperbolic.HyperbolaFit method) guess_limit() (mooonpy.fitting.dihedral.DihedralDist method) (mooonpy.fitting.fitting.CurveFit method) (mooonpy.fitting.hyperbolic.GaussianTurnFit method) (mooonpy.fitting.hyperbolic.HyperbolaFit method)

H

headers() (mooonpy.tools.tables.ArrayTable method) (mooonpy.tools.tables.ColTable method) (mooonpy.tools.tables.ListListTable method)

hello_world() (in module mooonpy.guis.hw) (in module mooonpy.xrdspace.hw) hyperbola() (in module mooonpy.tools.math_utils) HyperbolaFit (class in mooonpy.fitting.hyperbolic)

I

id_get() (mooonpy.molspace.topology.Angles method) (mooonpy.molspace.topology.Bonds method) (mooonpy.molspace.topology.Dihedrals method) (mooonpy.molspace.topology.Impropers method) id_set() (mooonpy.molspace.topology.Angles method) (mooonpy.molspace.topology.Bonds method) (mooonpy.molspace.topology.Dihedrals method) (mooonpy.molspace.topology.Impropers method)

improper_factory() (mooonpy.molspace.topology.Impropers method) Impropers (class in mooonpy.molspace.topology) IndexInfo (class in mooonpy.tools.loop_utils) is_float() (in module mooonpy.tools.string_utils) iterable (mooonpy.tools.loop_utils.DimensionEntry attribute)

J

join_restart() (mooonpy.Thermospace method) (mooonpy.thermospace.thermospace.Thermospace method)

K

key_rule() (mooonpy.molspace.topology.Angles method) (mooonpy.molspace.topology.Bonds method) (mooonpy.molspace.topology.Dihedrals method) (mooonpy.molspace.topology.Impropers method)

L

latex() (in module mooonpy.molspace.doc_examples) line_charge() (mooonpy.molspace.atom_styles.Styles method)

line_full() (mooonpy.molspace.atom_styles.Styles method) ListListTable (class in mooonpy.tools.tables)

M

MainClass1 (class in mooonpy.molspace.doc_examples) make_params() (mooonpy.fitting.dihedral.DihedralDist method) (mooonpy.fitting.fitting.CurveFit method) mass2element() (mooonpy.molspace.periodic_table.Elements method) matches() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method) MixingRule (class in mooonpy.tools.math_utils) module mooonpy mooonpy.fitting mooonpy.fitting.dihedral mooonpy.fitting.fitting mooonpy.fitting.hyperbolic mooonpy.guis mooonpy.guis.hw mooonpy.molspace mooonpy.molspace.atom_styles mooonpy.molspace.atoms mooonpy.molspace.bonds_from_distances mooonpy.molspace.box mooonpy.molspace.distance mooonpy.molspace.doc_examples mooonpy.molspace.force_field mooonpy.molspace.graph_theory mooonpy.molspace.graph_theory.interface mooonpy.molspace.graph_theory.ring_analysis mooonpy.molspace.molspace mooonpy.molspace.periodic_table mooonpy.molspace.topology mooonpy.programs mooonpy.programs.program mooonpy.programs.regression_fringe_response mooonpy.rcsetup mooonpy.thermospace mooonpy.thermospace.plotting mooonpy.thermospace.thermospace mooonpy.tools mooonpy.tools.file_utils mooonpy.tools.loop_utils mooonpy.tools.math_utils mooonpy.tools.misc_utils mooonpy.tools.signals mooonpy.tools.string_utils mooonpy.tools.tables mooonpy.xrdspace mooonpy.xrdspace.hw Molspace (class in mooonpy) (class in mooonpy.molspace.molspace) mooonpy module mooonpy.fitting module mooonpy.fitting.dihedral module mooonpy.fitting.fitting module mooonpy.fitting.hyperbolic module mooonpy.guis module mooonpy.guis.hw module mooonpy.molspace module

mooonpy.molspace.atom_styles module mooonpy.molspace.atoms module mooonpy.molspace.bonds_from_distances module mooonpy.molspace.box module mooonpy.molspace.distance module mooonpy.molspace.doc_examples module mooonpy.molspace.force_field module mooonpy.molspace.graph_theory module mooonpy.molspace.graph_theory.interface module mooonpy.molspace.graph_theory.ring_analysis module mooonpy.molspace.molspace module mooonpy.molspace.periodic_table module mooonpy.molspace.topology module mooonpy.programs module mooonpy.programs.program module mooonpy.programs.regression_fringe_response module mooonpy.rcsetup module mooonpy.thermospace module mooonpy.thermospace.plotting module mooonpy.thermospace.thermospace module mooonpy.tools module mooonpy.tools.file_utils module mooonpy.tools.loop_utils module mooonpy.tools.math_utils module mooonpy.tools.misc_utils module mooonpy.tools.signals module mooonpy.tools.string_utils module mooonpy.tools.tables module mooonpy.xrdspace module mooonpy.xrdspace.hw module multi_symmetric_gaussian() (in module mooonpy.fitting.dihedral) multiply() (in module mooonpy.molspace.doc_examples)

N

name (mooonpy.tools.loop_utils.DimensionEntry attribute) new_ext() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method)

new_log() (mooonpy.programs.program.ProgramResults class method)

O

open() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method)

P

Pair (class in mooonpy.molspace.distance) Pairs (class in mooonpy.molspace.distance) pairs_from_bonds() (in module mooonpy.molspace.distance) pairs_from_domains() (in module mooonpy.molspace.distance) parallels (mooonpy.tools.loop_utils.DimensionInfo attribute) Parameters (class in mooonpy.molspace.force_field) Path (class in mooonpy) (class in mooonpy.tools.file_utils)

plot() (mooonpy.tools.tables.Table method) plot_example() (in module mooonpy.thermospace.plotting) plot_mode_decomposition() (mooonpy.fitting.dihedral.DihedralDist method) pos2frac() (mooonpy.molspace.box.Box method) power_to_db() (in module mooonpy.tools.signals) ProgramResults (class in mooonpy.programs.program)

R

RCParams (class in mooonpy.rcsetup) read_charge() (mooonpy.molspace.atom_styles.Styles method) read_csv() (mooonpy.tools.tables.ColTable class method) (mooonpy.tools.tables.ListListTable class method) read_files() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) read_full() (mooonpy.molspace.atom_styles.Styles method) readlog_basic() (in module mooonpy.thermospace.thermospace) recent() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method) reset() (mooonpy.rcsetup.RCParams method) rfr_labeler() (in module mooonpy.programs.regression_fringe_response) rfr_plotter() (in module mooonpy.programs.regression_fringe_response)

RFR_tensile_analysis() (in module mooonpy.programs.regression_fringe_response) root() (mooonpy.Path method) (mooonpy.tools.file_utils.Path method) row() (mooonpy.tools.tables.ArrayTable method) (mooonpy.tools.tables.ColTable method) (mooonpy.tools.tables.ListListTable method) rowcol() (mooonpy.tools.tables.ArrayTable method) (mooonpy.tools.tables.ColTable method) (mooonpy.tools.tables.ListListTable method) rowlabels() (mooonpy.tools.tables.ArrayTable method) (mooonpy.tools.tables.ColTable method) (mooonpy.tools.tables.ListListTable method) run_default() (mooonpy.fitting.fitting.CurveFit method)

S

sect() (mooonpy.Thermospace method) (mooonpy.thermospace.thermospace.Thermospace method) shape() (mooonpy.tools.tables.ArrayTable method) (mooonpy.tools.tables.ColTable method) (mooonpy.tools.tables.ListListTable method) shift() (mooonpy.molspace.atoms.Atoms method) size (mooonpy.tools.loop_utils.DimensionInfo attribute)

smart_open() (in module mooonpy.tools.file_utils) sparse_eye_diff() (in module mooonpy.tools.signals) string2digit() (in module mooonpy.tools.string_utils) string_format() (mooonpy.tools.loop_utils.CartesianResult method) Styles (class in mooonpy.molspace.atom_styles) subtract() (in module mooonpy.molspace.doc_examples) symmetric_gaussian_periodic() (in module mooonpy.fitting.dihedral)

T

Table (class in mooonpy.tools.tables) Thermospace (class in mooonpy) (class in mooonpy.thermospace.thermospace)

to_dict() (mooonpy.programs.program.ProgramResults method) to_list() (mooonpy.programs.program.ProgramResults method)

U

update() (mooonpy.rcsetup.RCParams method) update_astyles() (mooonpy.molspace.atom_styles.Styles method) update_bonds() (mooonpy.molspace.distance.Pairs method)

update_elements() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method) useful_docstring() (in module mooonpy.molspace.doc_examples)

W

whitt_smooth() (in module mooonpy.tools.signals) wrap() (mooonpy.molspace.atoms.Atoms method)

write_files() (mooonpy.Molspace method) (mooonpy.molspace.molspace.Molspace method)

Y

yield_line() (mooonpy.tools.tables.Table method)