Index

A

add_angle() (sith.visualize.ngl.MoleculeNGL method) add_arc() (sith.visualize.ngl.MoleculeNGL method) add_axis() (sith.visualize.ngl.MoleculeNGL method) add_bond() (sith.visualize.ngl.MoleculeNGL method) add_bonds() (sith.visualize.ngl.MoleculeNGL method) add_color_per_amino() (sith.utils.sith_plots.SithPlotter method) add_dihedral() (sith.visualize.ngl.MoleculeNGL method) add_dof() (sith.visualize.ngl.MoleculeNGL method) align_axis() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method) align_molecules() (sith.utils.molecules.PCAMatcher method) align_plane() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method)

align_with_components() (sith.utils.molecules.Alignment static method) Alignment (class in sith.utils.molecules) all_hydrogen_atoms() (in module sith.utils.tools) all_xyz2pdb() (in module sith.utils.tools) amino_freq() (sith.utils.analysis.DataSetAnalysis method) analysis_energy_dof() (in module sith.utils.analysis) apply_trans() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method) arg() (sith.g09_stretching.protonate.Protonize method) asp() (sith.g09_stretching.protonate.Protonize method) atoms (sith.Utilities.Geometry attribute)

B

block_readers (sith.readers.g09_reader.FileReader attribute)

build_atoms() (sith.readers.g09_reader.FileReader method) build_proline_state() (sith.utils.peptides.PepSetter method)

C

center_geo() (sith.utils.molecules.Alignment static method) change_def() (in module sith.g09_stretching.change_dofs) (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) change_distance() (in module sith.utils.tools) change_prolines_dofs() (in module sith.g09_stretching.change_dofs) closest_indices() (in module sith.utils.analysis) color_distribution() (in module sith.Utilities) compute_angle() (sith.utils.peptides.PepSetter method)

compute_dihedrals() (sith.utils.peptides.PepSetter method) conf2pdb() (in module sith.utils.tools) construct_neigh_dic() (in module sith.utils.analysis) continuous_e2e() (in module sith.g09_stretching.from_extreme.info_from_opt) create_atoms() (sith.g09_stretching.protonate.Protonize method) create_blocks() (sith.utils.sith_plots.SithPlotter method) create_colorbar() (in module sith.Utilities) create_figure() (sith.visualize.vmol.EnergiesVMol method) create_gaussian_input() (sith.utils.molecules.MoleculeSetter method) cross_val() (in module sith.utils.analysis)

D

DataSetAnalysis (class in sith.utils.analysis) def_line() (in module sith.g09_stretching.change_dofs) delta_angles_continuous() (in module sith.g09_stretching.from_extreme.info_from_opt) diff_bonds() (in module sith.utils.tools) dim_indices (sith.Utilities.Geometry attribute) dims (sith.readers.g09_reader.FileReader attribute) (sith.Utilities.Geometry attribute)

distance() (in module sith.utils.tools) dof (sith.Utilities.Geometry attribute) dof_classificator_all() (in module sith.utils.analysis) dof_classificator_one() (in module sith.utils.analysis) dof_vs_energy() (sith.utils.analysis.DataSetAnalysis method) dof_vs_energy_rescaled() (sith.utils.analysis.DataSetAnalysis method) download_image() (sith.visualize.ngl.MoleculeNGL method)

E

endo_exo_proline() (sith.utils.peptides.PepSetter method) energies_all_dof() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) energies_angles() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) energies_bonds() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) energies_dihedrals() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method)

energies_some_dof() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) EnergiesNGL (class in sith.visualize.ngl) EnergiesVMol (class in sith.visualize.vmol) extract_bonds() (in module sith.utils.tools) extract_common() (in module sith.utils.compare_siths) extract_diff() (in module sith.utils.compare_siths) extract_dofs() (in module sith.g09_stretching.change_dofs) extract_proline_atoms() (in module sith.g09_stretching.change_dofs)

F

F_max_stretch() (in module sith.utils.tools)

F_stretch() (in module sith.utils.tools) FileReader (class in sith.readers.g09_reader)

G

G09Reader (class in sith.readers.g09_reader) gen_randpep() (in module sith.g09_stretching.sith_tools) Geometry (class in sith.Utilities)

geometry (sith.readers.g09_reader.FileReader attribute) get_jedi_dq() (sith.energy_analysis.jedi_analysis.JediAnalysis method) get_sith_dq() (sith.energy_analysis.sith_analysis.SithAnalysis method) glu() (sith.g09_stretching.protonate.Protonize method)

H

hessian (sith.Utilities.Geometry attribute)

I

increase_distance() (sith.utils.molecules.MoleculeSetter method) increase_distance_with_constraints() (sith.utils.molecules.MoleculeSetter method) index_dof() (in module sith.utils.compare_siths) (sith.utils.analysis.SithAnalysis method)

info_from_opt() (in module sith.g09_stretching.from_extreme.info_from_opt) inputfiles (sith.readers.g09_reader.G09Reader attribute) intermedia_vectors() (sith.visualize.ngl.MoleculeNGL method) internal_forces (sith.Utilities.Geometry attribute)

J

jedi_analysis() (sith.energy_analysis.jedi_analysis.JediAnalysis method)

JediAnalysis (class in sith.energy_analysis.jedi_analysis)

K

kill_dofs() (sith.Utilities.Geometry method)

L

le_dof_amino() (sith.utils.analysis.SithAnalysis method) le_same_aminoacids() (in module sith.utils.analysis) length_energy() (in module sith.utils.analysis)

log2xyz() (in module sith.g09_stretching.g09_xyz) log2xyz2() (in module sith.g09_stretching.g09_xyz) lys() (sith.g09_stretching.protonate.Protonize method)

M

matching() (sith.utils.molecules.PCAMatcher method) mean_n_std() (in module sith.utils.analysis) module sith.energy_analysis sith.energy_analysis.jedi_analysis sith.energy_analysis.sith_analysis sith.g09_stretching sith.g09_stretching.change_dofs sith.g09_stretching.from_extreme sith.g09_stretching.from_extreme.info_from_opt sith.g09_stretching.g09_xyz sith.g09_stretching.protonate sith.g09_stretching.sith_tools sith.readers sith.readers.g09_reader sith.SITH sith.SithWriter sith.Utilities sith.utils sith.utils.analysis sith.utils.compare_siths sith.utils.miscellaneous sith.utils.molecules sith.utils.peptides sith.utils.sith_plots sith.utils.tools sith.visualize sith.visualize.ngl sith.visualize.vmol

MoleculeNGL (class in sith.visualize.ngl) MoleculeSetter (class in sith.utils.molecules)

N

n_atoms (sith.Utilities.Geometry attribute)

name (sith.Utilities.Geometry attribute) Note (sith.Utilities.Geometry attribute)

O

organize_lengths() (in module sith.utils.compare_siths)

output_terminal() (in module sith.utils.miscellaneous)

P

pca_vectors() (sith.utils.molecules.Alignment static method) PCAMatcher (class in sith.utils.molecules) pep_per_x() (in module sith.utils.analysis) PepSetter (class in sith.utils.peptides) permute_atoms() (in module sith.g09_stretching.change_dofs) picked() (sith.visualize.ngl.MoleculeNGL method) plot_angles() (sith.utils.sith_plots.SithPlotter method) plot_averages_per_pos() (in module sith.utils.sith_plots) plot_DFT_ener() (sith.utils.analysis.DataSetAnalysis method) plot_energies_in_DOFs() (sith.utils.sith_plots.SithPlotter method)

plot_error() (sith.utils.sith_plots.SithPlotter method) plot_hessian() (sith.utils.sith_plots.SithPlotter method) plot_matrix() (in module sith.utils.sith_plots) plot_matrix2() (in module sith.utils.sith_plots) plot_matrix3() (in module sith.utils.sith_plots) plot_ramachandran() (sith.utils.sith_plots.SithPlotter method) plot_sith() (sith.utils.sith_plots.SithPlotter method) proline_state() (in module sith.g09_stretching.sith_tools) protonate() (in module sith.g09_stretching.protonate) Protonize (class in sith.g09_stretching.protonate)

R

rama_phi_psi() (sith.utils.peptides.PepSetter method) rectangle_integration() (sith.energy_analysis.sith_analysis.SithAnalysis method) reduce_data() (in module sith.utils.analysis) reduce_structs() (in module sith.g09_stretching.from_extreme.info_from_opt) remove_all_angles() (sith.visualize.ngl.MoleculeNGL method) remove_all_bonds() (sith.visualize.ngl.MoleculeNGL method) remove_all_dihedrals() (sith.visualize.ngl.MoleculeNGL method) remove_angle() (sith.visualize.ngl.MoleculeNGL method) remove_axis() (sith.visualize.ngl.MoleculeNGL method)

remove_bond() (sith.visualize.ngl.MoleculeNGL method) remove_bonds() (sith.visualize.ngl.MoleculeNGL method) remove_dihedral() (sith.visualize.ngl.MoleculeNGL method) reorder_prolines_atoms() (in module sith.g09_stretching.change_dofs) rot_x() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method) rot_y() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method) rot_z() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method)

S

scale_distance() (sith.utils.molecules.MoleculeSetter method) scf_energy (sith.Utilities.Geometry attribute) separate_by_position() (in module sith.utils.analysis) set1() (in module sith.g09_stretching.change_dofs) set2() (in module sith.g09_stretching.change_dofs) set3() (in module sith.g09_stretching.change_dofs) set4() (in module sith.g09_stretching.change_dofs) set_backbone() (in module sith.g09_stretching.change_dofs) set_hes_from_ref() (in module sith.utils.analysis) shake_except() (in module sith.utils.tools) show() (sith.visualize.ngl.MoleculeNGL method) show_bonds() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) show_bonds_of_DOF() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) show_dof() (sith.visualize.ngl.EnergiesNGL method) (sith.visualize.vmol.EnergiesVMol method) simpson_integration() (sith.energy_analysis.sith_analysis.SithAnalysis method) sith.energy_analysis module sith.energy_analysis.jedi_analysis module sith.energy_analysis.sith_analysis module sith.g09_stretching module sith.g09_stretching.change_dofs module sith.g09_stretching.from_extreme module sith.g09_stretching.from_extreme.info_from_opt module sith.g09_stretching.g09_xyz module sith.g09_stretching.protonate module sith.g09_stretching.sith_tools module

sith.readers module sith.readers.g09_reader module sith.SITH module sith.SithWriter module sith.Utilities module sith.utils module sith.utils.analysis module sith.utils.compare_siths module sith.utils.miscellaneous module sith.utils.molecules module sith.utils.peptides module sith.utils.sith_plots module sith.utils.tools module sith.visualize module sith.visualize.ngl module sith.visualize.vmol module sith_inDOFs() (sith.visualize.vmol.EnergiesVMol method) SithAnalysis (class in sith.energy_analysis.sith_analysis) (class in sith.utils.analysis) SithPlotter (class in sith.utils.sith_plots) statistics() (in module sith.utils.analysis) structures (sith.readers.g09_reader.G09Reader attribute) swaps_to_transform() (in module sith.g09_stretching.change_dofs)

T

test() (sith.utils.analysis.DataSetAnalysis method) test_continuity() (sith.utils.analysis.DataSetAnalysis method)

test_dofs() (in module sith.g09_stretching.change_dofs) traj_buttons() (sith.visualize.vmol.EnergiesVMol method) trapezoid_integration() (sith.energy_analysis.sith_analysis.SithAnalysis method)

U

update_frame() (sith.visualize.ngl.EnergiesNGL method)

update_stretching() (sith.visualize.vmol.EnergiesVMol method)

W

write_file() (sith.SithWriter.WriteSITH method)

write_sith_data() (in module sith.SithWriter) WriteSITH (class in sith.SithWriter)

X

xy_alignment() (sith.utils.molecules.MoleculeSetter method) (sith.visualize.ngl.MoleculeNGL method)