Index

A

add_0_to_kde() (slow_rotations.torsions.TorsionFinder static method), [1]

assign_bond_order_from_smiles() (in module slow_rotations.rdkit_wrapper), [1]

B

BadTorsionError, [1]

C

check_states() (in module slow_rotations.analysis), [1] check_symmetry() (in module slow_rotations.mappings), [1] check_transitions() (in module slow_rotations.analysis), [1] convert_dihedral() (in module slow_rotations.mappings), [1] convert_idx_to_sysidx() (slow_rotations.torsions.LigandTorsionFinder method), [1] (slow_rotations.torsions.TorsionFinder method), [1]

convert_torsion_indices() (slow_rotations.compare.LigandTorsionComparator method), [1] (slow_rotations.compare.TorsionComparator method), [1] count_transitions_into_state() (slow_rotations.transitions.TransitionMatrixCounter method) count_transitions_out_of_state() (slow_rotations.transitions.TransitionMatrixCounter method)

D

determine_chi_angle() (slow_rotations.torsions.ProteinTorsionFinder method), [1]

determine_chi_x() (slow_rotations.torsions.ProteinTorsionFinder method), [1]

E

export_pdb_from_traj() (slow_rotations.torsions.LigandTorsionFinder method), [1]

G

get_all_angles() (slow_rotations.compare.TorsionComparator method), [1] get_all_chi_x_torsions() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_angle_min() (slow_rotations.compare.TorsionComparator static method), [1] get_angle_shift_point() (slow_rotations.torsions.TorsionFinder static method), [1] get_atom_by_index() (in module slow_rotations.mappings), [1] get_atom_type() (in module slow_rotations.pdb_writer), [1] get_binding_residues() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_bounds_gmm() (slow_rotations.torsions.TorsionFinder method), [1] get_bounds_knn() (slow_rotations.torsions.TorsionFinder static method), [1] get_bounds_mindist() (slow_rotations.torsions.TorsionFinder static method), [1] get_chi1_torsions() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_chi_x_ags() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_chi_x_aid() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_chi_x_residues() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_chi_x_torsions() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_closest_peak() (slow_rotations.torsions.TorsionFinder static method), [1] get_cumulative_angles() (slow_rotations.compare.TorsionComparator method), [1] get_gmm() (slow_rotations.torsions.TorsionFinder static method), [1] get_index_convert() (in module slow_rotations.rdkit_wrapper), [1]

get_individual_gmm() (slow_rotations.torsions.TorsionFinder static method), [1] get_intersection() (slow_rotations.torsions.ProteinTorsionFinder static method), [1] get_kde() (slow_rotations.torsions.TorsionFinder static method), [1] get_kde_num_peaks() (slow_rotations.torsions.TorsionFinder static method), [1] get_mapped_bonds() (in module slow_rotations.rdkit_wrapper), [1] get_mapped_heavy_atom_indices() (in module slow_rotations.rdkit_wrapper), [1] get_rdmol() (slow_rotations.torsions.LigandTorsionFinder method), [1] get_rdmol_by_frame() (slow_rotations.torsions.LigandTorsionFinder method), [1] get_residue_from_torsion() (slow_rotations.torsions.TorsionFinder method), [1] get_residue_name_from_torsion() (slow_rotations.torsions.TorsionFinder method), [1] get_residues_ags() (slow_rotations.torsions.ProteinTorsionFinder method), [1] get_rotatable_bonds() (in module slow_rotations.rdkit_wrapper), [1] get_statistical_inefficiency() (slow_rotations.torsions.TorsionFinder static method), [1] get_torsion_angles() (slow_rotations.torsions.TorsionFinder method), [1] get_torsion_name() (slow_rotations.torsions.TorsionFinder method), [1] get_torsions() (slow_rotations.compare.ProteinTorsionComparator method), [1] (slow_rotations.compare.TorsionComparator method), [1] (slow_rotations.torsions.LigandTorsionFinder method), [1] (slow_rotations.torsions.TorsionFinder method), [1]

H

highlight_dihedral() (in module slow_rotations.rdkit_wrapper), [1] (slow_rotations.torsions.LigandTorsionFinder method), [1] (slow_rotations.torsions.ProteinTorsionFinder method), [1]

I

increment_in() (slow_rotations.transitions.TransitionCounter method)

increment_out() (slow_rotations.transitions.TransitionCounter method) increment_transition() (slow_rotations.transitions.TransitionMatrixCounter method)

L

LigandTorsionComparator (class in slow_rotations.compare), [1]

LigandTorsionFinder (class in slow_rotations.torsions), [1] load_rdmol_from_file() (in module slow_rotations.rdkit_wrapper), [1]

M

make_standard_atmname() (in module slow_rotations.pdb_writer), [1] make_torsion_img() (slow_rotations.torsions.LigandTorsionFinder method), [1] (slow_rotations.torsions.ProteinTorsionFinder method), [1] (slow_rotations.torsions.TorsionFinder method), [1] make_torsion_img_no_shift() (slow_rotations.torsions.LigandTorsionFinder method), [1] map_mols() (in module slow_rotations.mappings), [1] max_transitions() (slow_rotations.transitions.TransitionCounter method) (slow_rotations.transitions.TransitionMatrixCounter method) min_transitions() (slow_rotations.transitions.TransitionCounter method) (slow_rotations.transitions.TransitionMatrixCounter method)

mindist() (slow_rotations.torsions.TorsionFinder method), [1] module slow_rotations.analysis, [1] slow_rotations.compare, [1] slow_rotations.mappings, [1] slow_rotations.molconverter, [1] slow_rotations.pdb_writer, [1] slow_rotations.rdkit_wrapper, [1] slow_rotations.torsions, [1] slow_rotations.transitions slow_rotations.utils, [1]

N

NoMoleculeError, [1] NotImplementedError, [1]

num_states() (slow_rotations.transitions.TransitionCounter method) (slow_rotations.transitions.TransitionMatrixCounter method)

P

plot_all_distributions() (slow_rotations.compare.LigandTorsionComparator method), [1] (slow_rotations.compare.ProteinTorsionComparator method), [1] plot_cumulative_distribution() (slow_rotations.compare.TorsionComparator method), [1] plot_dihedral_histogram() (slow_rotations.torsions.TorsionFinder static method), [1] plot_dihedral_scatter() (slow_rotations.torsions.LigandTorsionFinder method), [1] (slow_rotations.torsions.TorsionFinder static method), [1]

plot_kde() (slow_rotations.torsions.TorsionFinder method), [1] plot_transition_counts() (slow_rotations.torsions.TorsionFinder static method), [1] ProteinTorsionComparator (class in slow_rotations.compare), [1] ProteinTorsionFinder (class in slow_rotations.torsions), [1]

R

rd_map_mols() (in module slow_rotations.mappings), [1]

rename_lig_pdb_atoms() (in module slow_rotations.pdb_writer), [1]

S

sanitize_rdmol() (in module slow_rotations.rdkit_wrapper), [1] save_traj_sel() (slow_rotations.torsions.ProteinTorsionFinder method), [1] shift_torsion_angles() (slow_rotations.torsions.TorsionFinder static method), [1] slow_rotations.analysis module, [1] slow_rotations.compare module, [1] slow_rotations.mappings module, [1] slow_rotations.molconverter module, [1]

slow_rotations.pdb_writer module, [1] slow_rotations.rdkit_wrapper module, [1] slow_rotations.torsions module, [1] slow_rotations.transitions module slow_rotations.utils module, [1] state_populations() (slow_rotations.torsions.TorsionFinder static method), [1]

T

to_dict() (slow_rotations.transitions.TransitionCounter method) (slow_rotations.transitions.TransitionMatrixCounter method) to_pandas() (slow_rotations.transitions.TransitionCounter method) (slow_rotations.transitions.TransitionMatrixCounter method) TorsionComparator (class in slow_rotations.compare), [1] TorsionFinder (class in slow_rotations.torsions), [1]

torsions_equivalent() (in module slow_rotations.mappings), [1] total_transitions() (slow_rotations.transitions.TransitionCounter method) (slow_rotations.transitions.TransitionMatrixCounter method) transition_counter() (slow_rotations.torsions.TorsionFinder static method), [1] transition_matrix() (slow_rotations.torsions.TorsionFinder static method), [1] TransitionCounter (class in slow_rotations.transitions) TransitionMatrixCounter (class in slow_rotations.transitions)

W

warn() (in module slow_rotations.utils), [1]