Index

A

add_atom() (fast_forward.map_file_parers.Mapping method)

add_residue() (fast_forward.universe_handler.ResidueIter method) apply_rotation() (in module fast_forward.linalg_functions)

B

beads (fast_forward.map_file_parers.Mapping property)

C

calc_rotation_matrix() (in module fast_forward.linalg_functions) calc_score() (in module fast_forward.score) cgsmiles_to_mapping() (in module fast_forward.cgsmiles)

COMMENT_CHAR (fast_forward.map_file_parers.MapDirector attribute) compute_coupling() (in module fast_forward.constraint_coupling) create_new_universe() (in module fast_forward.mapping) cross_product() (in module fast_forward.linalg_functions)

D

dihedral_angle() (in module fast_forward.linalg_functions)

dihedrals (fast_forward.interaction_fit.InteractionFitter property)

F

fast_forward module fast_forward.bonded_functions module fast_forward.cgsmiles module fast_forward.constraint_coupling module fast_forward.hydrogen module fast_forward.interaction_distribution module fast_forward.interaction_finalising module fast_forward.interaction_fit module fast_forward.interaction_plots module fast_forward.interactions_to_itp module fast_forward.itp_parser_sub module fast_forward.itp_to_ag module

fast_forward.linalg_functions module fast_forward.map_file_parers module fast_forward.mapping module fast_forward.ndx_parser module fast_forward.score module fast_forward.universe_handler module fast_forward.virtual_site_mass module FastForwardITPParser (class in fast_forward.itp_parser_sub) finalise_interaction_types() (in module fast_forward.interaction_finalising) finalize() (fast_forward.map_file_parers.MapDirector method) find_any_bonded_neighbor() (in module fast_forward.hydrogen) find_helper_atoms() (in module fast_forward.hydrogen) find_mol_indices() (in module fast_forward.itp_to_ag) find_one_graph_match() (in module fast_forward.cgsmiles) fit_interaction() (fast_forward.interaction_fit.InteractionFitter method) fit_to_gmx() (fast_forward.interaction_fit.InteractionFitter method) forward_map_indices() (in module fast_forward.mapping) forward_map_positions() (in module fast_forward.mapping)

G

generate_molecule_graphs() (fast_forward.universe_handler.UniverseHandler method) get_CH() (in module fast_forward.hydrogen) get_CH2() (in module fast_forward.hydrogen) get_CH3() (in module fast_forward.hydrogen)

get_CH_double_bond() (in module fast_forward.hydrogen) get_interactions_group() (fast_forward.itp_to_ag.ITPInteractionMapper method) get_mappings() (in module fast_forward.cgsmiles) get_pairwise_interaction() (fast_forward.itp_to_ag.ITPInteractionMapper method) guess_interactions() (in module fast_forward.itp_parser_sub)

H

hellinger() (in module fast_forward.score)

I

interaction_distribution() (in module fast_forward.interaction_distribution) interaction_finalising() (in module fast_forward.interaction_finalising) InteractionFitter (class in fast_forward.interaction_fit)

interactions_dict (fast_forward.interaction_fit.InteractionFitter attribute) itp_writer() (in module fast_forward.interactions_to_itp) ITPInteractionMapper (class in fast_forward.itp_to_ag)

L

load_cgsmiles_library() (in module fast_forward.cgsmiles)

M

make_distances_distribution_plot() (in module fast_forward.interaction_plots) make_distribution_plot() (in module fast_forward.interaction_plots) make_matrix_plot() (in module fast_forward.interaction_plots) MapDirector (class in fast_forward.map_file_parers) Mapping (class in fast_forward.map_file_parers) mass_redistribution() (in module fast_forward.virtual_site_mass) mass_to_element() (fast_forward.universe_handler.UniverseHandler method) match_attributes() (in module fast_forward.hydrogen) METH_DICT (fast_forward.itp_parser_sub.FastForwardITPParser attribute) (fast_forward.map_file_parers.MapDirector attribute) module fast_forward fast_forward.bonded_functions fast_forward.cgsmiles fast_forward.constraint_coupling fast_forward.hydrogen fast_forward.interaction_distribution fast_forward.interaction_finalising fast_forward.interaction_fit fast_forward.interaction_plots fast_forward.interactions_to_itp fast_forward.itp_parser_sub fast_forward.itp_to_ag fast_forward.linalg_functions fast_forward.map_file_parers fast_forward.mapping fast_forward.ndx_parser fast_forward.score fast_forward.universe_handler fast_forward.virtual_site_mass

molecule_graphs (fast_forward.universe_handler.UniverseHandler property)

N

n_atoms (fast_forward.universe_handler.UniverseHandler property) n_beads (fast_forward.map_file_parers.Mapping property)

n_residues (fast_forward.universe_handler.UniverseHandler property) ndx_to_ag() (in module fast_forward.ndx_parser)

P

parse() (fast_forward.itp_parser_sub.FastForwardITPParser method)

parse_header() (fast_forward.map_file_parers.MapDirector method) pbc_complete() (fast_forward.universe_handler.UniverseHandler method)

R

read_itp() (in module fast_forward.itp_parser_sub) read_mapping() (in module fast_forward.map_file_parers) remove_explicit_hydrogens() (in module fast_forward.cgsmiles) report_constraint_coupling() (in module fast_forward.constraint_coupling) res_as_mol() (in module fast_forward.universe_handler)

res_iter() (fast_forward.universe_handler.ResidueIter method) (fast_forward.universe_handler.UniverseHandler method) resids (fast_forward.universe_handler.UniverseHandler property) Residue (class in fast_forward.universe_handler) ResidueIter (class in fast_forward.universe_handler)

S

score_matrix() (in module fast_forward.score)

shift_united_atom_carbons() (fast_forward.universe_handler.UniverseHandler method) std_dev_hist() (in module fast_forward.score)

U

u_vect() (in module fast_forward.linalg_functions)

UniverseHandler (class in fast_forward.universe_handler)

V

vec2quaternion() (in module fast_forward.linalg_functions)

vector_angle() (in module fast_forward.linalg_functions) vector_angle_degrees() (in module fast_forward.linalg_functions)