fast_forward package

Submodules

• fast_forward.bonded_functions module
• fast_forward.cgsmiles module
  • cgsmiles_to_mapping()
  • find_one_graph_match()
  • get_mappings()
  • load_cgsmiles_library()
  • remove_explicit_hydrogens()
• fast_forward.constraint_coupling module
  • compute_coupling()
  • report_constraint_coupling()
• fast_forward.hydrogen module
  • find_any_bonded_neighbor()
  • find_helper_atoms()
  • get_CH()
  • get_CH2()
  • get_CH3()
  • get_CH_double_bond()
  • match_attributes()
• fast_forward.interaction_distribution module
  • interaction_distribution()
• fast_forward.interaction_finalising module
  • finalise_interaction_types()
  • interaction_finalising()
• fast_forward.interaction_fit module
  • InteractionFitter
    • InteractionFitter.dihedrals
    • InteractionFitter.fit_interaction()
    • InteractionFitter.fit_to_gmx()
    • InteractionFitter.interactions_dict
• fast_forward.interaction_plots module
  • make_distances_distribution_plot()
  • make_distribution_plot()
  • make_matrix_plot()
• fast_forward.interactions_to_itp module
  • itp_writer()
• fast_forward.itp_parser_sub module
  • FastForwardITPParser
    • FastForwardITPParser.METH_DICT
    • FastForwardITPParser.parse()
  • guess_interactions()
  • read_itp()
• fast_forward.itp_to_ag module
  • ITPInteractionMapper
    • ITPInteractionMapper.get_interactions_group()
    • ITPInteractionMapper.get_pairwise_interaction()
  • find_mol_indices()
• fast_forward.linalg_functions module
  • apply_rotation()
  • calc_rotation_matrix()
  • cross_product()
  • dihedral_angle()
  • u_vect()
  • vec2quaternion()
  • vector_angle()
  • vector_angle_degrees()
• fast_forward.map_file_parers module
  • MapDirector
    • MapDirector.COMMENT_CHAR
    • MapDirector.METH_DICT
    • MapDirector.finalize()
    • MapDirector.parse_header()
  • Mapping
    • Mapping.add_atom()
    • Mapping.beads
    • Mapping.n_beads
  • read_mapping()
• fast_forward.mapping module
  • create_new_universe()
  • forward_map_indices()
  • forward_map_positions()
• fast_forward.ndx_parser module
  • ndx_to_ag()
• fast_forward.score module
  • calc_score()
  • hellinger()
  • score_matrix()
  • std_dev_hist()
• fast_forward.universe_handler module
  • Residue
  • ResidueIter
    • ResidueIter.add_residue()
    • ResidueIter.res_iter()
  • UniverseHandler
    • UniverseHandler.generate_molecule_graphs()
    • UniverseHandler.mass_to_element()
    • UniverseHandler.molecule_graphs
    • UniverseHandler.n_atoms
    • UniverseHandler.n_residues
    • UniverseHandler.pbc_complete()
    • UniverseHandler.res_iter()
    • UniverseHandler.resids
    • UniverseHandler.shift_united_atom_carbons()
  • res_as_mol()
• fast_forward.virtual_site_mass module
  • mass_redistribution()

Module contents