Index _ | A | B | C | D | E | F | G | H | L | M | N | O | P | R | S | T | U | V | W | X _ __init__() (mofbuilder.visualization.Viewer method) _debug (mofbuilder.core.Framework attribute) (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzReader attribute) (mofbuilder.io.XyzWriter attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.md.SolvationBuilder attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) _dft_optimize() (mofbuilder.md.LinkerForceFieldGenerator method) _find_isomorphism_and_mapping() (mofbuilder.md.LinkerForceFieldGenerator method) _get_mapping_between_two_molecules() (mofbuilder.md.ForceFieldMapper method) _map_forcefield_sections() (mofbuilder.md.ForceFieldMapper method) _parse_itp_file() (mofbuilder.md.ForceFieldMapper method) _reconnect() (mofbuilder.md.LinkerForceFieldGenerator method) _reconnect_linker_molecule() (mofbuilder.md.LinkerForceFieldGenerator method) _reverse_eG_dict() (mofbuilder.visualization.Viewer method) _xtb_optimize() (mofbuilder.md.LinkerForceFieldGenerator method) A add_custom_solvent() (mofbuilder.md.SolvationBuilder method) add_virtual_edge (mofbuilder.core.Framework attribute) atom_site_sector (mofbuilder.io.CifReader attribute) B barostat_added (mofbuilder.md.OpenmmSetup attribute) best_solvents_dict (mofbuilder.md.SolvationBuilder attribute) box_size (mofbuilder.md.SolvationBuilder attribute) buffer (mofbuilder.md.SolvationBuilder attribute) build() (mofbuilder.MetalOrganicFrameworkBuilder method) C cell_info (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) ciffile_lines (mofbuilder.io.CifReader attribute) CifReader (class in mofbuilder.io) CifWriter (class in mofbuilder.io) clean_unsaturated_linkers (mofbuilder.core.Framework attribute) cleaved_graph (mofbuilder.core.Framework attribute) com_target_type (mofbuilder.io.PdbReader attribute) comm (mofbuilder.core.Framework attribute) (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzReader attribute) (mofbuilder.io.XyzWriter attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.md.OpenmmSetup attribute) (mofbuilder.md.SolvationBuilder attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) (mofbuilder.visualization.Viewer attribute) constant_length (mofbuilder.MetalOrganicFrameworkBuilder attribute) custom_solvent_data (mofbuilder.md.SolvationBuilder attribute) D data (mofbuilder.io.CifReader attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.XyzReader attribute) data_path (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) database_dir (mofbuilder.md.GromacsForcefieldMerger attribute) defectgenerator (mofbuilder.MetalOrganicFrameworkBuilder attribute) dest_linker_molecule (mofbuilder.md.LinkerForceFieldGenerator attribute) dest_molecule (mofbuilder.md.ForceFieldMapper attribute) dest_molecule_connectivity_matrix (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) dest_molecule_forcefield_itpfile (mofbuilder.md.ForceFieldMapper attribute) dummy_atom_node (mofbuilder.core.Framework attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) dummy_atom_node_dict (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) E EC_con (mofbuilder.io.CifReader attribute) eG_dict (mofbuilder.visualization.Viewer attribute) eG_name_idx_dict (mofbuilder.visualization.Viewer attribute) expand_arr2data() (mofbuilder.io.PdbReader method), [1] F fcoords (mofbuilder.io.CifReader attribute) file_dir (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzWriter attribute) filename (mofbuilder.core.Framework attribute) filepath (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzReader attribute) (mofbuilder.io.XyzWriter attribute) ForceFieldMapper (class in mofbuilder.md) frame_cell_info (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) frame_linker (mofbuilder.MetalOrganicFrameworkBuilder attribute) frame_net (mofbuilder.MetalOrganicFrameworkBuilder attribute) frame_nodes (mofbuilder.MetalOrganicFrameworkBuilder attribute) frame_terminations (mofbuilder.MetalOrganicFrameworkBuilder attribute) frame_unit_cell (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) Framework (class in mofbuilder.core) framework (mofbuilder.MetalOrganicFrameworkBuilder attribute) framework_data (mofbuilder.core.Framework attribute) framework_fcoords_data (mofbuilder.core.Framework attribute) free_opt_linker_mol (mofbuilder.md.LinkerForceFieldGenerator attribute) G generate_linker_forcefield() (mofbuilder.core.Framework method) generate_MOF_gromacsfile() (mofbuilder.md.GromacsForcefieldMerger method) generate_reconnected_molecule_forcefield() (mofbuilder.md.LinkerForceFieldGenerator method), [1] get_merged_data() (mofbuilder.core.Framework method) get_type_atoms_fcoords_in_primitive_cell() (mofbuilder.io.CifReader method) get_xyzlines() (mofbuilder.io.XyzWriter method), [1] graph (mofbuilder.core.Framework attribute) graph_index_name_dict (mofbuilder.core.Framework attribute) graph_matched_vnode_xind (mofbuilder.core.Framework attribute) grid_points_template() (mofbuilder.md.SolvationBuilder method) gro (mofbuilder.md.OpenmmSetup attribute) gro_file (mofbuilder.md.OpenmmSetup attribute) GromacsForcefieldMerger (class in mofbuilder.md) GroReader (class in mofbuilder.io) GroWriter (class in mofbuilder.io) H hall_number (mofbuilder.io.CifReader attribute) L lines_show() (mofbuilder.visualization.Viewer method), [1] linker_center_data (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_center_X_data (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_charge (mofbuilder.core.Framework attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_connectivity (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_fake_edge (mofbuilder.core.Framework attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_ff_name (mofbuilder.core.Framework attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) linker_frag_length (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_fragment_length (mofbuilder.core.Framework attribute) linker_itp_dir (mofbuilder.md.GromacsForcefieldMerger attribute) linker_itp_path (mofbuilder.md.LinkerForceFieldGenerator attribute) linker_molecule (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_multiplicity (mofbuilder.core.Framework attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_name (mofbuilder.md.GromacsForcefieldMerger attribute) linker_optimization (mofbuilder.md.LinkerForceFieldGenerator attribute) linker_outer_data (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_outer_X_data (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_reconnect_drv (mofbuilder.core.Framework attribute) linker_reconnect_opt (mofbuilder.core.Framework attribute) linker_residue_name (mofbuilder.md.LinkerForceFieldGenerator attribute) linker_smiles (mofbuilder.MetalOrganicFrameworkBuilder attribute) linker_xyzfile (mofbuilder.MetalOrganicFrameworkBuilder attribute) LinkerForceFieldGenerator (class in mofbuilder.md) list_available_metals() (mofbuilder.MetalOrganicFrameworkBuilder method) list_available_mof_families() (mofbuilder.MetalOrganicFrameworkBuilder method) list_available_solvents() (mofbuilder.MetalOrganicFrameworkBuilder method) list_available_terminations() (mofbuilder.MetalOrganicFrameworkBuilder method) load_framework() (mofbuilder.MetalOrganicFrameworkBuilder method) load_optimized_rotations (mofbuilder.MetalOrganicFrameworkBuilder attribute) load_solute_info() (mofbuilder.md.SolvationBuilder method) M make_supercell() (mofbuilder.MetalOrganicFrameworkBuilder method) map_existing_forcefield() (mofbuilder.md.LinkerForceFieldGenerator method), [1] matched_vnode_xind (mofbuilder.core.Framework attribute) max_fill_rounds (mofbuilder.md.SolvationBuilder attribute) md_prepare() (mofbuilder.core.Framework method) merged_lines (mofbuilder.visualization.Viewer attribute) MetalOrganicFrameworkBuilder (class in mofbuilder) mlp_model_path (mofbuilder.core.Framework attribute) mlp_type (mofbuilder.core.Framework attribute) mof_family (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) mof_name (mofbuilder.md.GromacsForcefieldMerger attribute) mof_top_library (mofbuilder.MetalOrganicFrameworkBuilder attribute) mofwriter (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) molecule_radii() (mofbuilder.md.SolvationBuilder method) mols_radii() (mofbuilder.md.SolvationBuilder method) N net_cell_info (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_name (mofbuilder.io.CifReader attribute) net_optimizer (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_pair_vertex_edge (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_sorted_edges (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_sorted_nodes (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_spacegroup (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_unit_cell (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) net_unit_cell_inv (mofbuilder.MetalOrganicFrameworkBuilder attribute) node_atoms (mofbuilder.io.PdbReader attribute) node_ccoords (mofbuilder.io.PdbReader attribute) node_connectivity (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) node_data (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) node_metal (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) node_metal_type (mofbuilder.md.GromacsForcefieldMerger attribute) node_x_ccoords (mofbuilder.io.PdbReader attribute) node_X_data (mofbuilder.MetalOrganicFrameworkBuilder attribute) nodes (mofbuilder.core.Framework attribute) (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzReader attribute) (mofbuilder.io.XyzWriter attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.md.OpenmmSetup attribute) (mofbuilder.md.SolvationBuilder attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) (mofbuilder.visualization.Viewer attribute) O OpenmmSetup (class in mofbuilder.md) optimize_drv (mofbuilder.md.LinkerForceFieldGenerator attribute) optimize_framework() (mofbuilder.MetalOrganicFrameworkBuilder method) original_solvents_dict (mofbuilder.md.SolvationBuilder attribute) ostream (mofbuilder.core.Framework attribute) (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzReader attribute) (mofbuilder.io.XyzWriter attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.md.OpenmmSetup attribute) (mofbuilder.md.SolvationBuilder attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) (mofbuilder.visualization.Viewer attribute) other_residues (mofbuilder.md.GromacsForcefieldMerger attribute) P PdbReader (class in mofbuilder.io) PdbWriter (class in mofbuilder.io) periodicity (mofbuilder.core.Framework attribute) positions (mofbuilder.md.OpenmmSetup attribute) preferred_region_box (mofbuilder.md.SolvationBuilder attribute) process_node_pdb() (mofbuilder.io.PdbReader method), [1] provided_linker_itpfile (mofbuilder.core.Framework attribute) R rank (mofbuilder.core.Framework attribute) (mofbuilder.io.CifReader attribute) (mofbuilder.io.CifWriter attribute) (mofbuilder.io.GroReader attribute) (mofbuilder.io.GroWriter attribute) (mofbuilder.io.PdbReader attribute) (mofbuilder.io.PdbWriter attribute) (mofbuilder.io.XyzReader attribute) (mofbuilder.io.XyzWriter attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.md.OpenmmSetup attribute) (mofbuilder.md.SolvationBuilder attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) (mofbuilder.visualization.Viewer attribute) rc_solute_coords (mofbuilder.md.SolvationBuilder attribute) read_cif() (mofbuilder.io.CifReader method) read_gro() (mofbuilder.io.GroReader method), [1] read_pdb() (mofbuilder.io.PdbReader method), [1] read_xyz() (mofbuilder.io.XyzReader method), [1] reconnected_linker_molecule (mofbuilder.core.Framework attribute) remove() (mofbuilder.core.Framework method) remove_edge_list (mofbuilder.MetalOrganicFrameworkBuilder attribute) remove_node_list (mofbuilder.MetalOrganicFrameworkBuilder attribute) remove_overlaps_kdtree() (mofbuilder.md.SolvationBuilder method) replace() (mofbuilder.core.Framework method) residues_info (mofbuilder.core.Framework attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) resp_charges (mofbuilder.core.Framework attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) rotation_filename (mofbuilder.MetalOrganicFrameworkBuilder attribute) run_em() (mofbuilder.md.OpenmmSetup method) run_npt() (mofbuilder.md.OpenmmSetup method) run_nvt() (mofbuilder.md.OpenmmSetup method) run_pipeline() (mofbuilder.md.OpenmmSetup method) S safe_box (mofbuilder.md.SolvationBuilder attribute) save_files (mofbuilder.core.Framework attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) sc_unit_cell (mofbuilder.core.Framework attribute) sc_unit_cell_inv (mofbuilder.core.Framework attribute) scalar (mofbuilder.md.SolvationBuilder attribute) show() (mofbuilder.core.Framework method) simulation (mofbuilder.md.OpenmmSetup attribute) skip_rotation_optimization (mofbuilder.MetalOrganicFrameworkBuilder attribute) solute_data (mofbuilder.md.SolvationBuilder attribute) solute_dict (mofbuilder.md.SolvationBuilder attribute) solute_file (mofbuilder.md.SolvationBuilder attribute) solvate() (mofbuilder.core.Framework method) (mofbuilder.md.SolvationBuilder method) solvated_gro_file (mofbuilder.core.Framework attribute) SolvationBuilder (class in mofbuilder.md) solvationbuilder (mofbuilder.core.Framework attribute) solvents (mofbuilder.core.Framework attribute) solvents_datalines (mofbuilder.md.SolvationBuilder attribute) solvents_dict (mofbuilder.core.Framework attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) solvents_files (mofbuilder.md.SolvationBuilder attribute) solvents_molecules (mofbuilder.core.Framework attribute) solvents_name (mofbuilder.md.GromacsForcefieldMerger attribute) solvents_names (mofbuilder.md.SolvationBuilder attribute) solvents_proportions (mofbuilder.core.Framework attribute) (mofbuilder.md.SolvationBuilder attribute) solvents_quantities (mofbuilder.core.Framework attribute) (mofbuilder.md.SolvationBuilder attribute) spacegroup (mofbuilder.io.CifReader attribute) src_linker_forcefield_itpfile (mofbuilder.md.LinkerForceFieldGenerator attribute) src_linker_molecule (mofbuilder.md.LinkerForceFieldGenerator attribute) src_molecule (mofbuilder.md.ForceFieldMapper attribute) src_molecule_forcefield_itpfile (mofbuilder.md.ForceFieldMapper attribute) supercell (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) supercell_boundary (mofbuilder.io.CifWriter attribute) supercell_info (mofbuilder.core.Framework attribute) symmetry_sector (mofbuilder.io.CifReader attribute) system (mofbuilder.md.OpenmmSetup attribute) system_datalines (mofbuilder.md.SolvationBuilder attribute) system_pbc (mofbuilder.md.OpenmmSetup attribute) T target_dir (mofbuilder.md.GromacsForcefieldMerger attribute) target_directory (mofbuilder.core.Framework attribute) (mofbuilder.md.ForceFieldMapper attribute) (mofbuilder.md.LinkerForceFieldGenerator attribute) (mofbuilder.md.SolvationBuilder attribute) target_fcoords (mofbuilder.io.CifReader attribute) temperature (mofbuilder.md.OpenmmSetup attribute) temperature_K (mofbuilder.md.OpenmmSetup attribute) termination (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) termination_data (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) termination_molecule (mofbuilder.MetalOrganicFrameworkBuilder attribute) termination_name (mofbuilder.core.Framework attribute) (mofbuilder.md.GromacsForcefieldMerger attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) termination_X_data (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) termination_Y_data (mofbuilder.core.Framework attribute) (mofbuilder.MetalOrganicFrameworkBuilder attribute) timestep (mofbuilder.md.OpenmmSetup attribute) timestep_fs (mofbuilder.md.OpenmmSetup attribute) top (mofbuilder.md.OpenmmSetup attribute) top_file (mofbuilder.md.OpenmmSetup attribute) top_path (mofbuilder.md.GromacsForcefieldMerger attribute) trial_rounds (mofbuilder.md.SolvationBuilder attribute) U unit_cell (mofbuilder.io.CifWriter attribute) unsaturated_linkers (mofbuilder.core.Framework attribute) unsaturated_nodes (mofbuilder.core.Framework attribute) update_node_termination (mofbuilder.core.Framework attribute) V V_con (mofbuilder.io.CifReader attribute) Viewer (class in mofbuilder.visualization) virtual_edge_max_neighbor (mofbuilder.core.Framework attribute) W write() (mofbuilder.core.Framework method) (mofbuilder.io.CifWriter method), [1] (mofbuilder.io.GroWriter method), [1] (mofbuilder.io.PdbWriter method), [1] (mofbuilder.io.XyzWriter method), [1] write_mapped_itp_file() (mofbuilder.md.ForceFieldMapper method), [1] write_output() (mofbuilder.md.SolvationBuilder method) X X_data (mofbuilder.io.PdbReader attribute) xoo_dict (mofbuilder.core.Framework attribute) XyzReader (class in mofbuilder.io) XyzWriter (class in mofbuilder.io)