Index

A

a_type (SMArt.md.incl.Dummy attribute) abc2vec() (SMArt.md.data_st.Box method) (SMArt.md.data_st.Configuration.Box method) add2container() (SMArt.incl.GeneralContainer method) add_a_type() (SMArt.md.data_st.FF method) add_atom() (SMArt.md.data_st.ChargeGroup method) (SMArt.md.data_st.GeneralTopology method) (SMArt.md.data_st.GeneralTopology.ChargeGroup method) (SMArt.md.data_st.GeneralTopology.Interaction method) (SMArt.md.data_st.MolTop method) (SMArt.md.data_st.MolTop.Residue method) (SMArt.md.data_st.Residue method) (SMArt.md.incl.Interaction method) (SMArt.md.incl.InteractionType method) add_atom_a_type_to_row() (in module SMArt.alchemy.top_matching_fnc) add_atom_m_to_row() (in module SMArt.alchemy.top_matching_fnc) add_atom_pair2EP_l() (SMArt.md.data_st.GeneralTopology method) add_atom_pch_to_row() (in module SMArt.alchemy.top_matching_fnc) add_atom_state() (SMArt.md.data_st.GeneralAtom method) add_atom_to_row() (in module SMArt.alchemy.top_matching_fnc) add_atom_types() (SMArt.md.incl.InteractionType method) add_bb() (SMArt.md.data_st.BBdb method) add_c() (SMArt.graph.incl.Vertex method) add_define() (SMArt.md.gromacs.io.incl.GromacsParser method) add_defs() (SMArt.md.gromacs.io.gm_io_defaults.gm_FF_Defaults method) (SMArt.md.gromacs.io.incl.gmFFParser.gm_FF_Defaults method) add_DUM_exclusions() (in module SMArt.alchemy.top_matching_fnc) add_edge() (SMArt.graph.incl.Graph method) add_edges() (SMArt.graph.incl.Graph method) add_excl() (SMArt.md.data_st.GeneralAtom method) add_exclusions_neigh() (SMArt.md.data_st.GeneralTopology method) add_genborn() (SMArt.md.incl.AtomType method) (SMArt.md.incl.AvailableInteractionTypes.AtomType method) add_gr_title() (SMArt.md.gromos.io.incl.GromosParser method) add_interactions() (SMArt.md.data_st.MolTop method) add_interactions2atoms_dict() (SMArt.md.data_st.GeneralTopology method) add_line() (SMArt.md.incl.DescriptionPart method) add_m_type() (SMArt.md.data_st.FF method) add_match2sol() (SMArt.alchemy.incl.AlchemicalSolution_base method) add_molecule() (SMArt.md.data_st.Topology method) add_molecule_type() (SMArt.md.data_st.Topology method) add_new_excl_pair() (in module SMArt.alchemy.top_matching_fnc) add_new_toptp_atom() (in module SMArt.alchemy.top_matching_fnc) add_p() (SMArt.graph.incl.Vertex method) add_p_type_flag() (SMArt.md.incl.InteractionType method) add_pair() (SMArt.md.data_st.GeneralAtom method) add_params() (SMArt.md.incl.InteractionType method)

add_residue() (SMArt.md.data_st.MolTop method) add_ring_path_3D() (in module SMArt.geometry) add_ring_path_simple() (in module SMArt.geometry) add_state() (SMArt.md.data_st.GeneralTopology.Interaction method) (SMArt.md.incl.Interaction method) add_state2EP_ND_states() (in module SMArt.alchemy.top_matching_fnc) add_vdw() (SMArt.md.data_st.FF method) AlchemicalSolution (class in SMArt.alchemy.incl) AlchemicalSolution_base (class in SMArt.alchemy.incl) Angle_r (class in SMArt.md.incl) Angle_r_z (class in SMArt.md.incl) AngleType (class in SMArt.md.incl) Atom (SMArt.md.data_st.BBdb.BuildingBlock attribute) (SMArt.md.data_st.BuildingBlock attribute) (SMArt.md.data_st.Configuration attribute) (SMArt.md.data_st.GeneralTopology attribute) (SMArt.md.data_st.MolTop attribute) atom_radius() (SMArt.md.data_st.FF method) AtomType (class in SMArt.md.incl) AvailableInteractionTypes (class in SMArt.md.incl) AvailableInteractionTypes.Angle_r (class in SMArt.md.incl) AvailableInteractionTypes.Angle_r_z (class in SMArt.md.incl) AvailableInteractionTypes.AngleType (class in SMArt.md.incl) AvailableInteractionTypes.AtomType (class in SMArt.md.incl) AvailableInteractionTypes.BondAtomType (class in SMArt.md.incl) AvailableInteractionTypes.BondType (class in SMArt.md.incl) AvailableInteractionTypes.cmap (class in SMArt.md.incl) AvailableInteractionTypes.ConstraintType (class in SMArt.md.incl) AvailableInteractionTypes.Dihedral_Check_atoms_int (class in SMArt.md.incl) AvailableInteractionTypes.Dihedral_r (class in SMArt.md.incl) AvailableInteractionTypes.DihedralType (class in SMArt.md.incl) AvailableInteractionTypes.Distance_r (class in SMArt.md.incl) AvailableInteractionTypes.ExclusionPairType (class in SMArt.md.incl) AvailableInteractionTypes.ExclusionType (class in SMArt.md.incl) AvailableInteractionTypes.ImproperType (class in SMArt.md.incl) AvailableInteractionTypes.MassType (class in SMArt.md.incl) AvailableInteractionTypes.Orientation_r (class in SMArt.md.incl) AvailableInteractionTypes.PairNBType (class in SMArt.md.incl) AvailableInteractionTypes.PairType (class in SMArt.md.incl) AvailableInteractionTypes.Position_r (class in SMArt.md.incl) AvailableInteractionTypes.SettleType (class in SMArt.md.incl) AvailableInteractionTypes.vdWAtomPairType (class in SMArt.md.incl) AvailableInteractionTypes.vdWType (class in SMArt.md.incl) AvailableInteractionTypes.VirtualSite2Type (class in SMArt.md.incl) AvailableInteractionTypes.VirtualSite3Type (class in SMArt.md.incl) AvailableInteractionTypes.VirtualSite4Type (class in SMArt.md.incl) AvailableInteractionTypes.VirtualSitenType (class in SMArt.md.incl)

B

BBAtom (class in SMArt.md.data_st) BBdb (class in SMArt.md.data_st) BBdb.BuildingBlock (class in SMArt.md.data_st) BBParsing (class in SMArt.md.gromos.io.incl) BBWriting (class in SMArt.md.gromos.io.incl) BFS() (SMArt.graph.incl.Graph method) BFS_d() (SMArt.graph.incl.Graph method) BFS_d_f() (SMArt.graph.incl.Graph method) BFS_f() (SMArt.graph.incl.Graph method)

BFS_l() (SMArt.graph.incl.Graph method) block_lines() (SMArt.md.gromos.io.incl.GromosStream method) block_names() (SMArt.md.gromos.io.incl.GromosStream property) block_split_fnc() (SMArt.md.gromos.io.incl.GromosStream property) BondAtomType (class in SMArt.md.incl) BondType (class in SMArt.md.incl) Box (class in SMArt.md.data_st) Branch (class in SMArt.alchemy.incl) BuildingBlock (class in SMArt.md.data_st)

C

c (SMArt.graph.incl.Vertex attribute) calc_dg_bar() (in module SMArt.md.ana.pert_FE) calc_dg_exTI_lin() (in module SMArt.md.ana.pert_FE) calc_dg_exTI_mbar() (in module SMArt.md.ana.pert_FE) calc_dg_mbar() (in module SMArt.md.ana.pert_FE) calc_dg_TI() (in module SMArt.md.ana.pert_FE) calc_exTI_err() (in module SMArt.md.ana.pert_FE) calc_OI_BAR() (in module SMArt.md.ana.pert_FE) calc_ptp_score() (SMArt.md.incl.InteractionType method) calc_score() (SMArt.alchemy.MCS.MCS method) calc_seg_props() (in module SMArt.md.ana.pert_FE) calculate_branch_pair_estimate() (SMArt.alchemy.incl.Branch static method) calculate_combined_branch_pair_estimate() (SMArt.alchemy.MCS.MCS static method) calculate_estimate_atom_dummy_pairs_in_sol() (SMArt.alchemy.MCS.MCS method) calculate_estimate_atom_pair_in_sol() (SMArt.alchemy.MCS.MCS method) calculate_estimate_atom_pair_in_sol_ring_ind() (SMArt.alchemy.MCS.MCS method) calculate_neigh_count_pair_estimate() (SMArt.alchemy.incl.Branch class method) calculate_pair_estimate() (SMArt.alchemy.incl.Branch method) calculate_stacked_neigh_count_pair_estimate() (SMArt.alchemy.incl.Branch static method) change_imd() (SMArt.md.data_st.MD_Parameters method) change_md_in() (SMArt.md.data_st.MD_Parameters method) change_mdp() (SMArt.md.data_st.MD_Parameters method) ChargeGroup (class in SMArt.md.data_st) check_at_types() (SMArt.md.incl.InteractionType static method) check_atom_types() (SMArt.md.incl.InteractionType method) check_atoms_int_match() (SMArt.md.data_st.GeneralTopology.Interaction method) (SMArt.md.incl.Interaction method) (SMArt.md.incl.InteractionType method) check_branches() (SMArt.alchemy.incl.TopGraphProperties method) check_eq_int_type() (SMArt.md.data_st.FF method) check_eq_params() (SMArt.md.incl.InteractionType method) check_eq_ptp_flag_params() (SMArt.md.incl.InteractionType method) check_fullseg_in_segs() (in module SMArt.md.ana.pert_FE) check_G() (in module SMArt.tests.test_graph.gen_test_graphs) (SMArt.graph.incl.Graph method) check_if_eq() (in module SMArt.md.incl) check_match_pair() (SMArt.alchemy.MCS.MCS method) check_molecule_atoms_order() (SMArt.md.data_st.Topology method) check_number_of_params() (SMArt.md.incl.InteractionType method) check_overlapping_segs() (in module SMArt.md.ana.pert_FE) check_param() (SMArt.md.incl.InteractionType static method) check_separate_groups() (SMArt.alchemy.incl.TopGraphProperties method) CI() (in module SMArt.md.ana.incl) cmap (class in SMArt.md.incl) cnfBlocksParser (class in SMArt.md.gromos.io.incl) cnfBlocksWriter (class in SMArt.md.gromos.io.incl) cog() (SMArt.md.data_st.Configuration method) comb_G() (in module SMArt.tests.test_graph.gen_test_graphs) combine_bar_dhdl() (in module SMArt.md.ana.pert_FE) combine_exTI() (in module SMArt.md.ana.pert_FE) combine_mutually_exclusive_neigh_count_list() (SMArt.alchemy.incl.Branch static method) combine_mutually_exclusive_neigh_count_list_with_max_Nv() (SMArt.alchemy.incl.Branch static method) combine_neigh_count() (SMArt.alchemy.incl.Branch method) combine_neigh_count_list() (SMArt.alchemy.incl.Branch static method) combine_neigh_count_Nv_general() (SMArt.alchemy.incl.TopGraphProperties method) combine_neigh_count_Nv_VinB_general() (SMArt.alchemy.incl.TopGraphProperties method) ConfAtom (class in SMArt.md.data_st) Configuration (class in SMArt.md.data_st) Configuration.Box (class in SMArt.md.data_st) connect_v() (in module SMArt.tests.test_graph.gen_test_graphs) ConstraintType (class in SMArt.md.incl) container2write (SMArt.md.data_st.BBdb.BuildingBlock attribute) (SMArt.md.data_st.BuildingBlock attribute) (SMArt.md.data_st.ChargeGroup attribute) (SMArt.md.data_st.ConfAtom attribute) (SMArt.md.data_st.GeneralAtom attribute) (SMArt.md.data_st.GeneralTopology.ChargeGroup attribute) (SMArt.md.data_st.Molecule attribute) (SMArt.md.data_st.MoleculeType attribute) (SMArt.md.data_st.MolTop.Residue attribute) (SMArt.md.data_st.Residue attribute) (SMArt.md.data_st.Topology.Molecule attribute) (SMArt.md.data_st.Topology.MoleculeType attribute) (SMArt.md.gromacs.io.additional_classes.Define attribute) (SMArt.md.gromacs.io.additional_classes.ParsedSegments attribute) (SMArt.md.gromacs.io.incl.GromacsParser.Define attribute) (SMArt.md.incl.Angle_r attribute) (SMArt.md.incl.Angle_r_z attribute) (SMArt.md.incl.AngleType attribute) (SMArt.md.incl.AtomType attribute) (SMArt.md.incl.AvailableInteractionTypes.Angle_r attribute) (SMArt.md.incl.AvailableInteractionTypes.Angle_r_z attribute) (SMArt.md.incl.AvailableInteractionTypes.AngleType attribute) (SMArt.md.incl.AvailableInteractionTypes.AtomType attribute) (SMArt.md.incl.AvailableInteractionTypes.BondAtomType attribute) (SMArt.md.incl.AvailableInteractionTypes.BondType attribute) (SMArt.md.incl.AvailableInteractionTypes.cmap attribute) (SMArt.md.incl.AvailableInteractionTypes.ConstraintType attribute) (SMArt.md.incl.AvailableInteractionTypes.Dihedral_r attribute) (SMArt.md.incl.AvailableInteractionTypes.DihedralType attribute) (SMArt.md.incl.AvailableInteractionTypes.Distance_r attribute) (SMArt.md.incl.AvailableInteractionTypes.ExclusionPairType attribute) (SMArt.md.incl.AvailableInteractionTypes.ExclusionType attribute) (SMArt.md.incl.AvailableInteractionTypes.ImproperType attribute) (SMArt.md.incl.AvailableInteractionTypes.MassType attribute) (SMArt.md.incl.AvailableInteractionTypes.Orientation_r attribute) (SMArt.md.incl.AvailableInteractionTypes.PairType attribute) (SMArt.md.incl.AvailableInteractionTypes.Position_r attribute) (SMArt.md.incl.AvailableInteractionTypes.SettleType attribute) (SMArt.md.incl.AvailableInteractionTypes.vdWAtomPairType attribute) (SMArt.md.incl.AvailableInteractionTypes.vdWType attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite2Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite3Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite4Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSitenType attribute) (SMArt.md.incl.BondAtomType attribute) (SMArt.md.incl.BondType attribute) (SMArt.md.incl.cmap attribute) (SMArt.md.incl.ConstraintType attribute) (SMArt.md.incl.DescriptionPart attribute) (SMArt.md.incl.Dihedral_r attribute) (SMArt.md.incl.DihedralType attribute) (SMArt.md.incl.Distance_r attribute) (SMArt.md.incl.ExclusionPairType attribute) (SMArt.md.incl.ExclusionType attribute) (SMArt.md.incl.ImproperType attribute) (SMArt.md.incl.MassType attribute) (SMArt.md.incl.Orientation_r attribute) (SMArt.md.incl.PairType attribute) (SMArt.md.incl.Position_r attribute) (SMArt.md.incl.SettleType attribute) (SMArt.md.incl.vdWAtomPairType attribute) (SMArt.md.incl.vdWType attribute) (SMArt.md.incl.VirtualSite2Type attribute) (SMArt.md.incl.VirtualSite3Type attribute) (SMArt.md.incl.VirtualSite4Type attribute) (SMArt.md.incl.VirtualSitenType attribute)

ContPref_g2g (class in SMArt.md.gro2gro.g2g) convert_c612_2_se() (SMArt.md.incl.AtomType method) (SMArt.md.incl.AvailableInteractionTypes.AtomType method) convert_harm_quad() (SMArt.md.incl.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.BondType method) (SMArt.md.incl.BondType method) convert_se_2_c612() (SMArt.md.incl.AtomType method) (SMArt.md.incl.AvailableInteractionTypes.AtomType method) coord (SMArt.md.incl.Dummy attribute) copy() (SMArt.alchemy.incl.AlchemicalSolution_base method) copy4update() (SMArt.alchemy.incl.AlchemicalSolution_base method) copy4update_new_sol_df() (SMArt.alchemy.incl.AlchemicalSolution_base method) copy_add_state() (SMArt.alchemy.incl.AlchemicalSolution_base method) create_adj_list() (SMArt.md.data_st.GeneralTopology method) create_estimate_top_pair_in_sol() (SMArt.alchemy.MCS.MCS method)

D

d2() (SMArt.md.data_st.Configuration method) d2_within() (SMArt.md.data_st.Configuration method) d2_within_c2() (SMArt.md.data_st.Configuration method) DataDumping (class in SMArt.incl) Defaults (class in SMArt.incl) Define (class in SMArt.md.gromacs.io.additional_classes) DescriptionPart (class in SMArt.md.incl) DFS() (SMArt.graph.incl.Graph method) DFS_f() (SMArt.graph.incl.Graph method)

dG_err_tols (class in SMArt.md.ana.pert_FE) Dihedral_Check_atoms_int (class in SMArt.md.incl) Dihedral_r (class in SMArt.md.incl) DihedralType (class in SMArt.md.incl) directed_BFS() (SMArt.graph.incl.GraphDirected method) dist() (SMArt.graph.incl.Graph method) Distance_r (class in SMArt.md.incl) do_warn() (in module SMArt.incl) Dummy (class in SMArt.md.incl) dump() (SMArt.incl.DataDumping method)

E

edges2adj() (SMArt.graph.incl.Graph method) end_block_split() (SMArt.md.gromos.io.incl.GromosStream method) enumerate_brute_force() (SMArt.alchemy.MCS.MCS method) enumerate_brute_force_call() (SMArt.alchemy.MCS.MCS method) enumerate_stepwise() (SMArt.alchemy.MCS.MCS method) enumerate_stepwise_call() (SMArt.alchemy.MCS.MCS method) enumerate_stepwise_call_partial_sol_invalid() (SMArt.alchemy.MCS.MCS method)

enumerate_stepwise_sorted() (SMArt.alchemy.MCS.MCS method) enumerate_stepwise_sorted_call() (SMArt.alchemy.MCS.MCS method) EP_l() (SMArt.md.data_st.GeneralTopology property) eq() (in module SMArt.md.pipeline) exchange_defs() (SMArt.md.gromacs.io.incl.GromacsParser static method) ExclusionPairType (class in SMArt.md.incl) ExclusionType (class in SMArt.md.incl)

F

f (SMArt.incl.StringStream attribute) FF (class in SMArt.md.data_st) ff_gm2gr() (SMArt.md.gro2gro.g2g.FFg2g method) ff_gr2gm() (SMArt.md.gro2gro.g2g.FFg2g method) ff_name (SMArt.md.gromos.incl.GromosDefaults attribute) FFg2g (class in SMArt.md.gro2gro.g2g) FileHandler (class in SMArt.incl) FileStream (class in SMArt.incl) find_atom() (SMArt.md.data_st.MolTop.Residue method) (SMArt.md.data_st.Residue method) find_atom_order() (in module SMArt.alchemy.top_matching_fnc) (SMArt.alchemy.MCS.MCS method) find_best_ptp_matches() (in module SMArt.alchemy.top_matching_fnc) find_common_atom_pair() (SMArt.alchemy.incl.AlchemicalSolution_base method) find_directive() (SMArt.md.gromacs.io.incl.GromacsStream static method) find_imp_pairs() (SMArt.md.data_st.FF method) find_int_container2write() (SMArt.md.incl.InteractionType class method) find_interaction_type() (SMArt.md.data_st.FF method) find_interactions() (SMArt.md.data_st.GeneralTopology method) find_interactions_ptp() (in module SMArt.alchemy.top_matching_fnc) find_matches_at_m_types() (SMArt.md.data_st.FF method) find_ND_state_tops_set() (in module SMArt.alchemy.top_matching_fnc) find_next_code() (SMArt.incl.GeneralContainer method) find_rings() (SMArt.graph.incl.Graph method) find_rings_graph() (SMArt.graph.incl.Graph method) find_shortest_rpath() (SMArt.graph.incl.GraphDirected method) find_sol_atom() (SMArt.alchemy.incl.AlchemicalSolution_base method) find_within() (SMArt.md.data_st.Configuration method) find_within_box() (SMArt.md.data_st.Configuration method) find_within_c2() (SMArt.md.data_st.Configuration method) fix() (SMArt.md.ana.incl.Real method) fix_float() (in module SMArt.md.ana.incl) (SMArt.md.ana.incl.Real class method) flag_traceback (SMArt.incl.WARN attribute) fnc (SMArt.md.incl.Angle_r attribute) (SMArt.md.incl.Angle_r_z attribute) (SMArt.md.incl.AngleType attribute) (SMArt.md.incl.AvailableInteractionTypes.Angle_r attribute) (SMArt.md.incl.AvailableInteractionTypes.Angle_r_z attribute) (SMArt.md.incl.AvailableInteractionTypes.AngleType attribute) (SMArt.md.incl.AvailableInteractionTypes.BondType attribute) (SMArt.md.incl.AvailableInteractionTypes.ConstraintType attribute) (SMArt.md.incl.AvailableInteractionTypes.Dihedral_r attribute) (SMArt.md.incl.AvailableInteractionTypes.DihedralType attribute) (SMArt.md.incl.AvailableInteractionTypes.Distance_r attribute) (SMArt.md.incl.AvailableInteractionTypes.ExclusionPairType attribute) (SMArt.md.incl.AvailableInteractionTypes.ExclusionType attribute) (SMArt.md.incl.AvailableInteractionTypes.ImproperType attribute) (SMArt.md.incl.AvailableInteractionTypes.Orientation_r attribute) (SMArt.md.incl.AvailableInteractionTypes.PairNBType attribute) (SMArt.md.incl.AvailableInteractionTypes.PairType attribute) (SMArt.md.incl.AvailableInteractionTypes.Position_r attribute) (SMArt.md.incl.AvailableInteractionTypes.SettleType attribute) (SMArt.md.incl.AvailableInteractionTypes.vdWType attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite2Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite3Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite4Type attribute) (SMArt.md.incl.BondType attribute) (SMArt.md.incl.ConstraintType attribute) (SMArt.md.incl.Dihedral_r attribute) (SMArt.md.incl.DihedralType attribute) (SMArt.md.incl.Distance_r attribute) (SMArt.md.incl.ExclusionPairType attribute) (SMArt.md.incl.ExclusionType attribute) (SMArt.md.incl.ImproperType attribute) (SMArt.md.incl.Orientation_r attribute) (SMArt.md.incl.PairNBType attribute) (SMArt.md.incl.PairType attribute) (SMArt.md.incl.Position_r attribute) (SMArt.md.incl.SettleType attribute) (SMArt.md.incl.vdWType attribute) (SMArt.md.incl.VirtualSite2Type attribute) (SMArt.md.incl.VirtualSite3Type attribute) (SMArt.md.incl.VirtualSite4Type attribute)

for_LPs_Es_nfr_mul() (SMArt.md.ana.pert_FE.LPs_Map method) for_neigh_Es_nfr() (SMArt.md.ana.pert_FE.LPs_Map method) FORCEFIELD (SMArt.md.gromos.incl.GromosBlockNames attribute)

G

G (SMArt.tests.test_alchemy.test_MCS_options.Test_MCS_RMSD attribute) g1 (SMArt.tests.test_alchemy.test_MCS_options.Test_MCS_RMSD attribute) g2 (SMArt.tests.test_alchemy.test_MCS_options.Test_MCS_RMSD attribute) g521 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) g522 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) g56 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) g621 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) g622 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) G7 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) g7 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) G_521 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) G_522 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) G_56 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) G_621 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) G_622 (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match attribute) gen_graph() (SMArt.md.data_st.GeneralTopology method) gen_int_container_01_list() (in module SMArt.alchemy.top_matching_fnc) gen_int_container_01_list_new() (in module SMArt.alchemy.top_matching_fnc) gen_slurm_job() (in module SMArt.md.pipeline) GeneralAtom (class in SMArt.md.data_st) GeneralCnfWriter (class in SMArt.md.gromos.io.incl) GeneralContainer (class in SMArt.incl) GeneralTopology (class in SMArt.md.data_st) GeneralTopology.ChargeGroup (class in SMArt.md.data_st) GeneralTopology.Interaction (class in SMArt.md.data_st) generate_2state_top() (in module SMArt.alchemy) generate_atom_states() (in module SMArt.alchemy.top_matching_fnc) generate_atom_top_state() (in module SMArt.alchemy.top_matching_fnc) generate_constraints() (SMArt.md.data_st.MolTop method) generate_EDS_top() (in module SMArt.alchemy) generate_excl_from_EP() (in module SMArt.alchemy.top_matching_fnc) generate_int_states() (in module SMArt.alchemy.top_matching_fnc) generate_mol_type() (SMArt.md.gro2gro.g2g.Top_g2g method) generate_mol_types() (SMArt.md.gro2gro.g2g.Top_g2g method) generate_multi_state_top() (in module SMArt.alchemy.top_matching_fnc) generate_new_coordinates() (in module SMArt.geometry) generate_params_gr_gm() (SMArt.md.gro2gro.g2g.IntType_g2g method) generate_params_khq() (SMArt.md.incl.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.BondType method) (SMArt.md.incl.BondType method) generate_ptp_excl_pair_single_atom() (in module SMArt.alchemy.top_matching_fnc) generate_sys_atoms_from_mols_types() (SMArt.md.gro2gro.g2g.Top_g2g method) generate_toptp() (in module SMArt.alchemy.top_matching_fnc) generate_vdw() (SMArt.md.data_st.FF method) generate_vdw_c612_se() (SMArt.md.data_st.FF method) get_2D_repr() (SMArt.graph.incl.Graph method) get_a_type() (SMArt.md.data_st.FF method) get_add_missing_groups() (SMArt.graph.incl.GraphDirected method) get_all_vs_all_estimate_matrix_top_pair() (SMArt.alchemy.MCS.MCS method) get_atom_ptp_states() (SMArt.md.data_st.GeneralTopology method) get_atoms() (SMArt.md.data_st.GeneralTopology method) get_bb() (SMArt.md.data_st.GeneralTopology method) get_branch_roots_parents() (SMArt.alchemy.incl.TopGraphProperties method) get_branch_Vpair() (SMArt.alchemy.incl.TopGraphProperties method) get_branches() (SMArt.alchemy.incl.TopGraphProperties method) get_c() (in module SMArt.tests.test_graph.gen_test_graphs) get_code() (SMArt.incl.GeneralContainer static method) get_combined_neigh_count_Nv() (SMArt.alchemy.incl.TopGraphProperties method) get_container() (SMArt.incl.GeneralContainer method) get_curr_stack() (SMArt.md.gromacs.io.additional_classes.ParsedSegments method) get_current_dvalues() (SMArt.incl.Defaults method) get_default_dg_err_tols() (SMArt.md.ana.pert_FE.dG_err_tols class method) get_defaults() (SMArt.incl.Defaults class method) get_DUM_type() (SMArt.md.data_st.FF property) get_dummy_branch() (SMArt.alchemy.incl.TopGraphProperties method) get_dummy_match_estimates() (SMArt.alchemy.incl.TopGraphProperties method) get_dummy_match_estimates_in_solution() (SMArt.alchemy.incl.TopGraphProperties method) get_edges() (SMArt.graph.incl.Graph method) get_EDS() (in module SMArt.alchemy) get_emin_missing_at_imd() (in module SMArt.md.gromos.md_functions.make_imd) get_emin_vac_imd() (in module SMArt.md.gromos.md_functions.make_imd) get_emin_water_imd() (in module SMArt.md.gromos.md_functions.make_imd) get_eq_imd() (in module SMArt.md.gromos.md_functions.make_imd) get_excl_pair() (SMArt.md.data_st.GeneralTopology method) get_exclusion_pair_state_from_EP() (in module SMArt.alchemy.top_matching_fnc) get_ext_TI_imd() (in module SMArt.md.gromos.md_functions.make_imd) get_f() (SMArt.incl.FileHandler method) get_first_non_ring_neighbour() (SMArt.alchemy.incl.TopGraphProperties method) get_form() (SMArt.md.incl.InteractionType method) get_frame_dtype() (SMArt.md.data_st.Trajectory method) get_FromRing_branches_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_FromRing_nonring_branches_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_FromRing_ring_branches_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_full_dG_err_from_segs() (in module SMArt.md.ana.pert_FE) get_full_dG_from_segs() (in module SMArt.md.ana.pert_FE) get_G_mol() (SMArt.md.data_st.Topology method) get_generator_ptp_excl_pair_single_atom() (in module SMArt.alchemy.top_matching_fnc) get_gm2gr_int_type() (SMArt.md.gro2gro.g2g.IntType_g2g method) get_gr2gm_def_pref() (SMArt.md.gro2gro.g2g.IntType_g2g method) get_gr2gm_def_pref_class() (SMArt.md.gro2gro.g2g.IntType_g2g class method) get_gr2gm_int_type() (SMArt.md.gro2gro.g2g.IntType_g2g class method) get_gr_gm_params() (SMArt.md.gro2gro.g2g.IntType_g2g method) get_Gs() (SMArt.graph.incl.Graph method) get_HH() (SMArt.md.data_st.GeneralTopology method) (SMArt.md.data_st.MolTop method) get_id_string() (in module SMArt.incl) get_initial_atom_brute_force() (SMArt.alchemy.MCS.MCS method) get_initial_pairs_brute_force() (SMArt.alchemy.MCS.MCS method) get_initial_pairs_stepwise() (SMArt.alchemy.MCS.MCS method) get_int_type() (SMArt.md.gro2gro.g2g.IntType_g2g class method) get_intDB() (SMArt.md.data_st.FF method) get_interaction_containers() (SMArt.md.data_st.GeneralAtom method) (SMArt.md.data_st.InteractionContainer method) get_item() (SMArt.incl.GeneralContainer method) get_khq() (SMArt.md.incl.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.BondType method) (SMArt.md.incl.BondType method) get_lifetime_trans() (in module SMArt.md.ana.incl) get_LPs_pos() (in module SMArt.md.ana.pert_FE) get_LPs_pred() (SMArt.md.data_st.MD_Parameters method) get_LPs_times() (in module SMArt.md.ana.pert_FE)

get_lset() (in module SMArt.md.ana.incl) get_max_Nv_combB_vDummy() (SMArt.alchemy.incl.TopGraphProperties method) get_molecules() (SMArt.md.data_st.Topology method) get_neigh_count_from_generator() (SMArt.alchemy.incl.TopGraphProperties static method) get_neigh_count_roots_parents() (SMArt.alchemy.incl.TopGraphProperties method) get_neigh_count_Vpair() (SMArt.alchemy.incl.TopGraphProperties method) get_new_pairs_brute_force() (SMArt.alchemy.MCS.MCS method) get_new_pairs_stepwise() (SMArt.alchemy.MCS.MCS method) get_nfr_from_nfr_mul() (in module SMArt.md.ana.pert_FE) get_nfr_from_NFRs() (in module SMArt.md.ana.pert_FE) get_nfr_LPs() (in module SMArt.md.ana.pert_FE) get_nfr_mul_from_NFRs() (in module SMArt.md.ana.pert_FE) get_nonring_branch_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_num_from_code() (SMArt.incl.GeneralContainer static method) get_p_c() (SMArt.graph.incl.GraphDirected method) get_parents() (SMArt.graph.incl.GraphDirected method) get_ptp_ligands() (in module SMArt.alchemy) get_ptp_states() (SMArt.md.data_st.GeneralTopology method) get_r() (in module SMArt.tests.test_graph.gen_test_graphs) get_rc() (in module SMArt.tests.test_graph.gen_test_graphs) get_reduced_state() (SMArt.md.data_st.Topology method) get_res_atom_names_v1() (in module SMArt.alchemy.top_matching_fnc) get_res_common_atoms() (in module SMArt.alchemy.top_matching_fnc) get_residues() (SMArt.md.data_st.GeneralTopology method) get_residues_v1() (in module SMArt.alchemy.top_matching_fnc) get_rev_top_ptp() (SMArt.md.data_st.Topology method) get_ring_branch_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_break_branches() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_combined_FromRing_branch_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_combined_linear_branch_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_combined_linear_branch_tot_Nv() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_ring_branch_from_generator_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_ring_branch_from_generator_VinB_recursive() (SMArt.alchemy.incl.TopGraphProperties method) get_ring_sorted_RLCB() (SMArt.alchemy.incl.TopGraphProperties method) get_segments2test() (in module SMArt.md.ana.pert_FE) get_separate_groups() (SMArt.alchemy.incl.TopGraphProperties method) get_separate_groups_brute_force() (SMArt.alchemy.incl.TopGraphProperties method) get_separate_groups_old() (SMArt.alchemy.incl.TopGraphProperties method) get_short_TI_imd() (in module SMArt.md.gromos.md_functions.make_imd) get_sim_l_from_fpath() (in module SMArt.md.gromos.io.ana) get_skips() (in module SMArt.md.ana.pert_FE) get_slurm_job_settings() (in module SMArt.md.pipeline) get_sorted_combined_branches() (SMArt.alchemy.incl.TopGraphProperties method) get_sorted_initial_pairs_stepwise() (SMArt.alchemy.MCS.MCS method) get_sorted_initial_pairs_stepwise_2() (SMArt.alchemy.MCS.MCS method) get_sorted_new_pairs_stepwise() (SMArt.alchemy.MCS.MCS method) get_state() (SMArt.md.data_st.GeneralTopology method) get_state_names() (in module SMArt.alchemy.top_matching_fnc) get_sys_title() (in module SMArt.alchemy.top_matching_fnc) get_TGP_top_available_atoms() (SMArt.alchemy.MCS.MCS method) get_v_dummy_match_estimate() (SMArt.alchemy.incl.TopGraphProperties method) get_vdw() (SMArt.md.data_st.FF method) get_xvg_labels() (in module SMArt.md.gromacs.io.ana) gm2gr() (SMArt.md.gro2gro.g2g.FFg2g method) (SMArt.md.gro2gro.g2g.IntType_g2g method) (SMArt.md.gro2gro.g2g.Top_g2g method) (SMArt.md.incl.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.BondType method) (SMArt.md.incl.BondType method) gm2gr_param_trans_fnc (SMArt.md.incl.AvailableInteractionTypes.ImproperType attribute) (SMArt.md.incl.ImproperType attribute) gm_FDs() (SMArt.local_config.paths class method) gm_FDs_Defaults (class in SMArt.md.gromacs.io.gm_io_defaults) gm_FF_Defaults (class in SMArt.md.gromacs.io.gm_io_defaults) gm_io_Defaults (class in SMArt.md.gromacs.io.gm_io_defaults) gm_ord() (SMArt.md.gromacs.io.additional_classes.ParsedSegments property) gm_params2define() (SMArt.md.gromacs.io.incl_md_only.gmInteractionTypeWriter method) gmCMAPWriter (class in SMArt.md.gromacs.io.incl_md_only) gmConfigurationIO (class in SMArt.md.gromacs.io.incl) gmFFParser (class in SMArt.md.gromacs.io.incl) gmFFParser.gm_FF_Defaults (class in SMArt.md.gromacs.io.incl) gmFFWriter (class in SMArt.md.gromacs.io.incl) gmFragmentMoleculeIO (class in SMArt.md.gromacs.io.incl) gmInteractionTypeWriter (class in SMArt.md.gromacs.io.incl_md_only) gmTopologyIO (class in SMArt.md.gromacs.io.incl) gmx() (SMArt.local_config.paths class method) gpp() (SMArt.local_config.paths class method) gr2gm() (SMArt.md.gro2gro.g2g.FFg2g method) (SMArt.md.gro2gro.g2g.IntType_g2g method) (SMArt.md.gro2gro.g2g.Top_g2g method) (SMArt.md.incl.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.AngleType method) (SMArt.md.incl.AvailableInteractionTypes.BondType method) (SMArt.md.incl.AvailableInteractionTypes.Distance_r method) (SMArt.md.incl.BondType method) (SMArt.md.incl.Distance_r method) gr2gm_param_trans_fnc (SMArt.md.incl.AvailableInteractionTypes.ImproperType attribute) (SMArt.md.incl.ImproperType attribute) gr_FDs() (SMArt.local_config.paths class method) gr_get_atom_element() (in module SMArt.md.gro2gro.g2g) gr_get_element() (SMArt.md.data_st.GeneralAtom method) gr_id_format (SMArt.md.gromos.io.incl.grAtomWriting attribute) (SMArt.md.gromos.io.incl.grBBAtomWriting attribute) (SMArt.md.gromos.io.incl.grTOPAtomWriting attribute) Graph (class in SMArt.graph.incl) GraphDirected (class in SMArt.graph.incl) grAtomWriting (class in SMArt.md.gromos.io.incl) grBBAtomWriting (class in SMArt.md.gromos.io.incl) GromacsFile (class in SMArt.md.gromacs.io.incl) GromacsParser (class in SMArt.md.gromacs.io.incl) GromacsParser.Define (class in SMArt.md.gromacs.io.incl) GromacsStream (class in SMArt.md.gromacs.io.incl) GromacsString (class in SMArt.md.gromacs.io.incl) GromacsWriter (class in SMArt.md.gromacs.io.incl) GromosBlockNames (class in SMArt.md.gromos.incl) GromosDefaults (class in SMArt.md.gromos.incl) GromosFile (class in SMArt.md.gromos.io.incl) GromosParser (class in SMArt.md.gromos.io.incl) GromosStream (class in SMArt.md.gromos.io.incl) GromosString (class in SMArt.md.gromos.io.incl) GromosWriter (class in SMArt.md.gromos.io.incl) grTOPAtomWriting (class in SMArt.md.gromos.io.incl) gxx() (SMArt.local_config.paths class method)

I

id_pref (SMArt.md.data_st.MoleculeType attribute) (SMArt.md.data_st.Topology.MoleculeType attribute) IFPBlocksParser (class in SMArt.md.gromos.io.incl) IFPBlocksWriter (class in SMArt.md.gromos.io.incl) improper_type() (SMArt.md.data_st.GeneralTopology method)

ImproperType (class in SMArt.md.incl) Interaction (class in SMArt.md.incl) InteractionContainer (class in SMArt.md.data_st) InteractionType (class in SMArt.md.incl) IntType_g2g (class in SMArt.md.gro2gro.g2g)

J

Jarz() (in module SMArt.md.ana.incl)

L

l (SMArt.graph.incl.Vertex attribute) lines() (SMArt.incl.FileStream method) (SMArt.incl.StringStream method) (SMArt.md.gromacs.io.incl.GromacsStream method)

LINKEXCLUSIONS (SMArt.md.gromos.incl.GromosBlockNames attribute) load() (SMArt.incl.DataDumping class method) load_trc_npz() (SMArt.md.data_st.Trajectory method) LPs_Map (class in SMArt.md.ana.pert_FE)

M

m (SMArt.md.incl.Dummy attribute) make_eq_job_list() (in module SMArt.md.gromos.md_functions.make_job_list) make_estimates() (SMArt.alchemy.MCS.MCS method) make_job_list() (in module SMArt.md.gromos.md_functions.make_job_list) MAKETOPVERSION (SMArt.md.gromos.incl.GromosBlockNames attribute) MassType (class in SMArt.md.incl) match_at_m_name() (SMArt.md.data_st.FF static method) MCS (class in SMArt.alchemy.MCS) MD_Parameters (class in SMArt.md.data_st) merge_EP_ND_states() (in module SMArt.alchemy.top_matching_fnc) module SMArt SMArt.alchemy SMArt.alchemy.incl SMArt.alchemy.MCS SMArt.alchemy.top_matching_fnc SMArt.geometry SMArt.graph SMArt.graph.incl SMArt.incl SMArt.local_config SMArt.md SMArt.md.ana SMArt.md.ana.incl SMArt.md.ana.pert_FE SMArt.md.data_st SMArt.md.gro2gro SMArt.md.gro2gro.g2g SMArt.md.gromacs SMArt.md.gromacs.FF_DB SMArt.md.gromacs.incl SMArt.md.gromacs.io SMArt.md.gromacs.io.additional_classes SMArt.md.gromacs.io.ana SMArt.md.gromacs.io.gm_io_defaults SMArt.md.gromacs.io.incl SMArt.md.gromacs.io.incl_md_only SMArt.md.gromacs.wrapper SMArt.md.gromos SMArt.md.gromos.FF_DB SMArt.md.gromos.incl SMArt.md.gromos.io SMArt.md.gromos.io.ana SMArt.md.gromos.io.incl SMArt.md.gromos.md_functions SMArt.md.gromos.md_functions.make_imd SMArt.md.gromos.md_functions.make_job_list SMArt.md.incl SMArt.md.pipeline SMArt.md.wrappers SMArt.mp_fnc SMArt.tests SMArt.tests.test_alchemy SMArt.tests.test_alchemy.test_MCS_options SMArt.tests.test_alchemy.test_partial_ring_match SMArt.tests.test_alchemy.test_point_mut SMArt.tests.test_graph SMArt.tests.test_graph.gen_test_graphs

Molecule (class in SMArt.md.data_st) MoleculeType (class in SMArt.md.data_st) MolSystem (class in SMArt.md.data_st) MolTop (class in SMArt.md.data_st) MolTop.Residue (class in SMArt.md.data_st) MolType_g2g (class in SMArt.md.gro2gro.g2g) MTBBlocksParser (class in SMArt.md.gromos.io.incl)

N

N (SMArt.tests.test_alchemy.test_MCS_options.Test_MCS_RMSD attribute) n_atoms_format (SMArt.md.gromos.io.incl.grAtomWriting attribute) (SMArt.md.gromos.io.incl.grBBAtomWriting attribute) (SMArt.md.gromos.io.incl.grTOPAtomWriting attribute) na (SMArt.md.incl.Angle_r attribute) (SMArt.md.incl.Angle_r_z attribute) (SMArt.md.incl.AngleType attribute) (SMArt.md.incl.AvailableInteractionTypes.Angle_r attribute) (SMArt.md.incl.AvailableInteractionTypes.Angle_r_z attribute) (SMArt.md.incl.AvailableInteractionTypes.AngleType attribute) (SMArt.md.incl.AvailableInteractionTypes.BondType attribute) (SMArt.md.incl.AvailableInteractionTypes.cmap attribute) (SMArt.md.incl.AvailableInteractionTypes.ConstraintType attribute) (SMArt.md.incl.AvailableInteractionTypes.Dihedral_r attribute) (SMArt.md.incl.AvailableInteractionTypes.DihedralType attribute) (SMArt.md.incl.AvailableInteractionTypes.Distance_r attribute) (SMArt.md.incl.AvailableInteractionTypes.ExclusionPairType attribute) (SMArt.md.incl.AvailableInteractionTypes.ExclusionType attribute) (SMArt.md.incl.AvailableInteractionTypes.Orientation_r attribute) (SMArt.md.incl.AvailableInteractionTypes.PairNBType attribute) (SMArt.md.incl.AvailableInteractionTypes.PairType attribute) (SMArt.md.incl.AvailableInteractionTypes.Position_r attribute) (SMArt.md.incl.AvailableInteractionTypes.SettleType attribute) (SMArt.md.incl.AvailableInteractionTypes.vdWType attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite2Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite3Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSite4Type attribute) (SMArt.md.incl.AvailableInteractionTypes.VirtualSitenType attribute) (SMArt.md.incl.BondType attribute) (SMArt.md.incl.cmap attribute) (SMArt.md.incl.ConstraintType attribute) (SMArt.md.incl.Dihedral_r attribute) (SMArt.md.incl.DihedralType attribute) (SMArt.md.incl.Distance_r attribute) (SMArt.md.incl.ExclusionPairType attribute) (SMArt.md.incl.ExclusionType attribute) (SMArt.md.incl.Orientation_r attribute) (SMArt.md.incl.PairNBType attribute) (SMArt.md.incl.PairType attribute) (SMArt.md.incl.Position_r attribute) (SMArt.md.incl.SettleType attribute) (SMArt.md.incl.vdWType attribute) (SMArt.md.incl.VirtualSite2Type attribute) (SMArt.md.incl.VirtualSite3Type attribute) (SMArt.md.incl.VirtualSite4Type attribute) (SMArt.md.incl.VirtualSitenType attribute)

new_line_format (SMArt.md.gromos.io.incl.grAtomWriting attribute) (SMArt.md.gromos.io.incl.grBBAtomWriting attribute) (SMArt.md.gromos.io.incl.grTOPAtomWriting attribute) nexcl (SMArt.md.gromos.incl.GromosDefaults attribute) next_block() (SMArt.md.gromos.io.incl.GromosStream method) next_line() (SMArt.md.gromacs.io.incl.GromacsStream method) normalize_RGB() (in module SMArt.md.ana.incl)

O

Orientation_r (class in SMArt.md.incl)

P

p (SMArt.graph.incl.Vertex attribute) p_ch (SMArt.md.incl.Dummy attribute) PairNBType (class in SMArt.md.incl) PairType (class in SMArt.md.incl) parse_bb() (SMArt.md.data_st.BBdb.BuildingBlock method) (SMArt.md.data_st.BuildingBlock method) parse_cnf() (in module SMArt.md) (SMArt.md.data_st.Configuration method) parse_dsr() (SMArt.md.gromos.io.incl.topBlocksParser method) parse_eds() (SMArt.md.data_st.Topology method) parse_ff() (in module SMArt.md) (SMArt.md.data_st.FF method) parse_ff_gm() (SMArt.md.gromacs.io.incl.gmFFParser method) parse_gm() (SMArt.md.gromacs.io.incl.GromacsParser method) parse_gro() (SMArt.md.gromacs.io.incl.gmConfigurationIO method) parse_ifp() (SMArt.md.gromos.io.incl.IFPBlocksParser method) parse_line() (SMArt.incl.FileStream method) (SMArt.incl.StringStream method)

parse_mtb() (in module SMArt.md) (SMArt.md.gromos.io.incl.MTBBlocksParser method) parse_top() (in module SMArt.md) (SMArt.md.data_st.Topology method) parse_top_gm() (SMArt.md.gromacs.io.incl.gmTopologyIO method) parse_top_gr() (SMArt.md.gromos.io.incl.topBlocksParser method) parse_trc() (in module SMArt.md) (SMArt.md.data_st.Trajectory method) ParsedSegments (class in SMArt.md.gromacs.io.additional_classes) paths (class in SMArt.local_config) pdb2pqr() (SMArt.local_config.paths class method) PHYSICALCONSTANTS (SMArt.md.gromos.incl.GromosBlockNames attribute) point_mutation() (in module SMArt.alchemy) Position_r (class in SMArt.md.incl) prep_mbar_input() (in module SMArt.md.ana.pert_FE) prep_pdb() (in module SMArt.md.pipeline) prune() (SMArt.alchemy.MCS.MCS method) PTP_EDS_BlocksParser (class in SMArt.md.gromos.io.incl)

R

read_bar_data() (in module SMArt.md.gromacs.io.ana) read_bar_dhdl() (in module SMArt.md.gromos.io.ana) read_data() (in module SMArt.md.ana.incl) read_define() (SMArt.md.gromacs.io.incl.GromacsStream static method) read_exTI() (in module SMArt.md.gromos.io.ana) read_lines() (SMArt.md.gromacs.io.incl.GromacsStream method) read_undef() (SMArt.md.gromacs.io.incl.GromacsStream static method) read_xvg_data() (in module SMArt.md.gromacs.io.ana) Real (class in SMArt.md.ana.incl) red_d_Es_nfr_mul() (in module SMArt.md.ana.pert_FE) reduce() (SMArt.md.data_st.GeneralTopology method) reduce_cnf() (SMArt.md.data_st.Configuration method) reduce_dummy_estimates_1() (SMArt.alchemy.MCS.MCS static method) reduce_dummy_estimates_2() (SMArt.alchemy.MCS.MCS static method) reduce_top() (SMArt.md.data_st.Topology method) remove_edge() (SMArt.graph.incl.Graph method) remove_V_in_branch() (SMArt.alchemy.incl.TopGraphProperties method) renumber() (SMArt.md.data_st.Configuration method) (SMArt.md.data_st.Topology method)

renumber_container() (SMArt.incl.GeneralContainer method) replace_v_in_G() (in module SMArt.tests.test_graph.gen_test_graphs) report_nl_block_split_fnc() (SMArt.md.gromos.io.incl.GromosStream property) reset_dvalues() (SMArt.incl.Defaults method) reset_overlapping_segs() (in module SMArt.md.ana.pert_FE) reset_stream() (SMArt.incl.FileStream method) (SMArt.incl.StringStream method) Residue (class in SMArt.md.data_st) RMSD() (in module SMArt.md.ana.incl) rot() (in module SMArt.geometry) rot_2D() (in module SMArt.geometry) run_comm_n_mp() (in module SMArt.mp_fnc) run_gm_prog() (in module SMArt.md.wrappers) run_gr_prog() (in module SMArt.md.wrappers) run_intial_FE() (in module SMArt.md.pipeline) run_n_mp() (in module SMArt.mp_fnc) run_prog() (in module SMArt.md.wrappers)

S

seg_check_conv_calc_score() (in module SMArt.md.ana.pert_FE) set_adj_type_format() (SMArt.graph.incl.Graph method) set_curr_stack() (SMArt.md.gromacs.io.additional_classes.ParsedSegments method) set_defaults() (SMArt.incl.Defaults method) set_N_frames() (SMArt.md.data_st.Trajectory method) set_params() (SMArt.md.incl.InteractionType method) set_parents() (SMArt.graph.incl.GraphDirected method) set_print_warnings() (in module SMArt.incl) set_tolerance() (SMArt.md.ana.incl.Real class method) set_top_state() (SMArt.md.data_st.GeneralTopology method) SettleType (class in SMArt.md.incl) si_data_bar_dhdl() (in module SMArt.md.ana.pert_FE) si_skips_data_dEs() (in module SMArt.md.ana.pert_FE) sim() (in module SMArt.md.ana.incl) sim_err() (in module SMArt.md.ana.incl) SMArt module SMArt.alchemy module SMArt.alchemy.incl module SMArt.alchemy.MCS module SMArt.alchemy.top_matching_fnc module SMArt.geometry module SMArt.graph module SMArt.graph.incl module SMArt.incl module SMArt.local_config module SMArt.md module SMArt.md.ana module SMArt.md.ana.incl module SMArt.md.ana.pert_FE module SMArt.md.data_st module SMArt.md.gro2gro module SMArt.md.gro2gro.g2g module SMArt.md.gromacs module SMArt.md.gromacs.FF_DB module SMArt.md.gromacs.incl module SMArt.md.gromacs.io module SMArt.md.gromacs.io.additional_classes module

SMArt.md.gromacs.io.ana module SMArt.md.gromacs.io.gm_io_defaults module SMArt.md.gromacs.io.incl module SMArt.md.gromacs.io.incl_md_only module SMArt.md.gromacs.wrapper module SMArt.md.gromos module SMArt.md.gromos.FF_DB module SMArt.md.gromos.incl module SMArt.md.gromos.io module SMArt.md.gromos.io.ana module SMArt.md.gromos.io.incl module SMArt.md.gromos.md_functions module SMArt.md.gromos.md_functions.make_imd module SMArt.md.gromos.md_functions.make_job_list module SMArt.md.incl module SMArt.md.pipeline module SMArt.md.wrappers module SMArt.mp_fnc module SMArt.tests module SMArt.tests.test_alchemy module SMArt.tests.test_alchemy.test_MCS_options module SMArt.tests.test_alchemy.test_partial_ring_match module SMArt.tests.test_alchemy.test_point_mut module SMArt.tests.test_graph module SMArt.tests.test_graph.gen_test_graphs module sort_atoms() (SMArt.md.data_st.GeneralTopology method) sort_container() (SMArt.incl.GeneralContainer method) sort_G() (in module SMArt.tests.test_graph.gen_test_graphs) split_gen() (in module SMArt.incl) states2df() (SMArt.alchemy.incl.AlchemicalSolution_base method) StringStream (class in SMArt.incl) sub_graph() (SMArt.graph.incl.Graph method) sum_neigh_count() (SMArt.alchemy.incl.Branch method) sum_neigh_count_list() (SMArt.alchemy.incl.Branch static method) sum_neigh_count_list_branches() (SMArt.alchemy.incl.Branch static method)

T

test_chain_ring_max_PRM0() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) test_chain_ring_max_PRM1() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) test_chain_ring_max_PRM2() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) Test_MCS_max_partial_ring_match (class in SMArt.tests.test_alchemy.test_partial_ring_match) Test_MCS_RMSD (class in SMArt.tests.test_alchemy.test_MCS_options) test_ring_ring_max_PRM0() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) test_ring_ring_max_PRM1() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) test_ring_ring_max_PRM2() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) test_ring_ring_partial() (SMArt.tests.test_alchemy.test_partial_ring_match.Test_MCS_max_partial_ring_match method) test_RMDS_pairwise() (SMArt.tests.test_alchemy.test_MCS_options.Test_MCS_RMSD method) test_RMDS_simpe() (SMArt.tests.test_alchemy.test_MCS_options.Test_MCS_RMSD method) test_time() (in module SMArt.incl) Top_g2g (class in SMArt.md.gro2gro.g2g) top_gm2gr() (SMArt.md.gro2gro.g2g.Top_g2g method) top_gr2gm() (SMArt.md.gro2gro.g2g.Top_g2g method)

TopAtom (class in SMArt.md.data_st) TopBBdb (class in SMArt.md.data_st) topBlocksParser (class in SMArt.md.gromos.io.incl) topBlocksWriter (class in SMArt.md.gromos.io.incl) TopGraphProperties (class in SMArt.alchemy.incl) Topology (class in SMArt.md.data_st) Topology.Molecule (class in SMArt.md.data_st) Topology.MoleculeType (class in SMArt.md.data_st) TOPVERSION (SMArt.md.gromos.incl.GromosBlockNames attribute) Trajectory (class in SMArt.md.data_st) transform_top_index_atom() (SMArt.alchemy.incl.AlchemicalSolution_base method) transform_top_index_atom_pair() (SMArt.alchemy.incl.AlchemicalSolution_base method) trap() (in module SMArt.md.ana.incl) trap_err() (in module SMArt.md.ana.incl) TrjCnfBlocksParser (class in SMArt.md.gromos.io.incl) TrjCnfBlocksWriter (class in SMArt.md.gromos.io.incl)

U

update() (SMArt.md.data_st.ChargeGroup method) (SMArt.md.data_st.GeneralTopology.ChargeGroup method) update_adj() (SMArt.graph.incl.Graph method) update_copy_sol_toptp() (SMArt.alchemy.incl.AlchemicalSolution_base method) update_copy_sol_toptp_add_state() (SMArt.alchemy.incl.AlchemicalSolution_base method) update_LPs_1() (in module SMArt.md.ana.pert_FE) update_LPs_2() (in module SMArt.md.ana.pert_FE) update_LPs_call() (in module SMArt.md.ana.pert_FE) update_LPs_times() (in module SMArt.md.ana.pert_FE) update_neigh_count() (SMArt.alchemy.incl.TopGraphProperties static method) update_neigh_count_Nv_general() (SMArt.alchemy.incl.TopGraphProperties method)

update_neigh_count_Nv_VinB_general() (SMArt.alchemy.incl.TopGraphProperties method) update_neigh_count_VinB() (SMArt.alchemy.incl.TopGraphProperties class method) update_overlapping_segs() (in module SMArt.md.ana.pert_FE) update_ptp() (in module SMArt.alchemy.top_matching_fnc) update_ptp_excl_pair_atom_atom_pair() (in module SMArt.alchemy.top_matching_fnc) update_ptp_excl_pair_row_atom_pair() (in module SMArt.alchemy.top_matching_fnc) update_ptp_excl_pair_row_row_pair() (in module SMArt.alchemy.top_matching_fnc) update_ptp_interactions() (in module SMArt.alchemy.top_matching_fnc) update_solution() (SMArt.alchemy.MCS.MCS method) update_solutions() (SMArt.alchemy.MCS.MCS method) update_tried_pairs() (SMArt.alchemy.incl.AlchemicalSolution_base method)

V

vdWAtomPairType (class in SMArt.md.incl) vdWType (class in SMArt.md.incl) vec2abc() (SMArt.md.data_st.Box method) (SMArt.md.data_st.Configuration.Box method)

Vertex (class in SMArt.graph.incl) VirtualSite2Type (class in SMArt.md.incl) VirtualSite3Type (class in SMArt.md.incl) VirtualSite4Type (class in SMArt.md.incl) VirtualSitenType (class in SMArt.md.incl)

W

WARN write() (SMArt.md.gromacs.io.incl.GromacsStream method) write_bb() (SMArt.md.data_st.BBdb.BuildingBlock method) (SMArt.md.data_st.BuildingBlock method) write_block() (SMArt.md.gromos.io.incl.GromosStream method) write_cnf() (SMArt.md.data_st.Configuration method) write_define() (SMArt.md.gromacs.io.additional_classes.Define method) (SMArt.md.gromacs.io.incl.GromacsParser.Define method) write_defs() (SMArt.md.gromacs.io.gm_io_defaults.gm_FF_Defaults method) (SMArt.md.gromacs.io.incl.gmFFParser.gm_FF_Defaults method) write_EDS() (SMArt.md.gromos.io.incl.PTP_EDS_BlocksParser method) write_ff() (SMArt.md.data_st.FF method) write_ff_itp() (SMArt.md.gromacs.io.incl.gmFFWriter method) write_gr_excl() (SMArt.md.gromos.io.incl.grBBAtomWriting property) (SMArt.md.gromos.io.incl.grTOPAtomWriting method) write_gr_id() (SMArt.md.gromos.io.incl.grAtomWriting property) write_gr_pairs() (SMArt.md.gromos.io.incl.grTOPAtomWriting method) write_gr_prop() (SMArt.md.gromos.io.incl.grBBAtomWriting property) (SMArt.md.gromos.io.incl.grTOPAtomWriting property)

write_gro() (SMArt.md.gromacs.io.incl.gmConfigurationIO method) write_gromacs_format() (SMArt.md.gromacs.io.incl.GromacsWriter method) write_gromos_format() (SMArt.md.gromos.io.incl.GromosWriter method) write_ifp() (SMArt.md.gromos.io.incl.IFPBlocksWriter method) write_imd() (SMArt.md.data_st.MD_Parameters method) write_itp() (SMArt.md.gromacs.io.incl.gmFragmentMoleculeIO method) write_lines() (SMArt.md.gromacs.io.incl.GromacsStream method) write_molecule_type() (SMArt.md.gromacs.io.incl.gmFragmentMoleculeIO method) write_mtb() (SMArt.md.data_st.BBdb method) write_por() (SMArt.md.data_st.Configuration method) write_ptp() (SMArt.md.gromos.io.incl.topBlocksWriter method) write_rev_prop() (SMArt.md.gromos.io.incl.grTOPAtomWriting property) write_rev_ptp_top_names() (SMArt.md.gromos.io.incl.topBlocksWriter method) write_rpr() (SMArt.md.data_st.Configuration method) write_top() (SMArt.md.data_st.Topology method) write_top_gm() (SMArt.md.gromacs.io.incl.gmTopologyIO method) write_top_gr() (SMArt.md.gromos.io.incl.topBlocksWriter method) write_trc() (SMArt.md.gromos.io.incl.TrjCnfBlocksWriter method) write_trc_npz() (SMArt.md.gromos.io.incl.TrjCnfBlocksWriter method)