Index

A

add_bonds() (htpolynet.core.topology.Topology method) add_length_attribute() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) add_restraints() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) adjacency_matrix() (htpolynet.geometry.bondlist.Bondlist method) adjust_charges() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) all_atoms() (htpolynet.geometry.ring.RingList method) allowed_keys (htpolynet.analysis.analyze.Analyze attribute) Analyze (class in htpolynet.analysis.analyze) analyze() (in module htpolynet.analysis.analyze) AnalyzeConfiguration (class in htpolynet.analysis.analyze) AnalyzeDensity (class in htpolynet.analysis.analyze)

AnalyzeFFV (class in htpolynet.analysis.analyze) append() (htpolynet.geometry.bondlist.Bondlist method) are_bonded() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.geometry.bondlist.Bondlist method) are_cellndx_neighbors() (htpolynet.geometry.linkcell.Linkcell method) are_ldx_neighbors() (htpolynet.geometry.linkcell.Linkcell method) as_list() (htpolynet.geometry.bondlist.Bondlist method) atom_count() (htpolynet.core.topocoord.TopoCoord method) atomcount() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topology.Topology method) atoms_w_same_attribute_as() (htpolynet.core.molecule.Molecule method) attenuate_bond_parameters() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) attenuate_pair_parameters() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method)

B

banner module banner() (in module htpolynet.utils.banner) basename() (htpolynet.cure.curecontroller.cure_step method) bond_source_check() (htpolynet.core.topology.Topology method) bondchain_expand_reactions() (in module htpolynet.cure.expandreactions) bondcycle_collective() (htpolynet.core.topocoord.TopoCoord method) Bondlist (class in htpolynet.geometry.bondlist) BondTemplate (class in htpolynet.cure.bondtemplate)

bondtest() (htpolynet.core.topocoord.TopoCoord method) bondtest_df() (htpolynet.core.topocoord.TopoCoord method) BTRC (class in htpolynet.core.topocoord) build (htpolynet.cure.reaction.reaction_stage attribute) build_interresidue_graph() (htpolynet.core.topology.Topology method) build_mdp() (htpolynet.analysis.postsim.PostSimAnneal method) (htpolynet.analysis.postsim.PostSimDeform method) (htpolynet.analysis.postsim.PostSimLadder method) (htpolynet.analysis.postsim.PostSimMD method) build_plots() (in module htpolynet.analysis.plot)

C

cap (htpolynet.cure.reaction.reaction_stage attribute) cap_bondsearch (htpolynet.cure.curecontroller.cure_step attribute) cap_equilibrate (htpolynet.cure.curecontroller.cure_step attribute) cap_relax (htpolynet.cure.curecontroller.cure_step attribute) cap_update (htpolynet.cure.curecontroller.cure_step attribute) cellndx_in_structure() (htpolynet.geometry.linkcell.Linkcell method) cellndx_of_ldx() (htpolynet.geometry.linkcell.Linkcell method) cellndx_of_point() (htpolynet.geometry.linkcell.Linkcell method) center_coords() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) cfg (htpolynet.cure.runtime.Runtime attribute) chain module Chain (class in htpolynet.cure.chain) chain_of() (htpolynet.cure.chain.ChainManager method) ChainManager (class in htpolynet.cure.chain) check_your_topology() (htpolynet.core.topocoord.TopoCoord method) checkbox() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) Checkpoint (class in htpolynet.utils.checkpoint) claim_parent() (htpolynet.core.coordinates.Coordinates method) cli() (in module htpolynet.driver) clusters() (in module htpolynet.analysis.utils) command module

Command (class in htpolynet.external.command) compute_E() (in module htpolynet.analysis.utils) compute_tg() (in module htpolynet.analysis.utils) Coordinates (class in htpolynet.core.coordinates) copy() (htpolynet.geometry.ring.Ring method) copy_bond_parameters() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) copy_coords() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) corners_of_cellndx() (htpolynet.geometry.linkcell.Linkcell method) count_H() (htpolynet.core.topocoord.TopoCoord method) create() (htpolynet.geometry.linkcell.Linkcell method) create_new_stereoisomers() (htpolynet.core.molecule.Molecule method) cure (htpolynet.cure.reaction.reaction_stage attribute) cure_bondsearch (htpolynet.cure.curecontroller.cure_step attribute) cure_drag (htpolynet.cure.curecontroller.cure_step attribute) cure_equilibrate (htpolynet.cure.curecontroller.cure_step attribute) cure_relax (htpolynet.cure.curecontroller.cure_step attribute) cure_step (class in htpolynet.cure.curecontroller) cure_update (htpolynet.cure.curecontroller.cure_step attribute) CureController (class in htpolynet.cure.curecontroller) curedict_defaults (htpolynet.cure.curecontroller.CureController attribute) CureState (class in htpolynet.cure.curecontroller)

D

decrement_gro_attribute_by_attributes() (htpolynet.core.topocoord.TopoCoord method) decrement_z() (htpolynet.core.coordinates.Coordinates method) default_class (htpolynet.analysis.analyze.AnalyzeConfiguration attribute) default_classes (htpolynet.analysis.postsim.PostsimConfiguration attribute) default_directives (htpolynet.cure.reaction.Reaction attribute) default_edict (htpolynet.cure.runtime.Runtime attribute) default_equilibration_sequence (htpolynet.cure.curecontroller.CureController attribute) default_filename (htpolynet.utils.checkpoint.Checkpoint attribute) default_params (htpolynet.analysis.analyze.Analyze attribute) (htpolynet.analysis.analyze.AnalyzeDensity attribute) (htpolynet.analysis.analyze.AnalyzeFFV attribute) (htpolynet.analysis.postsim.PostSimAnneal attribute) (htpolynet.analysis.postsim.PostSimDeform attribute) (htpolynet.analysis.postsim.PostSimLadder attribute) (htpolynet.analysis.postsim.PostSimMD attribute) delete_atoms() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) (htpolynet.geometry.bondlist.Bondlist method) density() (htpolynet.core.topocoord.TopoCoord method)

density_evolution() (in module htpolynet.analysis.utils) density_from_gro() (in module htpolynet.analysis.utils) detect_rings() (htpolynet.core.topology.Topology method) determine_sequence() (htpolynet.core.molecule.Molecule method) df_typeorder() (in module htpolynet.core.topology) dfrotate() (in module htpolynet.core.coordinates) diag_plots() (in module htpolynet.analysis.plot) diagnostics_graphs() (in module htpolynet.analysis.plot) do() (htpolynet.analysis.analyze.Analyze method) (htpolynet.analysis.postsim.PostSimMD method) do_capping() (htpolynet.cure.curecontroller.CureController method) do_cure() (htpolynet.cure.runtime.Runtime method) do_densification() (htpolynet.cure.runtime.Runtime method) do_E_plots() (in module htpolynet.analysis.plot) do_initialization() (htpolynet.cure.runtime.Runtime method) do_iter() (htpolynet.cure.curecontroller.CureController method) do_postcure() (htpolynet.cure.runtime.Runtime method) do_precure() (htpolynet.cure.runtime.Runtime method) do_tg_plots() (in module htpolynet.analysis.plot) do_workflow() (htpolynet.cure.runtime.Runtime method) dup_check() (htpolynet.core.topology.Topology method)

E

enableCheckpoint() (in module htpolynet.utils.checkpoint) enumerate_1_4_pairs() (htpolynet.core.topocoord.TopoCoord method)

equilibrate() (htpolynet.core.topocoord.TopoCoord method) extract_molecule_reactions() (in module htpolynet.cure.reaction)

F

failed_pierced_ring (htpolynet.core.topocoord.BTRC attribute) failed_shortcircuit (htpolynet.core.topocoord.BTRC attribute) fcc() (htpolynet.core.coordinates.Coordinates class method) fetch_example() (in module htpolynet.driver) filter() (htpolynet.geometry.ring.RingList method) find_sacrificial_H() (htpolynet.core.coordinates.Coordinates method) find_template() (in module htpolynet.core.topocoord) finished (htpolynet.cure.curecontroller.cure_step attribute)

flip_stereocenters() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) from_dataframe() (htpolynet.cure.chain.ChainManager method) from_ex() (htpolynet.core.topology.Topology class method) from_top_gro() (htpolynet.core.topocoord.TopoCoord class method) from_yaml() (htpolynet.cure.curecontroller.CureState class method) (htpolynet.utils.checkpoint.Checkpoint class method) fromDataFrame() (htpolynet.geometry.bondlist.Bondlist class method)

G

GAFFParameterize() (in module htpolynet.external.ambertools) generate() (htpolynet.core.molecule.Molecule method) generate_conformers() (htpolynet.core.molecule.Molecule method) generate_molecules() (htpolynet.cure.runtime.Runtime method) generate_product_name() (in module htpolynet.cure.reaction) generate_stereo_reactions() (in module htpolynet.core.molecule) generate_stereoisomers() (htpolynet.core.molecule.Molecule method) generate_symmetry_reactions() (in module htpolynet.core.molecule) geometric_center() (htpolynet.core.coordinates.Coordinates method) get_angles_dihedrals() (htpolynet.core.molecule.Molecule method) get_atom_attribute() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topology.Topology method) get_atoms_w_attribute() (htpolynet.core.coordinates.Coordinates method) get_atomtype() (htpolynet.core.topology.Topology method) get_bond_parameters() (htpolynet.core.topology.Topology method) get_bystanders() (htpolynet.core.topocoord.TopoCoord method) get_energy_menu() (in module htpolynet.external.gromacs) get_gro_attribute_by_attributes() (htpolynet.core.topocoord.TopoCoord method) get_gro_attributelist_by_attributes() (htpolynet.core.topocoord.TopoCoord method) get_idx() (htpolynet.core.coordinates.Coordinates method) get_molecular_weight() (htpolynet.core.molecule.Molecule method) get_oneaways() (htpolynet.core.topocoord.TopoCoord method) get_origin() (htpolynet.core.molecule.Molecule method)

get_R() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) get_r() (in module htpolynet.cure.reaction) get_resid_sets() (htpolynet.core.topocoord.TopoCoord method) get_resname() (htpolynet.core.molecule.Molecule method) get_row() (in module htpolynet.utils.dataframetools) get_row_as_string() (in module htpolynet.utils.dataframetools) get_row_attribute() (in module htpolynet.utils.dataframetools) get_rows_w_attribute() (in module htpolynet.utils.dataframetools) global_trace() (in module htpolynet.analysis.plot) gmx_command() (in module htpolynet.external.gromacs) gmx_energy_trace() (in module htpolynet.external.gromacs) gmx_traj_info() (in module htpolynet.external.gromacs) grab_files() (htpolynet.core.topocoord.TopoCoord method) graph() (htpolynet.geometry.bondlist.Bondlist method) graph_from_bondsfile() (in module htpolynet.analysis.utils) gro_attributes (htpolynet.core.coordinates.Coordinates attribute) gro_DataFrame() (htpolynet.core.topocoord.TopoCoord method) gro_from_trr() (in module htpolynet.external.gromacs) gromacs_distance() (in module htpolynet.external.gromacs) grompp_and_mdrun() (htpolynet.core.topocoord.TopoCoord method) (in module htpolynet.external.gromacs) GRX_ATTRIBUTES (in module htpolynet.core.coordinates)

H

half_as_list() (htpolynet.geometry.bondlist.Bondlist method) has_atom_attributes() (htpolynet.core.coordinates.Coordinates method) homog_trans() (htpolynet.core.coordinates.Coordinates method) htpolynet.analysis.analyze module htpolynet.analysis.plot module htpolynet.analysis.postsim module htpolynet.analysis.utils module htpolynet.core.coordinates module htpolynet.core.molecule module htpolynet.core.topocoord module htpolynet.core.topology module htpolynet.cure.bondtemplate module htpolynet.cure.chain module htpolynet.cure.curecontroller module htpolynet.cure.expandreactions module htpolynet.cure.reaction module

htpolynet.cure.runtime module htpolynet.driver module htpolynet.external.ambertools module htpolynet.external.command module htpolynet.external.gromacs module htpolynet.external.software module htpolynet.geometry.bondlist module htpolynet.geometry.linkcell module htpolynet.geometry.matrix4 module htpolynet.geometry.ring module htpolynet.utils.banner module htpolynet.utils.checkpoint module htpolynet.utils.dataframetools module htpolynet.utils.inputcheck module htpolynet.utils.stringthings module

I

idx_mappers() (htpolynet.core.molecule.Molecule method) idxorder() (in module htpolynet.core.topology) increment_gro_attribute_by_attributes() (htpolynet.core.topocoord.TopoCoord method) info() (in module htpolynet.driver) (in module htpolynet.external.software) inherit_grx_attributes_from_molecules() (htpolynet.core.topocoord.TopoCoord method) init_molecule_graph() (in module htpolynet.analysis.plot) initialize_molecule_rings() (htpolynet.core.molecule.Molecule method) initialize_monomer_grx_attributes() (htpolynet.core.molecule.Molecule method) injest_bond() (htpolynet.cure.chain.ChainManager method) injest_bonds() (htpolynet.cure.chain.ChainManager method)

injest_coordinates() (htpolynet.geometry.ring.Ring method) (htpolynet.geometry.ring.RingList method) injest_other() (htpolynet.cure.chain.ChainManager method) input_check() (in module htpolynet.utils.inputcheck) insert_molecules() (in module htpolynet.external.gromacs) interresidue_partners_of() (htpolynet.core.topocoord.TopoCoord method) is_cured() (htpolynet.cure.curecontroller.CureController method) is_head() (htpolynet.cure.chain.Chain method) is_reactant() (in module htpolynet.cure.reaction) is_reverse_of() (htpolynet.cure.bondtemplate.BondTemplate method) is_tail() (htpolynet.cure.chain.Chain method)

L

lawofcos() (in module htpolynet.geometry.ring) ldx_of_cellndx() (htpolynet.geometry.linkcell.Linkcell method) linelen (htpolynet.external.command.Command attribute) Linkcell (class in htpolynet.geometry.linkcell) linkcell_cleanup() (htpolynet.core.topocoord.TopoCoord method) linkcell_initialize() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method)

linkcelltest() (htpolynet.core.coordinates.Coordinates method) load_files() (htpolynet.core.topocoord.TopoCoord method) load_top_gro() (htpolynet.core.molecule.Molecule method) local_resid_cluster() (htpolynet.core.topology.Topology method) logrotate() (in module htpolynet.cure.runtime)

M

make_bonds() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) make_memberlists() (htpolynet.geometry.linkcell.Linkcell method) make_neighborlists() (htpolynet.geometry.linkcell.Linkcell method) make_resid_graph() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) makes_shortcircuit() (htpolynet.core.topocoord.TopoCoord method) map_from_templates() (htpolynet.core.topocoord.TopoCoord method) Matrix4 (class in htpolynet.geometry.matrix4) maxspan() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) mdp_get() (in module htpolynet.external.gromacs) mdp_modify() (in module htpolynet.external.gromacs) mdp_to_dict() (in module htpolynet.external.gromacs) merge() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) (htpolynet.cure.chain.Chain method) merge_ex() (htpolynet.core.topology.Topology method) merge_types() (htpolynet.core.topology.Topology method) mergechains() (htpolynet.cure.chain.ChainManager method) mic() (htpolynet.core.coordinates.Coordinates method) minimize() (htpolynet.core.molecule.Molecule method) minimum_distance() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) minmax() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) module banner chain command htpolynet.analysis.analyze htpolynet.analysis.plot htpolynet.analysis.postsim htpolynet.analysis.utils htpolynet.core.coordinates htpolynet.core.molecule htpolynet.core.topocoord htpolynet.core.topology htpolynet.cure.bondtemplate htpolynet.cure.chain htpolynet.cure.curecontroller htpolynet.cure.expandreactions htpolynet.cure.reaction htpolynet.cure.runtime htpolynet.driver htpolynet.external.ambertools htpolynet.external.command htpolynet.external.gromacs htpolynet.external.software htpolynet.geometry.bondlist htpolynet.geometry.linkcell htpolynet.geometry.matrix4 htpolynet.geometry.ring htpolynet.utils.banner htpolynet.utils.checkpoint htpolynet.utils.dataframetools htpolynet.utils.inputcheck htpolynet.utils.stringthings stringthings

mol2_atom_attributes (htpolynet.core.coordinates.Coordinates attribute) mol2_bond_attributes (htpolynet.core.coordinates.Coordinates attribute) mol2_bond_types (htpolynet.core.coordinates.Coordinates attribute) Molecule (class in htpolynet.core.molecule) molname_sequence_resnames() (in module htpolynet.cure.reaction) multi_trace() (in module htpolynet.analysis.plot) mwbxl() (in module htpolynet.analysis.utils) my_logger() (in module htpolynet.utils.stringthings)

N

neighbors_of_cellndx() (htpolynet.geometry.linkcell.Linkcell method) network_graph() (in module htpolynet.analysis.plot) New() (htpolynet.core.molecule.Molecule class method)

new_chain() (htpolynet.cure.chain.ChainManager method) next_iter() (htpolynet.cure.curecontroller.CureController method) null_check() (htpolynet.core.topology.Topology method)

O

overwrite_coords() (htpolynet.core.topocoord.TopoCoord method)

P

pack_example() (in module htpolynet.driver) param (htpolynet.cure.reaction.reaction_stage attribute) parameterize() (htpolynet.core.molecule.Molecule method) (in module htpolynet.driver) parse() (htpolynet.analysis.analyze.AnalyzeConfiguration method) (htpolynet.analysis.postsim.PostsimConfiguration method) parse_console_output() (htpolynet.analysis.analyze.Analyze method) parse_reaction_list() (in module htpolynet.cure.reaction) partners_of() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.geometry.bondlist.Bondlist method) passed (htpolynet.core.topocoord.BTRC attribute) pierced_by() (htpolynet.geometry.ring.Ring method) pierces() (htpolynet.core.coordinates.Coordinates method) pierces_ring() (htpolynet.core.topocoord.TopoCoord method) plots() (in module htpolynet.analysis.plot)

point_in_cellndx() (htpolynet.geometry.linkcell.Linkcell method) populate() (htpolynet.geometry.linkcell.Linkcell method) populate_par() (htpolynet.geometry.linkcell.Linkcell method) post_plots() (in module htpolynet.analysis.plot) postsim() (in module htpolynet.analysis.postsim) postsim_density_evolution() (in module htpolynet.analysis.utils) PostSimAnneal (class in htpolynet.analysis.postsim) PostsimConfiguration (class in htpolynet.analysis.postsim) PostSimDeform (class in htpolynet.analysis.postsim) PostSimLadder (class in htpolynet.analysis.postsim) PostSimMD (class in htpolynet.analysis.postsim) predefined_classes (htpolynet.analysis.analyze.AnalyzeConfiguration attribute) prepare_new_bonds() (htpolynet.core.molecule.Molecule method) previously_parameterized() (htpolynet.core.molecule.Molecule method) product_sequence_resnames() (in module htpolynet.cure.reaction)

R

reactant_resid_to_presid() (in module htpolynet.cure.reaction) Reaction (class in htpolynet.cure.reaction) reaction_stage (class in htpolynet.cure.reaction) ReactionBond (class in htpolynet.cure.bondtemplate) read() (htpolynet.analysis.analyze.AnalyzeConfiguration class method) (htpolynet.analysis.postsim.PostsimConfiguration class method) read_atomset_attributes() (htpolynet.core.coordinates.Coordinates method) read_checkpoint() (in module htpolynet.utils.checkpoint) read_gro() (htpolynet.core.coordinates.Coordinates class method) (htpolynet.core.topocoord.TopoCoord method) read_gro_attributes() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) read_mol2() (htpolynet.core.coordinates.Coordinates class method) (htpolynet.core.topocoord.TopoCoord method) read_top() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology class method) read_top_gro() (htpolynet.core.topocoord.TopoCoord method) read_tpx() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) reconcile_subcoords() (htpolynet.core.coordinates.Coordinates method) reindex() (htpolynet.cure.chain.ChainManager method) relax() (htpolynet.core.molecule.Molecule method) remap() (htpolynet.cure.chain.ChainManager method) (htpolynet.geometry.ring.Ring method) (htpolynet.geometry.ring.RingList method) remap_idx() (htpolynet.cure.chain.Chain method) remove_restraints() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) rep_ex() (htpolynet.core.topology.Topology method)

repeat_check() (in module htpolynet.core.topology) report_duplicate_types() (htpolynet.core.topology.Topology method) report_type() (htpolynet.core.topology.Topology method) required_keys (htpolynet.analysis.analyze.Analyze attribute) reset() (htpolynet.cure.curecontroller.CureController method) (htpolynet.cure.curecontroller.CureState method) reset_grx_attributes_from_idx_list() (htpolynet.core.topocoord.TopoCoord method) reset_idx_list_from_grx_attributes() (htpolynet.core.topocoord.TopoCoord method) reset_override_from_type() (htpolynet.core.topology.Topology method) reset_type() (htpolynet.core.topology.Topology method) resid_partners_of() (htpolynet.core.topocoord.TopoCoord method) restore_bond_parameters() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) return_bond_lengths() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) reverse() (htpolynet.cure.bondtemplate.BondTemplate method) (htpolynet.cure.bondtemplate.ReactionBond method) rij() (htpolynet.core.coordinates.Coordinates method) Ring (class in htpolynet.geometry.ring) RingList (class in htpolynet.geometry.ring) rot() (htpolynet.geometry.matrix4.Matrix4 method) rotate() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) rotate_axis() (htpolynet.geometry.matrix4.Matrix4 method) rotate_bond() (htpolynet.core.molecule.Molecule method) run() (htpolynet.external.command.Command method) (in module htpolynet.driver) Runtime (class in htpolynet.cure.runtime) runtime_defaults (htpolynet.cure.runtime.Runtime attribute)

S

sacH() (htpolynet.core.coordinates.Coordinates method) save_data() (htpolynet.cure.runtime.Runtime method) scatter() (in module htpolynet.analysis.plot) searchlist_of_ldx() (htpolynet.geometry.linkcell.Linkcell method) Segment (class in htpolynet.geometry.ring) select_topology_type_option() (in module htpolynet.core.topology) set_atom_attribute() (htpolynet.core.coordinates.Coordinates method) set_atomset_attribute() (htpolynet.core.coordinates.Coordinates method) set_box() (htpolynet.core.coordinates.Coordinates method) set_gmx_preferences() (in module htpolynet.external.software) set_gro_attribute() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) set_gro_attribute_by_attributes() (htpolynet.core.topocoord.TopoCoord method) set_grx_attributes() (htpolynet.core.topocoord.TopoCoord method) set_origin() (htpolynet.core.molecule.Molecule method) set_row_attribute() (in module htpolynet.utils.dataframetools)

set_rows_attributes_from_dict() (in module htpolynet.utils.dataframetools) set_sequence_from_coordinates() (htpolynet.core.molecule.Molecule method) set_sequence_from_moldict() (htpolynet.core.molecule.Molecule method) setup() (htpolynet.cure.curecontroller.CureController method) shift() (htpolynet.cure.chain.Chain method) (htpolynet.cure.chain.ChainManager method) (htpolynet.geometry.ring.Ring method) (htpolynet.geometry.ring.RingList method) shiftatomsidx() (htpolynet.core.topology.Topology method) show_z_report() (htpolynet.core.coordinates.Coordinates method) spew_atom() (htpolynet.core.coordinates.Coordinates method) stringthings module subcoords() (htpolynet.core.coordinates.Coordinates method) sw_setup() (in module htpolynet.external.software) swap_atom_names() (htpolynet.core.topocoord.TopoCoord method)

T

to_dataframe() (htpolynet.cure.chain.ChainManager method) to_string() (in module htpolynet.external.software) to_yaml() (htpolynet.utils.checkpoint.Checkpoint method) TopoCoord (class in htpolynet.core.topocoord) Topology (class in htpolynet.core.topology) total_charge() (htpolynet.core.topology.Topology method) total_mass() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) total_volume() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method)

trace() (in module htpolynet.analysis.plot) transform() (htpolynet.geometry.matrix4.Matrix4 method) transinvec() (htpolynet.geometry.matrix4.Matrix4 method) translate() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) (htpolynet.geometry.matrix4.Matrix4 method) transrot() (htpolynet.core.molecule.Molecule method) transvec() (htpolynet.geometry.matrix4.Matrix4 method) treadmill() (htpolynet.geometry.ring.Ring method) typedata() (in module htpolynet.core.topology) typeorder() (in module htpolynet.core.topology)

U

unknown (htpolynet.cure.curecontroller.cure_step attribute) unset (htpolynet.core.topocoord.BTRC attribute) (htpolynet.cure.reaction.reaction_stage attribute) unwrap() (htpolynet.core.coordinates.Coordinates method) (htpolynet.geometry.ring.Ring method)

update() (htpolynet.geometry.bondlist.Bondlist method) update_topology_and_coordinates() (htpolynet.core.topocoord.TopoCoord method) update_zrecs() (htpolynet.core.molecule.Molecule method)

V

vacuum_minimize() (htpolynet.core.topocoord.TopoCoord method)

vacuum_simulate() (htpolynet.core.topocoord.TopoCoord method)

W

wrap_coords() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) wrap_point() (htpolynet.core.coordinates.Coordinates method) write_atomset_attributes() (htpolynet.core.coordinates.Coordinates method) write_gro() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) write_gro_attributes() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method)

write_grx_attributes() (htpolynet.core.topocoord.TopoCoord method) write_mol2() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) write_top() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method) write_tpx() (htpolynet.core.topocoord.TopoCoord method) (htpolynet.core.topology.Topology method)

Y

yield_bonds() (in module htpolynet.core.molecule)

yield_bonds_as_df() (in module htpolynet.core.molecule)