Index

A

add_bonds() (HTPolyNet.topology.Topology method) add_enumerated_angles() (in module HTPolyNet.unused_symmetry_stuff) add_enumerated_dihedrals() (in module HTPolyNet.unused_symmetry_stuff) add_length_attribute() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) add_restraints() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) adjacency_matrix() (HTPolyNet.bondlist.Bondlist method) adjust_charges() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) all_atoms() (HTPolyNet.ring.RingList method) allowed_keys (HTPolyNet.analyze.Analyze attribute) ambertools module ambertools (HTPolyNet.software.Software attribute) analyze module Analyze (class in HTPolyNet.analyze)

analyze() (in module HTPolyNet.analyze) analyze_sea() (in module HTPolyNet.unused_symmetry_stuff) AnalyzeConfiguration (class in HTPolyNet.analyze) AnalyzeDensity (class in HTPolyNet.analyze) AnalyzeFFV (class in HTPolyNet.analyze) append() (HTPolyNet.bondlist.Bondlist method) are_bonded() (HTPolyNet.bondlist.Bondlist method) (HTPolyNet.topocoord.TopoCoord method) are_cellndx_neighbors() (HTPolyNet.linkcell.Linkcell method) are_ldx_neighbors() (HTPolyNet.linkcell.Linkcell method) as_list() (HTPolyNet.bondlist.Bondlist method) atom_count() (HTPolyNet.topocoord.TopoCoord method) atomcount() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topology.Topology method) atoms_w_same_attribute_as() (HTPolyNet.molecule.Molecule method) attenuate_bond_parameters() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) attenuate_pair_parameters() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method)

B

banner module banner() (in module HTPolyNet.banner) basename() (HTPolyNet.curecontroller.cure_step method) bond_source_check() (HTPolyNet.topology.Topology method) bondchain_expand_reactions() (in module HTPolyNet.expandreactions) bondcycle_collective() (HTPolyNet.topocoord.TopoCoord method) bondlist module Bondlist (class in HTPolyNet.bondlist) bondtemplate module

BondTemplate (class in HTPolyNet.bondtemplate) bondtest() (HTPolyNet.topocoord.TopoCoord method) bondtest_df() (HTPolyNet.topocoord.TopoCoord method) BTRC (class in HTPolyNet.topocoord) build (HTPolyNet.reaction.reaction_stage attribute) build_interresidue_graph() (HTPolyNet.topology.Topology method) build_mdp() (HTPolyNet.postsim.PostSimAnneal method) (HTPolyNet.postsim.PostSimDeform method) (HTPolyNet.postsim.PostSimLadder method) (HTPolyNet.postsim.PostSimMD method) build_plots() (in module HTPolyNet.plot)

C

calculate_maximum_conversion() (HTPolyNet.configuration.Configuration method) cap (HTPolyNet.reaction.reaction_stage attribute) cap_bondsearch (HTPolyNet.curecontroller.cure_step attribute) cap_equilibrate (HTPolyNet.curecontroller.cure_step attribute) cap_relax (HTPolyNet.curecontroller.cure_step attribute) cap_update (HTPolyNet.curecontroller.cure_step attribute) cdproj() (HTPolyNet.projectfilesystem.ProjectFileSystem method) cdroot() (HTPolyNet.projectfilesystem.ProjectFileSystem method) cellndx_in_structure() (HTPolyNet.linkcell.Linkcell method) cellndx_of_ldx() (HTPolyNet.linkcell.Linkcell method) cellndx_of_point() (HTPolyNet.linkcell.Linkcell method) center_coords() (HTPolyNet.molecule.Molecule method) (HTPolyNet.topocoord.TopoCoord method) cfg (HTPolyNet.runtime.Runtime attribute) check_your_topology() (HTPolyNet.topocoord.TopoCoord method) checkbox() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) checkin() (HTPolyNet.projectfilesystem.RuntimeLibrary method) (in module HTPolyNet.projectfilesystem) checkout() (HTPolyNet.projectfilesystem.RuntimeLibrary method) (in module HTPolyNet.projectfilesystem) checkpoint module Checkpoint (class in HTPolyNet.checkpoint) claim_parent() (HTPolyNet.coordinates.Coordinates method) cli() (in module HTPolyNet.driver) clusters() (in module HTPolyNet.utils) command module Command (class in HTPolyNet.command) compute_E() (in module HTPolyNet.utils) compute_tg() (in module HTPolyNet.utils)

configuration module Configuration (class in HTPolyNet.configuration) constituents (HTPolyNet.configuration.Configuration attribute) coordinates module Coordinates (class in HTPolyNet.coordinates) copy() (HTPolyNet.ring.Ring method) copy_bond_parameters() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) copy_coords() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) corners_of_cellndx() (HTPolyNet.linkcell.Linkcell method) count_H() (HTPolyNet.topocoord.TopoCoord method) countTime module countTime() (in module HTPolyNet.countTime) create() (HTPolyNet.linkcell.Linkcell method) create_new_stereoisomers() (HTPolyNet.molecule.Molecule method) cure (HTPolyNet.reaction.reaction_stage attribute) cure_bondsearch (HTPolyNet.curecontroller.cure_step attribute) cure_drag (HTPolyNet.curecontroller.cure_step attribute) cure_equilibrate (HTPolyNet.curecontroller.cure_step attribute) cure_relax (HTPolyNet.curecontroller.cure_step attribute) cure_step (class in HTPolyNet.curecontroller) cure_update (HTPolyNet.curecontroller.cure_step attribute) curecontroller module CureController (class in HTPolyNet.curecontroller) curedict_defaults (HTPolyNet.curecontroller.CureController attribute) CureState (class in HTPolyNet.curecontroller) cwd() (in module HTPolyNet.projectfilesystem)

D

dataframetools module decrement_gro_attribute_by_attributes() (HTPolyNet.topocoord.TopoCoord method) decrement_z() (HTPolyNet.coordinates.Coordinates method) default_class (HTPolyNet.analyze.AnalyzeConfiguration attribute) default_classes (HTPolyNet.postsim.PostsimConfiguration attribute) default_directives (HTPolyNet.configuration.Configuration attribute) (HTPolyNet.reaction.Reaction attribute) default_edict (HTPolyNet.runtime.Runtime attribute) default_equilibration_sequence (HTPolyNet.curecontroller.CureController attribute) default_filename (HTPolyNet.checkpoint.Checkpoint attribute) default_params (HTPolyNet.analyze.Analyze attribute) (HTPolyNet.analyze.AnalyzeDensity attribute) (HTPolyNet.analyze.AnalyzeFFV attribute) (HTPolyNet.postsim.PostSimAnneal attribute) (HTPolyNet.postsim.PostSimDeform attribute) (HTPolyNet.postsim.PostSimLadder attribute) (HTPolyNet.postsim.PostSimMD attribute) delete_atoms() (HTPolyNet.bondlist.Bondlist method) (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) density() (HTPolyNet.topocoord.TopoCoord method)

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

E

enableCheckpoint() (in module HTPolyNet.checkpoint) encluster() (in module HTPolyNet.unused_symmetry_stuff) enumerate_1_4_pairs() (HTPolyNet.topocoord.TopoCoord method) equilibrate() (HTPolyNet.topocoord.TopoCoord method)

exists() (HTPolyNet.projectfilesystem.RuntimeLibrary method) (in module HTPolyNet.projectfilesystem) expandreactions module extract_molecule_reactions() (in module HTPolyNet.reaction)

F

failed_pierced_ring (HTPolyNet.topocoord.BTRC attribute) failed_shortcircuit (HTPolyNet.topocoord.BTRC attribute) fcc() (HTPolyNet.coordinates.Coordinates class method) fetch_example() (in module HTPolyNet.driver) fetch_molecule_files() (in module HTPolyNet.projectfilesystem) filter() (HTPolyNet.ring.RingList method) find_sacrificial_H() (HTPolyNet.coordinates.Coordinates method) find_template() (in module HTPolyNet.topocoord)

finished (HTPolyNet.curecontroller.cure_step attribute) flip_stereocenters() (HTPolyNet.molecule.Molecule method) (HTPolyNet.topocoord.TopoCoord method) from_ex() (HTPolyNet.topology.Topology class method) from_top_gro() (HTPolyNet.topocoord.TopoCoord class method) from_yaml() (HTPolyNet.checkpoint.Checkpoint class method) (HTPolyNet.curecontroller.CureState class method) fromDataFrame() (HTPolyNet.bondlist.Bondlist class method)

G

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

get_r() (in module HTPolyNet.reaction) get_resid_sets() (HTPolyNet.topocoord.TopoCoord method) get_resname() (HTPolyNet.molecule.Molecule method) get_row() (in module HTPolyNet.dataframetools) get_row_as_string() (in module HTPolyNet.dataframetools) get_row_attribute() (in module HTPolyNet.dataframetools) get_rows_w_attribute() (in module HTPolyNet.dataframetools) getVersions() (HTPolyNet.software.Software method) global_trace() (in module HTPolyNet.plot) gmx_command() (in module HTPolyNet.gromacs) gmx_energy_trace() (in module HTPolyNet.gromacs) gmx_traj_info() (in module HTPolyNet.gromacs) go_proj() (in module HTPolyNet.projectfilesystem) go_root() (in module HTPolyNet.projectfilesystem) go_to() (HTPolyNet.projectfilesystem.ProjectFileSystem method) (in module HTPolyNet.projectfilesystem) grab_files() (HTPolyNet.topocoord.TopoCoord method) graph() (HTPolyNet.bondlist.Bondlist method) graph_from_bondsfile() (in module HTPolyNet.utils) gro_attributes (HTPolyNet.coordinates.Coordinates attribute) gro_DataFrame() (HTPolyNet.topocoord.TopoCoord method) gro_from_trr() (in module HTPolyNet.gromacs) gromacs module gromacs_distance() (in module HTPolyNet.gromacs) grompp_and_mdrun() (HTPolyNet.topocoord.TopoCoord method) (in module HTPolyNet.gromacs) GRX_ATTRIBUTES (in module HTPolyNet.coordinates)

H

half_as_list() (HTPolyNet.bondlist.Bondlist method) has_atom_attributes() (HTPolyNet.coordinates.Coordinates method) homog_trans() (HTPolyNet.coordinates.Coordinates method) HTPolyNet.ambertools module HTPolyNet.analyze module HTPolyNet.banner module HTPolyNet.bondlist module HTPolyNet.bondtemplate module HTPolyNet.checkpoint module HTPolyNet.command module HTPolyNet.configuration module HTPolyNet.coordinates module HTPolyNet.countTime module HTPolyNet.curecontroller module HTPolyNet.dataframetools module HTPolyNet.driver module HTPolyNet.expandreactions module HTPolyNet.gromacs module

HTPolyNet.inputcheck module HTPolyNet.linkcell module HTPolyNet.matrix4 module HTPolyNet.molecule module HTPolyNet.plot module HTPolyNet.postsim module HTPolyNet.projectfilesystem module HTPolyNet.reaction module HTPolyNet.ring module HTPolyNet.runtime module HTPolyNet.software module HTPolyNet.stringthings module HTPolyNet.topocoord module HTPolyNet.topology module HTPolyNet.unused_symmetry_stuff module HTPolyNet.utils module

I

idx_mappers() (HTPolyNet.molecule.Molecule method) idxorder() (in module HTPolyNet.topology) increment_gro_attribute_by_attributes() (HTPolyNet.topocoord.TopoCoord method) info() (HTPolyNet.projectfilesystem.RuntimeLibrary method) (HTPolyNet.software.Software method) (in module HTPolyNet.driver) (in module HTPolyNet.projectfilesystem) (in module HTPolyNet.software) inherit_grx_attributes_from_molecules() (HTPolyNet.topocoord.TopoCoord method) init_molecule_graph() (in module HTPolyNet.plot) initial_composition (HTPolyNet.configuration.Configuration attribute)

initialize_molecule_rings() (HTPolyNet.molecule.Molecule method) initialize_monomer_grx_attributes() (HTPolyNet.molecule.Molecule method) injest_coordinates() (HTPolyNet.ring.Ring method) (HTPolyNet.ring.RingList method) input_check() (in module HTPolyNet.inputcheck) inputcheck module insert_molecules() (in module HTPolyNet.gromacs) interresidue_partners_of() (HTPolyNet.topocoord.TopoCoord method) is_cured() (HTPolyNet.curecontroller.CureController method) is_reactant() (in module HTPolyNet.reaction) is_reverse_of() (HTPolyNet.bondtemplate.BondTemplate method)

L

lawofcos() (in module HTPolyNet.ring) ldx_of_cellndx() (HTPolyNet.linkcell.Linkcell method) lib_setup() (in module HTPolyNet.projectfilesystem) linelen (HTPolyNet.command.Command attribute) linkcell module Linkcell (class in HTPolyNet.linkcell) linkcell_cleanup() (HTPolyNet.topocoord.TopoCoord method)

linkcell_initialize() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) linkcelltest() (HTPolyNet.coordinates.Coordinates method) load_files() (HTPolyNet.topocoord.TopoCoord method) load_top_gro() (HTPolyNet.molecule.Molecule method) local_data_searchpath() (in module HTPolyNet.projectfilesystem) local_resid_cluster() (HTPolyNet.topology.Topology method) logrotate() (in module HTPolyNet.runtime)

M

make_bonds() (HTPolyNet.molecule.Molecule method) (HTPolyNet.topocoord.TopoCoord method) make_memberlists() (HTPolyNet.linkcell.Linkcell method) make_neighborlists() (HTPolyNet.linkcell.Linkcell method) make_resid_graph() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) makes_shortcircuit() (HTPolyNet.topocoord.TopoCoord method) map_from_templates() (HTPolyNet.topocoord.TopoCoord method) Matrix4 (class in HTPolyNet.matrix4) maxspan() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) mdp_get() (in module HTPolyNet.gromacs) mdp_modify() (in module HTPolyNet.gromacs) mdp_to_dict() (in module HTPolyNet.gromacs) merge() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.molecule.Molecule method) (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) merge_ex() (HTPolyNet.topology.Topology method) merge_types() (HTPolyNet.topology.Topology method) mic() (HTPolyNet.coordinates.Coordinates method) minimize() (HTPolyNet.molecule.Molecule method) minimum_distance() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) minmax() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.topocoord.TopoCoord method) module ambertools analyze banner bondlist bondtemplate checkpoint command configuration coordinates countTime curecontroller dataframetools driver expandreactions gromacs HTPolyNet.ambertools HTPolyNet.analyze HTPolyNet.banner HTPolyNet.bondlist HTPolyNet.bondtemplate HTPolyNet.checkpoint HTPolyNet.command HTPolyNet.configuration HTPolyNet.coordinates HTPolyNet.countTime HTPolyNet.curecontroller HTPolyNet.dataframetools HTPolyNet.driver HTPolyNet.expandreactions HTPolyNet.gromacs HTPolyNet.inputcheck HTPolyNet.linkcell HTPolyNet.matrix4 HTPolyNet.molecule HTPolyNet.plot HTPolyNet.postsim HTPolyNet.projectfilesystem HTPolyNet.reaction HTPolyNet.ring HTPolyNet.runtime HTPolyNet.software HTPolyNet.stringthings HTPolyNet.topocoord HTPolyNet.topology HTPolyNet.unused_symmetry_stuff HTPolyNet.utils inputcheck linkcell molecule plot postsim projectfilesystem reaction ring runtime software stringthings topocoords topology unused_symmetry_stuff utils

mol2_atom_attributes (HTPolyNet.coordinates.Coordinates attribute) mol2_bond_attributes (HTPolyNet.coordinates.Coordinates attribute) mol2_bond_types (HTPolyNet.coordinates.Coordinates attribute) molecule module Molecule (class in HTPolyNet.molecule) molecules (HTPolyNet.configuration.Configuration attribute) molname_sequence_resnames() (in module HTPolyNet.reaction) multi_trace() (in module HTPolyNet.plot) mwbxl() (in module HTPolyNet.utils) my_logger() (in module HTPolyNet.stringthings)

N

neighbors_of_cellndx() (HTPolyNet.linkcell.Linkcell method) network_graph() (in module HTPolyNet.plot) New() (HTPolyNet.molecule.Molecule class method)

NewMolecule() (HTPolyNet.configuration.Configuration method) next_iter() (HTPolyNet.curecontroller.CureController method) null_check() (HTPolyNet.topology.Topology method)

O

overwrite_coords() (HTPolyNet.topocoord.TopoCoord method)

P

pack_example() (in module HTPolyNet.driver) param (HTPolyNet.reaction.reaction_stage attribute) parameterize() (HTPolyNet.molecule.Molecule method) (in module HTPolyNet.driver) parse() (HTPolyNet.analyze.AnalyzeConfiguration method) (HTPolyNet.configuration.Configuration method) (HTPolyNet.postsim.PostsimConfiguration method) parse_console_output() (HTPolyNet.analyze.Analyze method) parse_reaction_list() (in module HTPolyNet.reaction) partners_of() (HTPolyNet.bondlist.Bondlist method) (HTPolyNet.topocoord.TopoCoord method) passed (HTPolyNet.topocoord.BTRC attribute) pfs_setup() (in module HTPolyNet.projectfilesystem) pierced_by() (HTPolyNet.ring.Ring method) pierces() (HTPolyNet.coordinates.Coordinates method) pierces_ring() (HTPolyNet.topocoord.TopoCoord method) plot module plots() (in module HTPolyNet.plot) point_in_cellndx() (HTPolyNet.linkcell.Linkcell method)

populate() (HTPolyNet.linkcell.Linkcell method) populate_par() (HTPolyNet.linkcell.Linkcell method) post_plots() (in module HTPolyNet.plot) postsim module postsim() (in module HTPolyNet.postsim) postsim_density_evolution() (in module HTPolyNet.utils) PostSimAnneal (class in HTPolyNet.postsim) PostsimConfiguration (class in HTPolyNet.postsim) PostSimDeform (class in HTPolyNet.postsim) PostSimLadder (class in HTPolyNet.postsim) PostSimMD (class in HTPolyNet.postsim) predefined_classes (HTPolyNet.analyze.AnalyzeConfiguration attribute) prepare_new_bonds() (HTPolyNet.molecule.Molecule method) previously_parameterized() (HTPolyNet.molecule.Molecule method) product_sequence_resnames() (in module HTPolyNet.reaction) proj() (in module HTPolyNet.projectfilesystem) proj_abspath() (in module HTPolyNet.projectfilesystem) projectfilesystem module ProjectFileSystem (class in HTPolyNet.projectfilesystem)

R

reactant_resid_to_presid() (in module HTPolyNet.reaction) reaction module Reaction (class in HTPolyNet.reaction) reaction_stage (class in HTPolyNet.reaction) ReactionBond (class in HTPolyNet.bondtemplate) reactions (HTPolyNet.configuration.Configuration attribute) read() (HTPolyNet.analyze.AnalyzeConfiguration class method) (HTPolyNet.configuration.Configuration class method) (HTPolyNet.postsim.PostsimConfiguration class method) read_atomset_attributes() (HTPolyNet.coordinates.Coordinates method) read_checkpoint() (in module HTPolyNet.checkpoint) read_gro() (HTPolyNet.coordinates.Coordinates class method) (HTPolyNet.topocoord.TopoCoord method) read_gro_attributes() (HTPolyNet.molecule.Molecule method) (HTPolyNet.topocoord.TopoCoord method) read_mol2() (HTPolyNet.coordinates.Coordinates class method) (HTPolyNet.topocoord.TopoCoord method) read_top() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology class method) read_top_gro() (HTPolyNet.topocoord.TopoCoord method) read_tpx() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) reconcile_subcoords() (HTPolyNet.coordinates.Coordinates method) relax() (HTPolyNet.molecule.Molecule method) remap() (HTPolyNet.ring.Ring method) (HTPolyNet.ring.RingList method) remove_restraints() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method) rep_ex() (HTPolyNet.topology.Topology method) repeat_check() (in module HTPolyNet.topology) report_duplicate_types() (HTPolyNet.topology.Topology method)

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

S

sacH() (HTPolyNet.coordinates.Coordinates method) save_data() (HTPolyNet.runtime.Runtime method) scatter() (in module HTPolyNet.plot) searchlist_of_ldx() (HTPolyNet.linkcell.Linkcell method) Segment (class in HTPolyNet.ring) select_topology_type_option() (in module HTPolyNet.topology) set_atom_attribute() (HTPolyNet.coordinates.Coordinates method) set_atomset_attribute() (HTPolyNet.coordinates.Coordinates method) set_box() (HTPolyNet.coordinates.Coordinates method) set_gmx_preferences() (HTPolyNet.software.Software method) (in module HTPolyNet.software) set_gro_attribute() (HTPolyNet.molecule.Molecule method) (HTPolyNet.topocoord.TopoCoord method) set_gro_attribute_by_attributes() (HTPolyNet.topocoord.TopoCoord method) set_grx_attributes() (HTPolyNet.topocoord.TopoCoord method) set_origin() (HTPolyNet.molecule.Molecule method) set_row_attribute() (in module HTPolyNet.dataframetools) set_rows_attributes_from_dict() (in module HTPolyNet.dataframetools) set_sequence_from_coordinates() (HTPolyNet.molecule.Molecule method)

set_sequence_from_moldict() (HTPolyNet.molecule.Molecule method) setup() (HTPolyNet.curecontroller.CureController method) shift() (HTPolyNet.ring.Ring method) (HTPolyNet.ring.RingList method) shiftatomsidx() (HTPolyNet.topology.Topology method) show_z_report() (HTPolyNet.coordinates.Coordinates method) software module Software (class in HTPolyNet.software) spew_atom() (HTPolyNet.coordinates.Coordinates method) stringthings module subcoords() (HTPolyNet.coordinates.Coordinates method) subpath() (in module HTPolyNet.projectfilesystem) sw_setup() (in module HTPolyNet.software) swap_atom_names() (HTPolyNet.topocoord.TopoCoord method) symm() (in module HTPolyNet.unused_symmetry_stuff) system() (HTPolyNet.projectfilesystem.RuntimeLibrary class method) (in module HTPolyNet.projectfilesystem)

T

Title (HTPolyNet.configuration.Configuration attribute) to_string() (in module HTPolyNet.software) to_yaml() (HTPolyNet.checkpoint.Checkpoint method) TopoCoord (class in HTPolyNet.topocoord) topocoords module topology module Topology (class in HTPolyNet.topology) total_charge() (HTPolyNet.topology.Topology method) total_mass() (HTPolyNet.topocoord.TopoCoord method) (HTPolyNet.topology.Topology method)

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

U

unknown (HTPolyNet.curecontroller.cure_step attribute) unset (HTPolyNet.reaction.reaction_stage attribute) (HTPolyNet.topocoord.BTRC attribute) unused_symmetry_stuff module unwrap() (HTPolyNet.coordinates.Coordinates method) (HTPolyNet.ring.Ring method)

update() (HTPolyNet.bondlist.Bondlist method) update_topology_and_coordinates() (HTPolyNet.topocoord.TopoCoord method) update_zrecs() (HTPolyNet.molecule.Molecule method) user() (HTPolyNet.projectfilesystem.RuntimeLibrary class method) utils module

V

vacuum_minimize() (HTPolyNet.topocoord.TopoCoord method)

vacuum_simulate() (HTPolyNet.topocoord.TopoCoord method)

W

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

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

Y

yield_bonds() (in module HTPolyNet.molecule)

yield_bonds_as_df() (in module HTPolyNet.molecule)