Index

A

add_bonds() (htpolynet.core.topology.Topology method) add_length_attribute() (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.topology.Topology method) all_atoms() (htpolynet.geometry.ring.RingList method) allowed_keys (htpolynet.analysis.analyze.Analyze attribute) Analyze (class in htpolynet.analysis.analyze) analyze (htpolynet.core.projectfilesystem.Dirs attribute) analyze() (in module htpolynet.analysis.analyze) analyze_topdirs (htpolynet.core.projectfilesystem.Dirs attribute) 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.geometry.bondlist.Bondlist method) are_cellndx_neighbors() (htpolynet.geometry.linkcell.Linkcell method) as_list() (htpolynet.geometry.bondlist.Bondlist method) assign() (htpolynet.geometry.linkcell.Linkcell 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.topology.Topology method) attenuate_pair_parameters() (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.core.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) cdproj() (htpolynet.core.projectfilesystem.ProjectFileSystem method) cdroot() (htpolynet.core.projectfilesystem.ProjectFileSystem method) 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) 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) checkin() (htpolynet.core.projectfilesystem.UserCache method) (in module htpolynet.core.projectfilesystem) checkout() (htpolynet.core.projectfilesystem.SystemLibrary method) (htpolynet.core.projectfilesystem.UserCache method) (htpolynet.core.projectfilesystem.UserLibrary method) (in module htpolynet.core.projectfilesystem)

Checkpoint (class in htpolynet.utils.checkpoint) claim_parent() (htpolynet.core.coordinates.Coordinates method) clusters() (in module htpolynet.analysis.utils) compute_E() (in module htpolynet.analysis.utils) compute_tg() (in module htpolynet.analysis.utils) Configuration (class in htpolynet.core.configuration) Coordinates (class in htpolynet.core.coordinates) copy() (htpolynet.geometry.ring.Ring method) copy_bond_parameters() (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) cwd() (in module htpolynet.core.projectfilesystem)

D

decrement_gro_attribute_by_attributes() (htpolynet.core.topocoord.TopoCoord 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.core.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) diag_plots() (in module htpolynet.analysis.plot) diagnostics_graphs() (in module htpolynet.analysis.plot) Dirs (class in htpolynet.core.projectfilesystem) do() (htpolynet.analysis.analyze.Analyze method) (htpolynet.analysis.postsim.PostSimMD method) do_capping() (htpolynet.cure.curecontroller.CureController method) do_cure() (htpolynet.core.runtime.Runtime method) do_densification() (htpolynet.core.runtime.Runtime method) do_E_plots() (in module htpolynet.analysis.plot) do_initialization() (htpolynet.core.runtime.Runtime method) do_iter() (htpolynet.cure.curecontroller.CureController method) do_postcure() (htpolynet.core.runtime.Runtime method) do_precure() (htpolynet.core.runtime.Runtime method) do_tg_plots() (in module htpolynet.analysis.plot) do_workflow() (htpolynet.core.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) exists() (htpolynet.core.projectfilesystem.SystemLibrary method) (htpolynet.core.projectfilesystem.UserCache method) (htpolynet.core.projectfilesystem.UserLibrary method) (in module htpolynet.core.projectfilesystem)

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_molecule_files() (in module htpolynet.core.projectfilesystem) filter() (htpolynet.geometry.ring.RingList 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.core.runtime.Runtime method) generate_product_name() (in module htpolynet.cure.reaction) generate_stereo_reactions() (in module htpolynet.cure.expandreactions) generate_stereoisomers() (htpolynet.core.molecule.Molecule method) generate_symmetry_reactions() (in module htpolynet.cure.expandreactions) 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_example_depot_location() (htpolynet.core.projectfilesystem.SystemLibrary method) get_example_names() (htpolynet.core.projectfilesystem.SystemLibrary method) get_gro_attribute_by_attributes() (htpolynet.core.topocoord.TopoCoord method) get_gro_attributelist_by_attributes() (htpolynet.core.topocoord.TopoCoord method) get_molecular_weight() (htpolynet.core.molecule.Molecule method) get_molecule_info() (in module htpolynet.core.projectfilesystem) get_molecule_names() (htpolynet.core.projectfilesystem.SystemLibrary method) (htpolynet.core.projectfilesystem.UserCache method) get_oneaways() (htpolynet.core.topocoord.TopoCoord 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_as_string() (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) go_proj() (in module htpolynet.core.projectfilesystem) go_root() (in module htpolynet.core.projectfilesystem) go_to() (htpolynet.core.projectfilesystem.ProjectFileSystem method) (in module htpolynet.core.projectfilesystem) 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.io.gro) GRX_GLOBALLY_UNIQUE (in module htpolynet.io.gro) GRX_UNSET_DEFAULTS (in module htpolynet.io.gro)

H

half_as_list() (htpolynet.geometry.bondlist.Bondlist 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.bondtemplate module htpolynet.core.configuration module htpolynet.core.coordinates module htpolynet.core.molecule module htpolynet.core.projectfilesystem module htpolynet.core.runtime module htpolynet.core.topocoord module htpolynet.core.topology module htpolynet.cure.chain module htpolynet.cure.curecontroller module htpolynet.cure.expandreactions module htpolynet.cure.reaction 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.io.gro module htpolynet.io.mol2 module htpolynet.io.pdb module htpolynet.utils.banner module htpolynet.utils.checkpoint module htpolynet.utils.dataframetools module htpolynet.utils.inputcheck module htpolynet.utils.logsetup 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() (htpolynet.core.projectfilesystem.SystemLibrary method) (htpolynet.core.projectfilesystem.UserCache method) (htpolynet.core.projectfilesystem.UserLibrary method) (in module htpolynet.core.projectfilesystem) (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.core.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) lib_setup() (in module htpolynet.core.projectfilesystem) 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)

load_files() (htpolynet.core.topocoord.TopoCoord method) load_top_gro() (htpolynet.core.molecule.Molecule method) local_data_searchpath() (in module htpolynet.core.projectfilesystem) local_resid_cluster() (htpolynet.core.topology.Topology method) logrotate() (in module htpolynet.core.runtime)

M

make_bonds() (htpolynet.core.molecule.Molecule method) (htpolynet.core.topocoord.TopoCoord method) make_neighborlists() (htpolynet.geometry.linkcell.Linkcell method) make_resid_graph() (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 (htpolynet.core.projectfilesystem.Dirs attribute) mdp_file() (htpolynet.core.projectfilesystem.Dirs static 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 htpolynet.analysis.analyze htpolynet.analysis.plot htpolynet.analysis.postsim htpolynet.analysis.utils htpolynet.core.bondtemplate htpolynet.core.configuration htpolynet.core.coordinates htpolynet.core.molecule htpolynet.core.projectfilesystem htpolynet.core.runtime htpolynet.core.topocoord htpolynet.core.topology htpolynet.cure.chain htpolynet.cure.curecontroller htpolynet.cure.expandreactions htpolynet.cure.reaction 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.io.gro htpolynet.io.mol2 htpolynet.io.pdb htpolynet.utils.banner htpolynet.utils.checkpoint htpolynet.utils.dataframetools htpolynet.utils.inputcheck htpolynet.utils.logsetup 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) molecules (htpolynet.core.projectfilesystem.Dirs attribute) molecules_inputs (htpolynet.core.projectfilesystem.Dirs attribute) molecules_parameterized (htpolynet.core.projectfilesystem.Dirs attribute) 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

nearby_atom_ids() (htpolynet.geometry.linkcell.Linkcell method) neighbor_cell_set() (htpolynet.geometry.linkcell.Linkcell method) 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

opts() (in module htpolynet.external.command)

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

P

param (htpolynet.cure.reaction.reaction_stage attribute) parameterize() (htpolynet.core.molecule.Molecule method) 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.geometry.bondlist.Bondlist method) passed (htpolynet.core.topocoord.BTRC attribute) pfs_setup() (in module htpolynet.core.projectfilesystem) pierced_by() (htpolynet.geometry.ring.Ring method) pierces() (htpolynet.core.coordinates.Coordinates method) pierces_ring() (htpolynet.core.topocoord.TopoCoord method) plots (htpolynet.core.projectfilesystem.Dirs attribute) plots() (in module htpolynet.analysis.plot) point_in_cellndx() (htpolynet.geometry.linkcell.Linkcell method) post_plots() (in module htpolynet.analysis.plot)

postsim (htpolynet.core.projectfilesystem.Dirs attribute) postsim() (in module htpolynet.analysis.postsim) postsim_density_evolution() (in module htpolynet.analysis.utils) postsim_topdirs (htpolynet.core.projectfilesystem.Dirs attribute) 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) proj() (in module htpolynet.core.projectfilesystem) proj_abspath() (in module htpolynet.core.projectfilesystem) ProjectFileSystem (class in htpolynet.core.projectfilesystem)

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.core.bondtemplate) read() (htpolynet.analysis.analyze.AnalyzeConfiguration class method) (htpolynet.analysis.postsim.PostsimConfiguration class method) (htpolynet.core.configuration.Configuration class method) (in module htpolynet.io.gro) (in module htpolynet.io.mol2) (in module htpolynet.io.pdb) 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_grx() (in module htpolynet.io.gro) read_mol2() (htpolynet.core.coordinates.Coordinates class method) (htpolynet.core.topocoord.TopoCoord method) read_pdb() (htpolynet.core.coordinates.Coordinates class 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) 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.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.topology.Topology method) return_bond_lengths() (htpolynet.core.coordinates.Coordinates method) (htpolynet.core.topocoord.TopoCoord method) reverse() (htpolynet.core.bondtemplate.BondTemplate method) (htpolynet.core.bondtemplate.ReactionBond method) rij() (htpolynet.core.coordinates.Coordinates method) Ring (class in htpolynet.geometry.ring) RingList (class in htpolynet.geometry.ring) root (htpolynet.core.projectfilesystem.SystemLibrary property) root() (in module htpolynet.core.projectfilesystem) 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() (in module htpolynet.external.command) run_topdirs (htpolynet.core.projectfilesystem.Dirs attribute) Runtime (class in htpolynet.core.runtime) runtime_defaults (htpolynet.core.runtime.Runtime attribute)

S

save_data() (htpolynet.core.runtime.Runtime method) scatter() (in module htpolynet.analysis.plot) 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_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) setup_logging() (in module htpolynet.utils.logsetup) 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) stringthings module subcoords() (htpolynet.core.coordinates.Coordinates method) subpath() (in module htpolynet.core.projectfilesystem) sw_setup() (in module htpolynet.external.software) swap_atom_names() (htpolynet.core.topocoord.TopoCoord method) system() (in module htpolynet.core.projectfilesystem) SystemLibrary (class in htpolynet.core.projectfilesystem) systems (htpolynet.core.projectfilesystem.Dirs attribute) systems_capping (htpolynet.core.projectfilesystem.Dirs attribute) systems_densification (htpolynet.core.projectfilesystem.Dirs attribute) systems_final (htpolynet.core.projectfilesystem.Dirs attribute) systems_init (htpolynet.core.projectfilesystem.Dirs attribute) systems_iter() (htpolynet.core.projectfilesystem.Dirs static method) systems_postcure (htpolynet.core.projectfilesystem.Dirs attribute) systems_precure (htpolynet.core.projectfilesystem.Dirs attribute)

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.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) UserCache (class in htpolynet.core.projectfilesystem) UserLibrary (class in htpolynet.core.projectfilesystem)

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() (in module htpolynet.io.gro) (in module htpolynet.io.mol2) 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() (in module htpolynet.io.gro) 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)