Index

A

a (polymerist.maths.lattices.bravais.LatticeParameters attribute) ABE10Charger (class in polymerist.mdtools.openfftools.partialcharge.molchargers) ABERRANT_RDKIT_ATOM_SMARTS (in module polymerist.polymers.monomers.specification) Accumulate (class in polymerist.polymers.smidgelib.smidgeread) Accumulator (class in polymerist.mdtools.openfftools.partialcharge.rescharge.calculation) add_monomer() (polymerist.polymers.monomers.MonomerGroup method) (polymerist.polymers.monomers.repr.MonomerGroup method) add_type_serializer() (polymerist.genutils.fileutils.jsonio.MultiTypeSerializer method) (polymerist.genutils.fileutils.jsonio.serialize.MultiTypeSerializer method) ADDED (polymerist.rdutils.reactions.BondChange attribute) (polymerist.rdutils.reactions.reactinfo.BondChange attribute) affine_transformation() (polymerist.maths.lattices.coordinates.Coordinates method) AffineMatrix (in module polymerist.maths.linearalg.affine) aggregate_atom_prop() (in module polymerist.rdutils.rdprops.atomprops) aggregate_bond_prop() (in module polymerist.rdutils.rdprops.bondprops) ALL_AVAILABLE_TKWRAPPERS (in module polymerist.mdtools.openfftools) ALL_IMPORTABLE_TKWRAPPERS (in module polymerist.mdtools.openfftools) allow_openff_units() (in module polymerist.mdtools.openfftools.unitsys) allow_openmm_units() (in module polymerist.mdtools.openfftools.unitsys) allow_pathlib_paths() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) allow_string_paths() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) alpha (polymerist.maths.lattices.bravais.LatticeParameters attribute) AlreadySolvated alt_sign() (in module polymerist.maths.combinatorics.numbers) alternating_group() (polymerist.maths.combinatorics.permutations.Permutation class method) ALWAYS_FALSE_FILTER (in module polymerist.genutils.filters) ALWAYS_TRUE_FILTER (in module polymerist.genutils.filters) ANDERSEN (polymerist.mdtools.openmmtools.thermo.Thermostat attribute) angles (polymerist.maths.lattices.bravais.LatticeParameters property) annotate_atom_ids() (in module polymerist.rdutils.rdprops.atomprops) annotate_atom_prop() (in module polymerist.rdutils.rdprops.atomprops) annotate_bond_ids() (in module polymerist.rdutils.rdprops.bondprops) annotate_bond_prop() (in module polymerist.rdutils.rdprops.bondprops) AnnotatedReaction (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.reactions) append_to_json() (in module polymerist.genutils.fileutils.jsonio) (in module polymerist.genutils.fileutils.jsonio.update) apply_atom_info_to_product() (polymerist.rdutils.reactions.AnnotatedReaction static method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction static method) apply_bond_info_to_product() (polymerist.rdutils.reactions.AnnotatedReaction static method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction static method)

apply_residue_charges() (in module polymerist.mdtools.openfftools.partialcharge.rescharge) (in module polymerist.mdtools.openfftools.partialcharge.rescharge.calculation) apply_state_to_context() (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.state) are_bondable() (polymerist.rdutils.bonding.portlib.Port static method) Array4x4 (in module polymerist.maths.linearalg.affine) as_cycle() (polymerist.maths.combinatorics.permutations.Permutation method) as_identity (polymerist.maths.combinatorics.permutations.Permutation property) as_proper() (polymerist.maths.fractions.ratios.Rational method) ascents (polymerist.maths.combinatorics.permutations.Permutation property) ascii_printable (in module polymerist.genutils.textual) asiterable() (in module polymerist.genutils.iteration) aspath() (in module polymerist.genutils.fileutils.pathutils) assemble_path() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) assemble_rxn() (polymerist.rdutils.reactions.assembly.ReactionAssembler method) (polymerist.rdutils.reactions.ReactionAssembler method) assign_atom_map_nums_by_ids() (in module polymerist.rdutils.chemlabel) assign_contiguous_atom_map_nums() (in module polymerist.rdutils.chemlabel) assign_ordered_atom_map_nums() (in module polymerist.rdutils.chemlabel) assign_props_from_dict() (in module polymerist.rdutils.rdprops) asstrpath() (in module polymerist.genutils.fileutils.pathutils) atom_adjoins_linker (in module polymerist.rdutils.selection) atom_ids_with_prop() (in module polymerist.rdutils.rdprops.atomprops) atom_idxs_by_map_numbers() (in module polymerist.rdutils.chemlabel) atom_is_mapped (in module polymerist.rdutils.selection) atom_label_width (polymerist.molfiles.pdb.pdbatoms.SerialAtomLabeller attribute) (polymerist.molfiles.pdb.SerialAtomLabeller attribute) atom_neighbors (in module polymerist.rdutils.selection) atom_neighbors_by_condition() (in module polymerist.rdutils.selection) AtomCondition (in module polymerist.rdutils.selection) atomic_time (in module polymerist.unitutils.extraunits) atomic_time_base_unit (in module polymerist.unitutils.extraunits) AtomLike (in module polymerist.rdutils.selection) atoms (in module polymerist.rdutils.selection) atoms_by_condition() (in module polymerist.rdutils.selection) AtomTraceInfo (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.reactinfo) attr_val (in module polymerist.unitutils.unitstr) autoreduce (polymerist.maths.fractions.ratios.Rational attribute) available_force_fields_summary() (in module polymerist.mdtools.openfftools) average (polymerist.mdtools.openfftools.partialcharge.rescharge.calculation.Accumulator property) axial_angles() (polymerist.maths.lattices.bravais.LatticeParameters method) axial_lengths (polymerist.maths.lattices.bravais.LatticeParameters property)

B

b (polymerist.maths.lattices.bravais.LatticeParameters attribute) BadNumberReactants BALANCED (polymerist.genutils.textual.delimiters.DelimiterBalanceState attribute) Barostat (class in polymerist.mdtools.openmmtools.thermo) barostat (polymerist.mdtools.openmmtools.thermo.BarostatParameters attribute) barostat_params (polymerist.mdtools.openmmtools.thermo.ThermoParameters attribute) BarostatParameters (class in polymerist.mdtools.openmmtools.thermo) BarostatSerializer (in module polymerist.mdtools.openmmtools.thermo) base (polymerist.maths.numbersys.commonbases.FixedRadixNumberSystem attribute) (polymerist.maths.numbersys.FixedRadixNumberSystem attribute) base_bond_cost (polymerist.rdutils.reactions.CutMinimumCostBondsStrategy attribute) (polymerist.rdutils.reactions.fragment.CutMinimumCostBondsStrategy attribute) base_sys (in module polymerist.maths.numbersys) bases (polymerist.maths.numbersys.positional.PositionalNumberingSystem attribute) bell() (in module polymerist.maths.combinatorics.numbers) bernoulli() (in module polymerist.maths.combinatorics.numbers) bernoulli_up_to() (in module polymerist.maths.combinatorics.numbers) best_rational_approx() (in module polymerist.maths.fractions.continued) beta (polymerist.maths.lattices.bravais.LatticeParameters attribute) bijective_atom_id_iter() (in module polymerist.rdutils.rdprops.bijection) bin_index_map (polymerist.genutils.sequences.discernment.inventory.SymbolInventory property) (polymerist.genutils.sequences.discernment.SymbolInventory property) binomial_coeff() (in module polymerist.maths.combinatorics.numbers) bits (polymerist.genutils.sequences.similarity.edits.EditOperation property) block_size (polymerist.polymers.building.sequencing.LinearCopolymerSequencer property) bond (polymerist.rdutils.bonding.portlib.Port attribute) bond_adjoins_linker (in module polymerist.rdutils.reactions.fragment) BOND_CHANGE_PROPNAME (in module polymerist.rdutils.reactions.reactinfo) bond_change_type (polymerist.rdutils.reactions.BondTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.BondTraceInfo attribute) bond_condition_by_atom_condition_factory() (in module polymerist.rdutils.selection) bond_cost_keyword (polymerist.rdutils.reactions.CutMinimumCostBondsStrategy attribute) (polymerist.rdutils.reactions.fragment.CutMinimumCostBondsStrategy attribute) bond_derangement (polymerist.rdutils.reactions.assembly.ReactionAssembler attribute) (polymerist.rdutils.reactions.ReactionAssembler attribute) bond_discounts (polymerist.rdutils.reactions.CutMinimumCostBondsStrategy attribute) (polymerist.rdutils.reactions.fragment.CutMinimumCostBondsStrategy attribute) bond_ids_with_prop() (in module polymerist.rdutils.rdprops.bondprops) bond_info (polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister attribute) (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) BOND_INITIALIZERS (in module polymerist.smileslib.primitives) bond_is_newly_formed() (in module polymerist.rdutils.reactions.fragment) BOND_PRIMITIVES (in module polymerist.smileslib.primitives) BOND_PRIMITIVES_FOR_REGEX (in module polymerist.polymers.smidgelib) (in module polymerist.smileslib.primitives)

bond_str (polymerist.polymers.smidgelib.MonomerGraphBondInfo property) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo property) BOND_TOKEN_RE (in module polymerist.polymers.smidgelib) (in module polymerist.polymers.smidgelib.smidgebonds) bondable_flavors (polymerist.rdutils.bonding.portlib.Port attribute) BondChange (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.reactinfo) BondCondition (in module polymerist.rdutils.selection) bonded_pairs() (in module polymerist.rdutils.selection) BondEnd (class in polymerist.polymers.smidgelib.smidgeread) BondInfoDict (in module polymerist.mdtools.openfftools.partition) BondLike (in module polymerist.rdutils.selection) BondOrderModificationError bonds (in module polymerist.rdutils.selection) bonds_between_mapped_atoms() (in module polymerist.rdutils.selection) bonds_by_condition() (in module polymerist.rdutils.selection) BondStart (class in polymerist.polymers.smidgelib.smidgeread) BondTraceInfo (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.reactinfo) bondtype (polymerist.polymers.smidgelib.MonomerGraphBondInfo attribute) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo attribute) BONDTYPE_ATTR (polymerist.polymers.monographs.MonomerGraph attribute) BoundingBox (class in polymerist.maths.lattices.coordinates) box_vectors_flexible() (in module polymerist.mdtools.openfftools.boxvectors) BoxVectorError BoxVectors (in module polymerist.mdtools.openfftools.boxvectors) BoxVectorsQuantity (in module polymerist.mdtools.openfftools.boxvectors) BranchEnd (class in polymerist.polymers.smidgelib.smidgeread) (class in polymerist.polymers.smidgelib.smidgewrite) BranchStart (class in polymerist.polymers.smidgelib.smidgeread) (class in polymerist.polymers.smidgelib.smidgewrite) bridgehead (polymerist.rdutils.bonding.portlib.Port attribute) bridgehead_atom_ids() (in module polymerist.rdutils.reactions.fragment) BROWNIAN (polymerist.mdtools.openmmtools.thermo.Thermostat attribute) build_linear_polymer() (in module polymerist.polymers.building) (in module polymerist.polymers.building.linear) BUILTIN_TYPES (in module polymerist.genutils.typetools.categorical) byproduct_map_nums (polymerist.rdutils.reactions.assembly.ReactionAssembler property) (polymerist.rdutils.reactions.ReactionAssembler property) byproduct_relabeling (polymerist.rdutils.reactions.assembly.ReactionAssembler property) (polymerist.rdutils.reactions.ReactionAssembler property) byproducts (polymerist.rdutils.reactions.assembly.ReactionAssembler attribute) (polymerist.rdutils.reactions.ReactionAssembler attribute)

C

C (in module polymerist.genutils.decorators.classmod) (in module polymerist.genutils.fileutils.jsonio.jsonify) c (polymerist.maths.lattices.bravais.LatticeParameters attribute) camel_case_to_snake_case() (in module polymerist.genutils.textual.casing) canonical_SMILES_from_mol() (in module polymerist.smileslib) (in module polymerist.smileslib.cleanup) canvas() (in module polymerist.polymerist) capacity (polymerist.maths.lattices.integral.CubicIntegerLattice property) cartesian_grid() (in module polymerist.genutils.iteration) catalan() (in module polymerist.maths.combinatorics.numbers) category (polymerist.smileslib.functgroups.FnGroupSMARTSEntry attribute) category_desc (polymerist.smileslib.functgroups.FnGroupSMARTSEntry attribute) CENTER (polymerist.genutils.textual.prettyprint.Justification attribute) centroid (polymerist.maths.lattices.coordinates.Coordinates property) ChainNew (class in polymerist.polymers.smidgelib.smidgeread) chains (polymerist.polymers.monographs.MonomerGraph property) charge (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) CHARGE_METHODS_BY_TOOLKIT (in module polymerist.mdtools.openfftools) (in module polymerist.mdtools.openfftools.partialcharge) charge_molecule() (polymerist.mdtools.openfftools.partialcharge.molchargers.MolCharger method) ChargedResidue (class in polymerist.mdtools.openfftools.partialcharge.rescharge) (class in polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes) ChargeMap (in module polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes) ChargeMismatch ChargeRedistributionStrategy (class in polymerist.mdtools.openfftools.partialcharge.rescharge) (class in polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution) charges (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargedResidue attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargesByResidue attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargedResidue attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargesByResidue attribute) charges_by_residue (polymerist.mdtools.openfftools.partialcharge.rescharge.interface.LibraryCharger attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.LibraryCharger attribute) ChargesByResidue (class in polymerist.mdtools.openfftools.partialcharge.rescharge) (class in polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes) check_balanced_delimiters() (in module polymerist.genutils.textual.delimiters) CheckIsVisitedNode (class in polymerist.polymers.smidgelib.smidgewrite) checkpoint_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) chem_info_from_match() (in module polymerist.polymers.monomers.specification) ChemDBServiceQueryStrategy (class in polymerist.smileslib.chemdbqueries) chemical_graph() (in module polymerist.rdutils.rdgraphs) ChemicalDataQueryFailed children (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler attribute) children() (polymerist.genutils.fileutils.filetree.PathToNodeCorrespondence method) (polymerist.genutils.importutils.pkgiter.ModuleToNodeCorrespondence method) (polymerist.genutils.trees.NodeCorrespondence method) (polymerist.genutils.trees.treebase.NodeCorrespondence method) CHK_REPORTERS (in module polymerist.mdtools.openmmtools.reporters) choice_bins (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample attribute) choice_solutions_exist() (polymerist.genutils.sequences.discernment.DISCERNMENTSolver method) (polymerist.genutils.sequences.discernment.enumeration.DISCERNMENTSolver method) choose (in module polymerist.maths.combinatorics.numbers) cirpy_error (in module polymerist.smileslib.chemdbqueries) class_reg (in module polymerist.genutils.typetools.categorical) clear() (polymerist.genutils.containers.UnorderedRegistry method) clear_atom_annotations() (in module polymerist.rdutils.rdprops.atomprops) clear_atom_isotopes() (in module polymerist.rdutils.chemlabel) clear_atom_map_nums() (in module polymerist.rdutils.chemlabel)

clear_atom_props() (in module polymerist.rdutils.rdprops.atomprops) clear_bond_annotations() (in module polymerist.rdutils.rdprops.bondprops) clear_bond_props() (in module polymerist.rdutils.rdprops.bondprops) clear_dir() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.filetree) clear_highlights() (in module polymerist.rdutils.rdkdraw) Color (in module polymerist.graphics.colors) ColorMapper (in module polymerist.graphics.plotutils) combined_rdmol() (in module polymerist.rdutils.bonding) COMMON_BASES (in module polymerist.maths.numbersys) COMMON_DELIMITERS (in module polymerist.genutils.textual.delimiters) COMMON_UNIT_LATTICE_VECTORS (in module polymerist.maths.lattices.bravais) compile_argfree_getable_attrs() (in module polymerist.genutils.attrs) compile_functional_group_inventory() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) compile_tree_factory() (in module polymerist.genutils.trees) (in module polymerist.genutils.trees.treebase) compliant_atom_query_from_info() (in module polymerist.polymers.monomers.specification) compliant_atom_query_from_rdatom() (in module polymerist.polymers.monomers.specification) compliant_atom_query_from_re_match() (in module polymerist.polymers.monomers.specification) COMPLIANT_ATOM_SMARTS (in module polymerist.polymers.monomers.specification) compliant_mol_SMARTS() (in module polymerist.polymers.monomers) (in module polymerist.polymers.monomers.specification) compose (polymerist.maths.combinatorics.permutations.Permutation attribute) compute_residue_charges() (in module polymerist.mdtools.openfftools.partialcharge.rescharge) (in module polymerist.mdtools.openfftools.partialcharge.rescharge.calculation) compute_wf_matrix() (in module polymerist.genutils.sequences.similarity.edits) const_with_units (in module polymerist.unitutils.physconsts) contains_word() (polymerist.genutils.sequences.discernment.inventory.SymbolInventory method) (polymerist.genutils.sequences.discernment.SymbolInventory method) continuant_matrix() (in module polymerist.maths.fractions.continued) continued_fraction_to_continuants() (in module polymerist.maths.fractions.continued) contributions() (polymerist.polymers.monomers.MonomerGroup method) (polymerist.polymers.monomers.repr.MonomerGroup method) Coordinates (class in polymerist.maths.lattices.coordinates) copy() (polymerist.maths.combinatorics.permutations.Cycle method) (polymerist.maths.combinatorics.permutations.Permutation method) (polymerist.polymers.building.sequencing.LinearCopolymerSequencer method) copy_atom_metadata() (in module polymerist.mdtools.openfftools.topology) copy_node_unbound() (in module polymerist.genutils.trees.treecopy) copy_rdobj_props() (in module polymerist.rdutils.rdprops) copy_tree() (in module polymerist.genutils.trees) (in module polymerist.genutils.trees.treecopy) count (polymerist.mdtools.openfftools.partialcharge.rescharge.calculation.Accumulator attribute) count_connected_labelled_graphs() (in module polymerist.maths.combinatorics.numbers) count_labelled_graphs() (in module polymerist.maths.combinatorics.numbers) counts_along_dims (polymerist.maths.lattices.integral.CubicIntegerLattice attribute) counts_along_dims_as_str() (polymerist.maths.lattices.integral.CubicIntegerLattice method) crop_borders() (in module polymerist.graphics.imageutils) CubicIntegerLattice (class in polymerist.maths.lattices.integral) curr_idx (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) curr_token (polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister attribute) CutMinimumCostBondsStrategy (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.fragment) Cycle (class in polymerist.maths.combinatorics.permutations) cycle_index() (polymerist.maths.combinatorics.permutations.Permutation static method) cycle_index_sym() (polymerist.maths.combinatorics.permutations.Cycle static method) cycle_items() (in module polymerist.genutils.sequences) (in module polymerist.genutils.sequences.seqops) cycle_type (polymerist.maths.combinatorics.permutations.Permutation property) cycle_type() (polymerist.maths.combinatorics.permutations.Cycle static method) cycles (polymerist.maths.combinatorics.permutations.Permutation property) cycles_are_disjoint() (polymerist.maths.combinatorics.permutations.Cycle static method) cycles_canonical (polymerist.maths.combinatorics.permutations.Permutation property) cycles_produce_partition() (polymerist.maths.combinatorics.permutations.Cycle static method) cyclic_group() (polymerist.maths.combinatorics.permutations.Permutation class method)

D

D (in module polymerist.genutils.typetools.numpytypes) dataclass_serializer_factory() (in module polymerist.genutils.fileutils.jsonio.jsonify) day (polymerist.genutils.duration.Duration attribute) decode() (polymerist.genutils.fileutils.jsonio.PathSerializer static method) (polymerist.genutils.fileutils.jsonio.QuantitySerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.NDArraySerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.PathSerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.QuantitySerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.TypeSerializer static method) (polymerist.genutils.fileutils.jsonio.TypeSerializer static method) (polymerist.polymers.monographs.MonomerGraphSerializer static method) decoder_hook() (polymerist.genutils.fileutils.jsonio.MultiTypeSerializer method) (polymerist.genutils.fileutils.jsonio.serialize.MultiTypeSerializer method) (polymerist.genutils.fileutils.jsonio.serialize.TypeSerializer class method) (polymerist.genutils.fileutils.jsonio.TypeSerializer class method) Decorator (in module polymerist.genutils.decorators.meta) decrease_bond_order() (in module polymerist.rdutils.bonding.dissolution) deepcopy() (polymerist.genutils.sequences.discernment.inventory.SymbolInventory method) (polymerist.genutils.sequences.discernment.SymbolInventory method) DEFAULT_ATOM_PROPS (in module polymerist.rdutils.rdgraphs) DEFAULT_BOND_PROPS (in module polymerist.rdutils.rdgraphs) DEFAULT_BONDTYPE (polymerist.polymers.smidgelib.MonomerGraphBondInfo attribute) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo attribute) default_elem_idx (polymerist.molfiles.pdb.pdbatoms.SerialAtomLabeller attribute) (polymerist.molfiles.pdb.SerialAtomLabeller attribute) DEFAULT_EPS (in module polymerist.maths.fractions.continued) DEFAULT_FLAVOR (polymerist.polymers.smidgelib.MonomerGraphBondInfo attribute) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo attribute) DEFAULT_INT_TYPE (in module polymerist.maths.fractions.continued) DEFAULT_STATE_DATA_PROPS (in module polymerist.mdtools.openmmtools.reporters) DEFAULT_STATE_PROPS (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.state) default_suffix() (in module polymerist.genutils.fileutils.pathutils) DEFAULT_TOL (in module polymerist.maths.fractions.continued) degree (polymerist.maths.combinatorics.permutations.Permutation property) DELETED (polymerist.rdutils.reactions.BondChange attribute) (polymerist.rdutils.reactions.reactinfo.BondChange attribute) DELETION (polymerist.genutils.sequences.similarity.edits.EditOperation attribute) delimit_substrs_from_choices() (in module polymerist.genutils.textual.delimiters) delimit_substrs_from_regex() (in module polymerist.genutils.textual.delimiters) delimiter (polymerist.genutils.duration.TimeTemplate attribute) DelimiterBalanceState (class in polymerist.genutils.textual.delimiters) denom (polymerist.maths.fractions.ratios.Ratio attribute) (polymerist.maths.fractions.ratios.Rational attribute) density (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) dependencies() (polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy class method) (polymerist.smileslib.chemdbqueries.NIHCACTUSQueryStrategy class method) (polymerist.smileslib.chemdbqueries.PubChemQueryStrategy class method) descents (polymerist.maths.combinatorics.permutations.Permutation property) describe_edits() (in module polymerist.genutils.sequences.similarity.edits) describe_ensemble() (polymerist.mdtools.openmmtools.thermo.ThermoParameters method) describe_force() (in module polymerist.mdtools.openmmtools.forces) describe_forces() (in module polymerist.mdtools.openmmtools.forces) describe_order() (polymerist.polymers.building.sequencing.LinearCopolymerSequencer method) describe_tally() (polymerist.polymers.building.sequencing.LinearCopolymerSequencer method) desired_net_charge (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargeRedistributionStrategy attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution.ChargeRedistributionStrategy attribute) detach_parent() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) detailed_rdobj_info() (in module polymerist.rdutils.rdprops)

detect_ring_is_pierced() (in module polymerist.rdutils.rdcoords.piercing) DetermineNodeSuccessors (class in polymerist.polymers.smidgelib.smidgewrite) diagonalize() (in module polymerist.maths.linearalg.decomposition) dict_to_indented_str() (in module polymerist.genutils.textual.prettyprint) difference_rdmol() (in module polymerist.rdutils.rdprops.bijection) digits_to_int() (polymerist.maths.numbersys.positional.PositionalNumberingSystem method) dihedral_group() (polymerist.maths.combinatorics.permutations.Permutation class method) dimensions (polymerist.maths.lattices.coordinates.Coordinates property) dipole (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) dipole_moment (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) dir_tree (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.filetree) disable_kekulized_drawing() (in module polymerist.rdutils) (in module polymerist.rdutils.rdkdraw) disable_substruct_highlights() (in module polymerist.rdutils) (in module polymerist.rdutils.rdkdraw) disambiguate_formal_charge() (in module polymerist.polymers.monomers.specification) DISCERNMENTExample (class in polymerist.genutils.sequences.discernment.examples) DISCERNMENTSolver (class in polymerist.genutils.sequences.discernment) (class in polymerist.genutils.sequences.discernment.enumeration) DISCERNMENTStrategy (class in polymerist.genutils.sequences.discernment.strategies) DISCERNMENTStrategyCartesian (class in polymerist.genutils.sequences.discernment) (class in polymerist.genutils.sequences.discernment.strategies) DISCERNMENTStrategyRecursive (class in polymerist.genutils.sequences.discernment) (class in polymerist.genutils.sequences.discernment.strategies) DISCERNMENTStrategyStack (class in polymerist.genutils.sequences.discernment) (class in polymerist.genutils.sequences.discernment.strategies) dissolve_bond() (in module polymerist.rdutils.bonding.dissolution) distance (polymerist.genutils.sequences.similarity.edits.EditInfo attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) dists_to_centroid() (polymerist.maths.lattices.coordinates.Coordinates method) dists_to_point() (polymerist.maths.lattices.coordinates.Coordinates method) dotless() (in module polymerist.genutils.fileutils.pathutils) dozen (in module polymerist.unitutils.extraunits) dozen_base_unit (in module polymerist.unitutils.extraunits) draw() (polymerist.polymers.monographs.MonomerGraph method) draw_colorbar() (in module polymerist.graphics.plotutils) dt (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) DType (in module polymerist.genutils.typetools.numpytypes) Duration (class in polymerist.genutils.duration) dynamic_viscosity (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute)

E

edit_op (polymerist.genutils.sequences.similarity.edits.EditInfo attribute) EditInfo (class in polymerist.genutils.sequences.similarity.edits) EditOperation (class in polymerist.genutils.sequences.similarity.edits) effective_radius() (in module polymerist.mdtools.openfftools.physprops) electric_field (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) electronvolt_base_unit (in module polymerist.unitutils.extraunits) element_counter (polymerist.molfiles.pdb.pdbatoms.SerialAtomLabeller attribute) (polymerist.molfiles.pdb.SerialAtomLabeller attribute) element_set (polymerist.maths.combinatorics.permutations.Permutation property) elements (polymerist.genutils.containers.UnorderedRegistry attribute) elems (polymerist.maths.combinatorics.permutations.Permutation attribute) EmptyBlockSequence enable_kekulized_drawing() (in module polymerist.rdutils) (in module polymerist.rdutils.rdkdraw) enable_substruct_highlights() (in module polymerist.rdutils) (in module polymerist.rdutils.rdkdraw) encloses_box_vectors() (in module polymerist.mdtools.openfftools.boxvectors) encode() (polymerist.genutils.fileutils.jsonio.PathSerializer static method) (polymerist.genutils.fileutils.jsonio.QuantitySerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.NDArraySerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.PathSerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.QuantitySerializer static method) (polymerist.genutils.fileutils.jsonio.serialize.TypeSerializer static method) (polymerist.genutils.fileutils.jsonio.TypeSerializer static method) (polymerist.polymers.monographs.MonomerGraphSerializer static method) encoder_default() (polymerist.genutils.fileutils.jsonio.MultiTypeSerializer method) (polymerist.genutils.fileutils.jsonio.serialize.MultiTypeSerializer method) (polymerist.genutils.fileutils.jsonio.serialize.TypeSerializer class method) (polymerist.genutils.fileutils.jsonio.TypeSerializer class method) EndGroupDominatedChain energy (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute)

Ensemble (class in polymerist.mdtools.openmmtools.thermo) ensemble (polymerist.mdtools.openmmtools.thermo.ThermoParameters property) enum_serializer_factory() (in module polymerist.genutils.fileutils.jsonio.serialize) enumerate_bondable_port_pairs() (in module polymerist.rdutils.bonding.identification) enumerate_bondable_port_pairs_internal() (in module polymerist.rdutils.bonding.identification) enumerate_choice_labels() (polymerist.genutils.sequences.discernment.DISCERNMENTStrategyCartesian method) (polymerist.genutils.sequences.discernment.DISCERNMENTStrategyRecursive method) (polymerist.genutils.sequences.discernment.DISCERNMENTStrategyStack method) (polymerist.genutils.sequences.discernment.strategies.DISCERNMENTStrategy method) (polymerist.genutils.sequences.discernment.strategies.DISCERNMENTStrategyCartesian method) (polymerist.genutils.sequences.discernment.strategies.DISCERNMENTStrategyRecursive method) (polymerist.genutils.sequences.discernment.strategies.DISCERNMENTStrategyStack method) enumerate_choices() (polymerist.genutils.sequences.discernment.DISCERNMENTSolver method) (polymerist.genutils.sequences.discernment.enumeration.DISCERNMENTSolver method) enumerate_test_inputs() (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample method) enumerate_valid_reactant_orderings() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) EspalomaCharger (class in polymerist.mdtools.openfftools.partialcharge.molchargers) estimate_n_atoms_linear() (in module polymerist.polymers.estimation) estimate_n_monomers_infimum() (in module polymerist.polymers.estimation) estimate_n_monomers_supremum() (in module polymerist.polymers.estimation) eval_openmm_energies (in module polymerist.mdtools.openmmtools.evaluation) eval_openmm_energies_separated (in module polymerist.mdtools.openmmtools.evaluation) even_idxs (polymerist.maths.lattices.integral.CubicIntegerLattice property) even_points (polymerist.maths.lattices.integral.CubicIntegerLattice attribute) even_sublattice (polymerist.maths.lattices.integral.CubicIntegerLattice property) ExcessiveChainLength exchange_parent() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) expanded_SMILES() (in module polymerist.smileslib) (in module polymerist.smileslib.cleanup) explicit_mol_from_SMILES() (in module polymerist.rdutils.sanitization) EXT_REG (in module polymerist.genutils.fileutils.extensions) extend_to_methods() (in module polymerist.genutils.decorators.meta) extended_euclidean_algorithm() (in module polymerist.maths.fractions.continued) extension (polymerist.mdtools.openmmtools.reporters.ReporterConfig attribute) extra_kwargs (polymerist.mdtools.openmmtools.reporters.ReporterConfig attribute) extract_datetime() (polymerist.genutils.logutils.timestamps.Timestamp method) extract_imports_from_dir() (in module polymerist.genutils.importutils.pyimports) extract_imports_from_module() (in module polymerist.genutils.importutils.pyimports) extract_imports_from_pyfile() (in module polymerist.genutils.importutils.pyimports) extrema (polymerist.maths.lattices.coordinates.Coordinates property)

F

face_coords (polymerist.maths.lattices.coordinates.BoundingBox property) face_indices (polymerist.maths.lattices.coordinates.BoundingBox property) Factoradic (in module polymerist.maths.numbersys) FactorialNumberSystem (class in polymerist.maths.numbersys) (class in polymerist.maths.numbersys.commonbases) Factorization (in module polymerist.maths.primes) FF_DIR_REGISTRY (in module polymerist.mdtools.openfftools) FF_PATH_REGISTRY (in module polymerist.mdtools.openfftools) FFDIR (in module polymerist.mdtools.openfftools) FileTypeError Filter (in module polymerist.genutils.filters) final_bond_type (polymerist.rdutils.reactions.BondTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.BondTraceInfo attribute) find_repr_residues() (in module polymerist.mdtools.openfftools.partialcharge.rescharge) (in module polymerist.mdtools.openfftools.partialcharge.rescharge.calculation) finished (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) FixedRadixNumberSystem (class in polymerist.maths.numbersys) (class in polymerist.maths.numbersys.commonbases) flavor (polymerist.rdutils.bonding.portlib.Port property) FLAVOR_DICT_ATTR (polymerist.polymers.monographs.MonomerGraph attribute) FLEXIBLE (polymerist.mdtools.openmmtools.thermo.Barostat attribute) flexible_listlike_input() (in module polymerist.genutils.decorators.functional) flexible_module_pass() (in module polymerist.genutils.importutils.pkginspect) fmt (polymerist.genutils.duration.Duration attribute) fmt_str (polymerist.genutils.logutils.timestamps.Timestamp attribute) FN_GROUP_ENTRIES (in module polymerist.smileslib.functgroups) FN_GROUP_TABLE (in module polymerist.smileslib.functgroups) FnGroupSMARTSEntry (class in polymerist.smileslib.functgroups) force (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) force_added_by_polymerist() (in module polymerist.mdtools.openmmtools.forces)

force_groups_are_unique() (in module polymerist.mdtools.openmmtools.forces) forces() (polymerist.mdtools.openmmtools.thermo.BarostatParameters method) (polymerist.mdtools.openmmtools.thermo.ThermoParameters method) (polymerist.mdtools.openmmtools.thermo.ThermostatParameters method) forces_by_force_group() (in module polymerist.mdtools.openmmtools.forces) format() (polymerist.genutils.duration.Duration method) fragment_strategy (polymerist.rdutils.reactions.PolymerizationReactor attribute) (polymerist.rdutils.reactions.reactors.PolymerizationReactor attribute) from_bin_sequence() (polymerist.genutils.sequences.discernment.inventory.SymbolInventory class method) (polymerist.genutils.sequences.discernment.SymbolInventory class method) from_bin_sequence_mapping() (polymerist.genutils.sequences.discernment.inventory.SymbolInventory class method) (polymerist.genutils.sequences.discernment.SymbolInventory class method) from_bins() (polymerist.genutils.sequences.discernment.inventory.SymbolInventory class method) (polymerist.genutils.sequences.discernment.SymbolInventory class method) from_cycle() (polymerist.maths.combinatorics.permutations.Permutation class method) from_cycles() (polymerist.maths.combinatorics.permutations.Permutation class method) from_degree() (polymerist.maths.combinatorics.permutations.Permutation class method) from_dict() (polymerist.polymers.smidgelib.MonomerGraphBondInfo class method) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo class method) from_dir_and_parameters() (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths class method) (polymerist.mdtools.openmmtools.serialization.SimulationPaths class method) from_file() (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample class method) from_lattice_vectors() (polymerist.maths.lattices.bravais.LatticeParameters class method) from_lehmer() (polymerist.maths.combinatorics.permutations.Permutation class method) from_match() (polymerist.polymers.smidgelib.MonomerGraphBondInfo class method) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo class method) from_matrix() (polymerist.maths.combinatorics.permutations.Permutation class method) from_rdmols() (polymerist.rdutils.reactions.AnnotatedReaction class method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction class method) from_rxnfile() (polymerist.rdutils.reactions.AnnotatedReaction class method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction class method) from_seconds() (polymerist.genutils.duration.Duration class method) from_smarts() (polymerist.rdutils.reactions.AnnotatedReaction class method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction class method) from_smidge_string() (polymerist.polymers.monographs.MonomerGraph class method) from_word() (polymerist.maths.combinatorics.permutations.Permutation class method) full_arr_builtin() (in module polymerist.genutils.sequences.discernment.inventory)

G

gamma (polymerist.maths.lattices.bravais.LatticeParameters attribute) generate_int_lattice() (in module polymerist.maths.lattices.integral) generate_repr() (in module polymerist.genutils.decorators.classmod) generate_water_TIP3P() (in module polymerist.mdtools.openfftools.solvation.solvents) get_active_loggers() (in module polymerist.genutils.logutils.IOHandlers) get_atom_label() (polymerist.molfiles.pdb.pdbatoms.SerialAtomLabeller method) (polymerist.molfiles.pdb.SerialAtomLabeller method) get_axis_bounds() (in module polymerist.graphics.imageutils) get_bond_by_map_num_pair() (in module polymerist.rdutils.chemlabel) get_bondable_port_pairs() (in module polymerist.rdutils.bonding.identification) get_box_volume() (in module polymerist.mdtools.openfftools.boxvectors) get_chemical_property() (in module polymerist.smileslib.chemdbqueries) get_context_positions() (in module polymerist.mdtools.openmmtools.evaluation) get_dir_path_within_package() (in module polymerist.genutils.importutils.pkginspect) get_file_path_within_package() (in module polymerist.genutils.importutils.pkginspect) get_first_bondable_port_pair() (in module polymerist.rdutils.bonding.identification) get_flavor_dict_at_node_index() (polymerist.polymers.monographs.MonomerGraph method) get_greek_prefix() (in module polymerist.maths.greek) (in module polymerist.maths.greek.prefixes) get_index_after_positionals() (in module polymerist.genutils.decorators.signatures) get_lammps_energies() (in module polymerist.mdtools.lammpstools.lammpseval) get_lammps_lattice_parameters() (in module polymerist.mdtools.lammpstools.lammpseval) get_lammps_unit_style() (in module polymerist.mdtools.lammpstools.lammpseval) get_largest_offmol() (in module polymerist.mdtools.openfftools.topology) get_linker_ids() (in module polymerist.rdutils.bonding.portlib) get_logger_registry() (in module polymerist.genutils.logutils.IOHandlers) get_monomer_name_at_node_index() (polymerist.polymers.monographs.MonomerGraph method)

get_node_attrs() (in module polymerist.genutils.trees) (in module polymerist.genutils.trees.treecopy) get_num_bondable_port_pairs() (in module polymerist.rdutils.bonding.identification) get_num_linkers() (in module polymerist.rdutils.bonding.portlib) get_num_ports() (in module polymerist.rdutils.bonding.portlib) get_openmm_energies() (in module polymerist.mdtools.openmmtools.evaluation) get_openmm_energies_separated() (in module polymerist.mdtools.openmmtools.evaluation) get_port_ids() (in module polymerist.rdutils.bonding.portlib) get_ports() (in module polymerist.rdutils.bonding.portlib) get_property() (polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy method) get_resource_path_within_package() (in module polymerist.genutils.importutils.pkginspect) get_shortest_path_bonds() (in module polymerist.rdutils.reactions.fragment) get_single_port() (in module polymerist.rdutils.bonding.portlib) get_tight_bbox() (in module polymerist.graphics.imageutils) get_topology_bbox() (in module polymerist.mdtools.openfftools.boxvectors) get_total_port_degree_on_atom() (in module polymerist.rdutils.bonding.identification) GREEK_LETTER_NAMES (in module polymerist.maths.greek) (in module polymerist.maths.greek.alphabet) GREEK_PREFIXES (in module polymerist.maths.greek) (in module polymerist.maths.greek.prefixes), [1] GREEK_PREFIXES_POW_TENS (in module polymerist.maths.greek.prefixes) GREEK_PREFIXES_SPECIAL (in module polymerist.maths.greek.prefixes) GREEK_PREFIXES_TEENS (in module polymerist.maths.greek.prefixes) GREEK_PREFIXES_TENS (in module polymerist.maths.greek.prefixes) GREEK_PREFIXES_UNITS (in module polymerist.maths.greek.prefixes) group_name (polymerist.smileslib.functgroups.FnGroupSMARTSEntry attribute) group_type (polymerist.smileslib.functgroups.FnGroupSMARTSEntry attribute) GTR (in module polymerist.mdtools.openfftools)

H

hamming_distance() (in module polymerist.genutils.sequences.similarity.distances) has_atom_neighbors (in module polymerist.rdutils.selection) has_atom_neighbors_by_condition() (in module polymerist.rdutils.selection) has_children() (polymerist.genutils.fileutils.filetree.PathToNodeCorrespondence method) (polymerist.genutils.importutils.pkgiter.ModuleToNodeCorrespondence method) (polymerist.genutils.trees.NodeCorrespondence method) (polymerist.genutils.trees.treebase.NodeCorrespondence method) has_fully_mapped_atoms() (in module polymerist.rdutils.chemlabel) has_partial_charges() (in module polymerist.mdtools.openfftools.partialcharge.molchargers) has_reactable_subset() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method)

has_residual (polymerist.polymers.building.sequencing.LinearCopolymerSequencer property) has_uniquely_mapped_atoms() (in module polymerist.rdutils.chemlabel) hash_as_alphanum (in module polymerist.genutils.textual.encoding) hash_as_alphanumeric() (in module polymerist.genutils.textual.encoding) hasunits() (in module polymerist.unitutils) (in module polymerist.unitutils.dimensions) HEAVY_FORMER_LINKER_QUERY_ATOM (in module polymerist.rdutils.reactions.fragment) hertz (in module polymerist.unitutils.extraunits) hertz_base_unit (in module polymerist.unitutils.extraunits) hour (polymerist.genutils.duration.Duration attribute) hydrogenate_rdmol_ports() (in module polymerist.rdutils.bonding.substitution) hypergeometric_ratios() (in module polymerist.maths.numbersys.commonbases)

I

I (in module polymerist.maths.fractions.continued) IBIS (in module polymerist.rdutils.reactions) (in module polymerist.rdutils.reactions.fragment) id (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler attribute) identify_bravais_points_within_bbox() (in module polymerist.maths.lattices.bravais) identity() (polymerist.maths.combinatorics.permutations.Permutation class method) image() (polymerist.maths.combinatorics.permutations.Permutation method) img_from_bytes() (in module polymerist.graphics.imageutils) img_to_array() (in module polymerist.graphics.imageutils) ImportedObjectInfo (class in polymerist.genutils.importutils.pyimports) impose_unique_force_groups() (in module polymerist.mdtools.openmmtools.forces) in_line_fmt (in module polymerist.smileslib.primitives) include_elem_idx (polymerist.molfiles.pdb.pdbatoms.SerialAtomLabeller attribute) (polymerist.molfiles.pdb.SerialAtomLabeller attribute) incoming_flavor (polymerist.polymers.smidgelib.MonomerGraphBondInfo attribute) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo attribute) increase_bond_order() (in module polymerist.rdutils.bonding.formation) INDENT (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample attribute) IndexableIterable (class in polymerist.genutils.typetools.interfaces) indices (polymerist.genutils.sequences.similarity.edits.EditInfo attribute) init_reporter_paths() (polymerist.mdtools.openmmtools.reporters.ReporterParameters method) init_top_and_sys_paths() (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths method) (polymerist.mdtools.openmmtools.serialization.SimulationPaths method) initial_bond_type (polymerist.rdutils.reactions.BondTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.BondTraceInfo attribute) initialize_simulation_and_files() (in module polymerist.mdtools.openmmtools.preparation) initializer (polymerist.mdtools.openmmtools.reporters.ReporterConfig property) input_as_counter() (polymerist.genutils.containers.UnorderedRegistry method) insert() (polymerist.genutils.containers.UnorderedRegistry method) insert_chemical_info() (polymerist.polymers.monographs.MonomerGraph method) insert_into_text_periodic() (in module polymerist.genutils.textual.interpolation) insert_into_text_periodic_re() (in module polymerist.genutils.textual.interpolation) insert_parameter_at_index() (in module polymerist.genutils.decorators.signatures) INSERTION (polymerist.genutils.sequences.similarity.edits.EditOperation attribute) InsufficientChainLength int_complement() (in module polymerist.genutils.sequences) (in module polymerist.genutils.sequences.seqops) int_partitions() (in module polymerist.maths.combinatorics.partitions) INT_REGEX (in module polymerist.genutils.textual.encoding) int_to_bits() (in module polymerist.genutils.bits) int_to_digits() (polymerist.maths.numbersys.positional.PositionalNumberingSystem method) int_to_digits_iter() (polymerist.maths.numbersys.positional.PositionalNumberingSystem method) int_value (in module polymerist.mdtools.openmmtools.forces) integ_params (polymerist.mdtools.openmmtools.parameters.SimulationParameters attribute) integrator() (polymerist.mdtools.openmmtools.thermo.BarostatParameters method) (polymerist.mdtools.openmmtools.thermo.ThermoParameters method) (polymerist.mdtools.openmmtools.thermo.ThermostatParameters method) IntegratorParameters (class in polymerist.mdtools.openmmtools.parameters) IntermonomerBondIdentificationStrategy (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.fragment) inv_left() (in module polymerist.maths.linearalg.decomposition) inv_right() (in module polymerist.maths.linearalg.decomposition) InvalidChemicalLineNotation, [1]

InvalidInChI, [1] InvalidPropertyError InvalidSMARTS, [1] InvalidSMILES, [1] inverse (polymerist.maths.combinatorics.permutations.Permutation property) involution (polymerist.genutils.sequences.discernment.inventory.SymbolInventory property) (polymerist.genutils.sequences.discernment.SymbolInventory property) is_branchable (polymerist.polymers.monomers.MonomerGroup property) (polymerist.polymers.monomers.repr.MonomerGroup property) is_empty() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) is_empty_dir() (in module polymerist.genutils.fileutils.pathutils) is_empty_file() (in module polymerist.genutils.fileutils.pathutils) is_even (polymerist.maths.combinatorics.permutations.Permutation property) is_homopolymer() (polymerist.polymers.monomers.MonomerGroup method) (polymerist.polymers.monomers.repr.MonomerGroup method) is_linear (polymerist.polymers.monographs.MonomerGraph attribute) (polymerist.polymers.monomers.MonomerGroup property) (polymerist.polymers.monomers.repr.MonomerGroup property) is_linear_homopolymer (polymerist.polymers.monomers.MonomerGroup property) (polymerist.polymers.monomers.repr.MonomerGroup property) is_linker() (in module polymerist.rdutils.bonding.portlib) is_module() (in module polymerist.genutils.importutils) (in module polymerist.genutils.importutils.pkginspect) is_odd (polymerist.maths.combinatorics.permutations.Permutation property) is_online() (polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy class method) (polymerist.smileslib.chemdbqueries.NIHCACTUSQueryStrategy class method) (polymerist.smileslib.chemdbqueries.PubChemQueryStrategy class method) is_package() (in module polymerist.genutils.importutils) (in module polymerist.genutils.importutils.pkginspect) is_prime() (in module polymerist.maths.primes) is_prime_alt() (in module polymerist.maths.primes) is_relative (polymerist.genutils.importutils.pyimports.ImportedObjectInfo attribute) is_terminal() (polymerist.polymers.monomers.MonomerGroup static method) (polymerist.polymers.monomers.repr.MonomerGroup static method) is_unbranched (polymerist.polymers.monographs.MonomerGraph property) is_unique() (in module polymerist.genutils.sequences) (in module polymerist.genutils.sequences.discernment.strategies) (in module polymerist.genutils.sequences.seqops) is_valid_SMARTS() (in module polymerist.smileslib) (in module polymerist.smileslib.cleanup) is_valid_SMILES() (in module polymerist.smileslib) (in module polymerist.smileslib.cleanup) is_volume() (in module polymerist.unitutils) (in module polymerist.unitutils.dimensions) isrdobj (in module polymerist.rdutils.rdprops) istimeable (in module polymerist.genutils.duration) iter_len() (in module polymerist.genutils.iteration) iter_rdmols() (polymerist.polymers.monomers.MonomerGroup method) (polymerist.polymers.monomers.repr.MonomerGroup method) iter_submodule_info() (in module polymerist.genutils.importutils.pkgiter) iter_submodules() (in module polymerist.genutils.importutils) (in module polymerist.genutils.importutils.pkgiter)

J

jaccard_distance() (in module polymerist.genutils.sequences.similarity.distances) json_path (polymerist.genutils.fileutils.jsonio.JSONDict attribute) (polymerist.genutils.fileutils.jsonio.update.JSONDict attribute) JSONDict (class in polymerist.genutils.fileutils.jsonio) (class in polymerist.genutils.fileutils.jsonio.update)

JSONifiable (class in polymerist.genutils.fileutils.jsonio) (class in polymerist.genutils.fileutils.jsonio.jsonify) JSONSerializable (in module polymerist.genutils.fileutils.jsonio) (in module polymerist.genutils.fileutils.jsonio.serialize) Just (in module polymerist.genutils.textual.prettyprint) Justification (class in polymerist.genutils.textual.prettyprint)

K

KEYWORD_PARAMETER_TYPES (in module polymerist.genutils.decorators.signatures)

L

L (in module polymerist.genutils.sequences.discernment.examples) (in module polymerist.genutils.sequences.discernment.inventory) (in module polymerist.rdutils.reactions.reactions) label (polymerist.mdtools.openmmtools.reporters.ReporterConfig attribute) label_discrete_cmap() (in module polymerist.graphics.plotutils) label_linkers() (in module polymerist.rdutils.rdprops.atomprops) label_R_groups (in module polymerist.rdutils.rdprops.atomprops) LAMMPS_ENERGY_KW_ALIASES (in module polymerist.mdtools.lammpstools.lammpseval) LAMMPSUnitStyle (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleCGS (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleElectron (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleMetal (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleMicro (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleNano (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleReal (class in polymerist.mdtools.lammpstools.unitstyles) LAMMPSUnitStyleSI (class in polymerist.mdtools.lammpstools.unitstyles) LANGEVIN (polymerist.mdtools.openmmtools.thermo.Thermostat attribute) LANGEVIN_MIDDLE (polymerist.mdtools.openmmtools.thermo.Thermostat attribute) LANGEVINMIDDLE (polymerist.mdtools.openmmtools.thermo.Thermostat attribute) lattice_generator (in module polymerist.maths.lattices.bravais) lattice_vectors (polymerist.maths.lattices.bravais.LatticeParameters property) LatticeParameters (class in polymerist.maths.lattices.bravais) LEFT (polymerist.genutils.textual.prettyprint.Justification attribute) lehmer_code (polymerist.maths.combinatorics.permutations.Permutation property) lengths (polymerist.maths.lattices.bravais.LatticeParameters attribute) lengths_are_positive (polymerist.maths.lattices.bravais.LatticeParameters property) levenshtein_distance() (in module polymerist.genutils.sequences.similarity.edits) lex_order_points() (polymerist.maths.lattices.coordinates.Coordinates method) lex_ordered_idxs (polymerist.maths.lattices.coordinates.Coordinates property) lex_ordered_points (polymerist.maths.lattices.coordinates.Coordinates property) lex_ordered_weights (polymerist.maths.lattices.integral.CubicIntegerLattice property) LibraryCharger (class in polymerist.mdtools.openfftools.partialcharge.rescharge) (class in polymerist.mdtools.openfftools.partialcharge.rescharge.interface) line_number (polymerist.genutils.importutils.pyimports.ImportedObjectInfo attribute) linear_end_groups() (polymerist.polymers.monomers.MonomerGroup method) (polymerist.polymers.monomers.repr.MonomerGroup method) linear_transformation() (polymerist.maths.lattices.coordinates.Coordinates method) LinearCopolymerSequencer (class in polymerist.polymers.building.sequencing)

linker (polymerist.rdutils.bonding.portlib.Port attribute) load_state_flexible() (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.state) local_rename() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) local_restem() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) locate_intermonomer_bonds() (polymerist.rdutils.reactions.fragment.IntermonomerBondIdentificationStrategy method) (polymerist.rdutils.reactions.IntermonomerBondIdentificationStrategy method) LOG_FORMATTER (in module polymerist.genutils.logutils.IOHandlers) LOGGER (in module polymerist.genutils.importutils.pkgiter) (in module polymerist.genutils.sequences.discernment.inventory) (in module polymerist.mdtools.openfftools.partialcharge.molchargers) (in module polymerist.mdtools.openfftools.partialcharge.rescharge.calculation) (in module polymerist.mdtools.openfftools.solvation.packing) (in module polymerist.mdtools.openfftools.topology) (in module polymerist.mdtools.openmmtools.execution) (in module polymerist.mdtools.openmmtools.preparation) (in module polymerist.mdtools.openmmtools.reporters) (in module polymerist.mdtools.openmmtools.serialization.state) (in module polymerist.mdtools.openmmtools.serialization.topology) (in module polymerist.mdtools.openmmtools.thermo) (in module polymerist.polymers.building.linear) (in module polymerist.polymers.building.sequencing) (in module polymerist.polymers.monomers.repr) (in module polymerist.polymers.monomers.specification) (in module polymerist.polymers.smidgelib.smidgeread) (in module polymerist.polymers.smidgelib.smidgewrite) (in module polymerist.rdutils.bonding.dissolution) (in module polymerist.rdutils.bonding.formation) (in module polymerist.rdutils.bonding.permutation) (in module polymerist.rdutils.reactions.fragment) (in module polymerist.rdutils.reactions.reactors) (in module polymerist.smileslib.chemdbqueries) (in module polymerist.smileslib.functgroups) LongRangeNonbondedMethod (in module polymerist.mdtools.openmmtools.forces) lumen_base_unit (in module polymerist.unitutils.extraunits) lux (in module polymerist.unitutils.extraunits) lux_base_unit (in module polymerist.unitutils.extraunits)

M

M (in module polymerist.genutils.typetools.numpytypes) make_change_greedy() (in module polymerist.maths.combinatorics.partitions) make_cmapper() (in module polymerist.graphics.plotutils) make_jsonifiable() (in module polymerist.genutils.fileutils.jsonio) (in module polymerist.genutils.fileutils.jsonio.jsonify) map_number (polymerist.rdutils.reactions.AtomTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.AtomTraceInfo attribute) map_numbers_by_atom_idxs() (in module polymerist.rdutils.chemlabel) map_numbers_to_neighbor_bonds() (in module polymerist.rdutils.reactions.reactions) map_nums (polymerist.rdutils.reactions.BondTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.BondTraceInfo attribute) mapped_atom_info (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) mapped_atom_info_by_map_number (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) mapped_atom_info_by_product_idx (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) mapped_atoms() (in module polymerist.rdutils.selection) mapped_bond_info (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) mapped_bond_info_by_change_type (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) mapped_bond_info_by_product_idx (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) mapped_neighbors() (in module polymerist.rdutils.selection) mapping (polymerist.maths.combinatorics.permutations.Cycle property) mass (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) matches_flavor() (polymerist.rdutils.bonding.portlib.Port method) matrix (polymerist.maths.combinatorics.permutations.Permutation property) max_bondable_order_between_atoms() (in module polymerist.rdutils.bonding.identification) max_bonds_per_cut (polymerist.rdutils.reactions.CutMinimumCostBondsStrategy attribute) (polymerist.rdutils.reactions.fragment.CutMinimumCostBondsStrategy attribute) max_elem_in_cycles() (polymerist.maths.combinatorics.permutations.Cycle static method) maximum (polymerist.maths.lattices.coordinates.Coordinates property) mbmol_from_mono_rdmol() (in module polymerist.polymers.building) (in module polymerist.polymers.building.mbconvert) mbmol_to_openmm_pdb() (in module polymerist.polymers.building) (in module polymerist.polymers.building.mbconvert) mbmol_to_rdkit_pdb() (in module polymerist.polymers.building) (in module polymerist.polymers.building.mbconvert) mbmol_to_rdmol() (in module polymerist.polymers.building) (in module polymerist.polymers.building.mbconvert) MC (polymerist.mdtools.openmmtools.thermo.Barostat attribute) microsecond (polymerist.genutils.duration.Duration attribute) millisecond (polymerist.genutils.duration.Duration attribute) minimum (polymerist.maths.lattices.coordinates.Coordinates property) minute (polymerist.genutils.duration.Duration attribute) MissingMonomerData MissingPrerequisitePackage, [1], [2], [3] MissingStructureData MissingUnitsError, [1] MODIFIED (polymerist.rdutils.reactions.BondChange attribute) (polymerist.rdutils.reactions.reactinfo.BondChange attribute) modify_dict() (in module polymerist.genutils.iteration) modify_param_annotation_by_index() (in module polymerist.genutils.decorators.signatures) modify_param_annotation_by_name() (in module polymerist.genutils.decorators.signatures) module polymerist polymerist.genutils polymerist.genutils.attrs polymerist.genutils.bits polymerist.genutils.containers polymerist.genutils.decorators polymerist.genutils.decorators.classmod polymerist.genutils.decorators.functional polymerist.genutils.decorators.meta polymerist.genutils.decorators.signatures polymerist.genutils.duration polymerist.genutils.fileutils polymerist.genutils.fileutils.extensions polymerist.genutils.fileutils.filetree polymerist.genutils.fileutils.jsonio polymerist.genutils.fileutils.jsonio.jsonify polymerist.genutils.fileutils.jsonio.serialize polymerist.genutils.fileutils.jsonio.update polymerist.genutils.fileutils.pathutils polymerist.genutils.filters polymerist.genutils.importutils polymerist.genutils.importutils.dependencies polymerist.genutils.importutils.pkginspect polymerist.genutils.importutils.pkgiter polymerist.genutils.importutils.pyimports polymerist.genutils.iteration polymerist.genutils.logutils polymerist.genutils.logutils.IOHandlers polymerist.genutils.logutils.timestamps polymerist.genutils.sequences polymerist.genutils.sequences.discernment polymerist.genutils.sequences.discernment.enumeration polymerist.genutils.sequences.discernment.examples polymerist.genutils.sequences.discernment.inventory polymerist.genutils.sequences.discernment.strategies polymerist.genutils.sequences.seqops polymerist.genutils.sequences.similarity polymerist.genutils.sequences.similarity.distances polymerist.genutils.sequences.similarity.edits polymerist.genutils.textual polymerist.genutils.textual.casing polymerist.genutils.textual.delimiters polymerist.genutils.textual.encoding polymerist.genutils.textual.interpolation polymerist.genutils.textual.ordinals polymerist.genutils.textual.prettyprint polymerist.genutils.textual.substrings polymerist.genutils.trees polymerist.genutils.trees.treebase polymerist.genutils.trees.treecopy polymerist.genutils.trees.treeviz polymerist.genutils.typetools polymerist.genutils.typetools.categorical polymerist.genutils.typetools.interfaces polymerist.genutils.typetools.numpytypes polymerist.graphics polymerist.graphics.colors polymerist.graphics.imageutils polymerist.graphics.plotutils polymerist.maths polymerist.maths.combinatorics polymerist.maths.combinatorics.numbers polymerist.maths.combinatorics.partitions polymerist.maths.combinatorics.permutations polymerist.maths.combinatorics.tables polymerist.maths.fractions polymerist.maths.fractions.continued polymerist.maths.fractions.ratios polymerist.maths.greek polymerist.maths.greek.alphabet polymerist.maths.greek.prefixes polymerist.maths.lattices polymerist.maths.lattices.bravais polymerist.maths.lattices.coordinates polymerist.maths.lattices.integral polymerist.maths.linearalg polymerist.maths.linearalg.affine polymerist.maths.linearalg.decomposition polymerist.maths.numbersys polymerist.maths.numbersys.commonbases polymerist.maths.numbersys.positional polymerist.maths.primes polymerist.mdtools polymerist.mdtools.lammpstools polymerist.mdtools.lammpstools.lammpseval polymerist.mdtools.lammpstools.unitstyles polymerist.mdtools.openfftools polymerist.mdtools.openfftools.boxvectors polymerist.mdtools.openfftools.partialcharge polymerist.mdtools.openfftools.partialcharge.molchargers polymerist.mdtools.openfftools.partialcharge.rescharge polymerist.mdtools.openfftools.partialcharge.rescharge.calculation polymerist.mdtools.openfftools.partialcharge.rescharge.interface polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution polymerist.mdtools.openfftools.partition polymerist.mdtools.openfftools.physprops polymerist.mdtools.openfftools.solvation polymerist.mdtools.openfftools.solvation.packing polymerist.mdtools.openfftools.solvation.solvents polymerist.mdtools.openfftools.topology polymerist.mdtools.openfftools.unitsys polymerist.mdtools.openmmtools polymerist.mdtools.openmmtools.evaluation polymerist.mdtools.openmmtools.execution polymerist.mdtools.openmmtools.forces polymerist.mdtools.openmmtools.parameters polymerist.mdtools.openmmtools.preparation polymerist.mdtools.openmmtools.reporters polymerist.mdtools.openmmtools.serialization polymerist.mdtools.openmmtools.serialization.paths polymerist.mdtools.openmmtools.serialization.state polymerist.mdtools.openmmtools.serialization.system polymerist.mdtools.openmmtools.serialization.topology polymerist.mdtools.openmmtools.thermo polymerist.molfiles polymerist.molfiles.pdb polymerist.molfiles.pdb.pdbatoms polymerist.polymerist polymerist.polymers polymerist.polymers.building polymerist.polymers.building.linear polymerist.polymers.building.mbconvert polymerist.polymers.building.sequencing polymerist.polymers.estimation polymerist.polymers.exceptions polymerist.polymers.monographs polymerist.polymers.monomers polymerist.polymers.monomers.fragments polymerist.polymers.monomers.repr polymerist.polymers.monomers.specification polymerist.polymers.smidgelib polymerist.polymers.smidgelib.smidgebonds polymerist.polymers.smidgelib.smidgeread polymerist.polymers.smidgelib.smidgewrite polymerist.rdutils polymerist.rdutils.bonding polymerist.rdutils.bonding.dissolution polymerist.rdutils.bonding.formation polymerist.rdutils.bonding.identification polymerist.rdutils.bonding.permutation polymerist.rdutils.bonding.portlib polymerist.rdutils.bonding.substitution polymerist.rdutils.chemlabel polymerist.rdutils.rdcoords polymerist.rdutils.rdcoords.piercing polymerist.rdutils.rdcoords.tiling polymerist.rdutils.rdgraphs polymerist.rdutils.rdkdraw polymerist.rdutils.rdprops polymerist.rdutils.rdprops.atomprops polymerist.rdutils.rdprops.bijection polymerist.rdutils.rdprops.bondprops polymerist.rdutils.reactions polymerist.rdutils.reactions.assembly polymerist.rdutils.reactions.fragment polymerist.rdutils.reactions.reactexc polymerist.rdutils.reactions.reactinfo polymerist.rdutils.reactions.reactions polymerist.rdutils.reactions.reactors polymerist.rdutils.sanitization polymerist.rdutils.selection polymerist.rdutils.substructures polymerist.smileslib polymerist.smileslib.chemdbqueries polymerist.smileslib.cleanup polymerist.smileslib.functgroups polymerist.smileslib.primitives polymerist.smileslib.special polymerist.unitutils polymerist.unitutils.dimensions polymerist.unitutils.extraunits polymerist.unitutils.physconsts polymerist.unitutils.unitstr

module_hierarchy() (in module polymerist) (in module polymerist.genutils.importutils) (in module polymerist.genutils.importutils.pkgiter) module_installed() (in module polymerist.genutils.importutils.dependencies) module_parts() (in module polymerist.genutils.importutils.pkginspect) module_stem() (in module polymerist.genutils.importutils.pkginspect) module_tree (in module polymerist.genutils.importutils) (in module polymerist.genutils.importutils.pkgiter) module_tree_direct() (in module polymerist.genutils.importutils) (in module polymerist.genutils.importutils.pkgiter) modules_installed() (in module polymerist.genutils.importutils.dependencies) (in module polymerist.genutils.trees) (in module polymerist.mdtools.openfftools) (in module polymerist.polymers.building) ModuleToNodeCorrespondence (class in polymerist.genutils.importutils.pkgiter) mol_fragment (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargedResidue attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargedResidue attribute) mol_to_smiles_and_atom_permutation() (in module polymerist.rdutils.chemlabel) MolCharger (class in polymerist.mdtools.openfftools.partialcharge.molchargers) molecular_weight() (in module polymerist.mdtools.openfftools.physprops) MolPortError MolSizeMismatchError MonoGraph (in module polymerist.polymers.monographs) monograph (polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister attribute) (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) MONOMER_NAME_ATTR (polymerist.polymers.monographs.MonomerGraph attribute) MonomerEnd (class in polymerist.polymers.smidgelib.smidgeread) MonomerGraph (class in polymerist.polymers.monographs) MonomerGraphBondInfo (class in polymerist.polymers.smidgelib) (class in polymerist.polymers.smidgelib.smidgebonds) MonomerGraphSerializer (class in polymerist.polymers.monographs) MonomerGroup (class in polymerist.polymers.monomers) (class in polymerist.polymers.monomers.repr) monomers (polymerist.polymers.monomers.MonomerGroup attribute) (polymerist.polymers.monomers.repr.MonomerGroup attribute) MonomerStart (class in polymerist.polymers.smidgelib.smidgeread) MONTE_CARLO (polymerist.mdtools.openmmtools.thermo.Barostat attribute) MONTE_CARLO_FLEXIBLE (polymerist.mdtools.openmmtools.thermo.Barostat attribute) MONTECARLO (polymerist.mdtools.openmmtools.thermo.Barostat attribute) MorphologyError MPD_TMC_FRAGMENTS (in module polymerist.polymers.monomers) (in module polymerist.polymers.monomers.fragments) MSFHandler (in module polymerist.genutils.logutils.IOHandlers) MSFHandlerFlex (in module polymerist.genutils.logutils.IOHandlers) multinomial_coeff() (in module polymerist.maths.combinatorics.numbers) multinomial_coeff_native() (in module polymerist.maths.combinatorics.numbers) multiset_coeff() (in module polymerist.maths.combinatorics.numbers) multiset_partition() (in module polymerist.maths.combinatorics.partitions) MultiStreamFileHandler (class in polymerist.genutils.logutils.IOHandlers) MultiStreamFileHandlerFlexible (class in polymerist.genutils.logutils.IOHandlers) MultiTypeSerializer (class in polymerist.genutils.fileutils.jsonio) (class in polymerist.genutils.fileutils.jsonio.serialize)

N

N (in module polymerist.genutils.typetools.numpytypes) (in module polymerist.maths.fractions.ratios) (in module polymerist.rdutils.rdcoords.piercing) n_dims (polymerist.maths.lattices.coordinates.Coordinates attribute) n_full_periods (polymerist.polymers.building.sequencing.LinearCopolymerSequencer property) n_monomers (polymerist.polymers.monomers.MonomerGroup property) (polymerist.polymers.monomers.repr.MonomerGroup property) n_points (polymerist.maths.lattices.coordinates.Coordinates property) n_repeat_units (polymerist.polymers.building.sequencing.LinearCopolymerSequencer attribute) n_repeat_units_middle (polymerist.polymers.building.sequencing.LinearCopolymerSequencer property) n_repeat_units_terminal (polymerist.polymers.building.sequencing.LinearCopolymerSequencer attribute) n_residual_repeat_units (polymerist.polymers.building.sequencing.LinearCopolymerSequencer property) NAGLCharger (class in polymerist.mdtools.openfftools.partialcharge.molchargers) name() (polymerist.genutils.fileutils.filetree.PathToNodeCorrespondence method) (polymerist.genutils.importutils.pkgiter.ModuleToNodeCorrespondence method) (polymerist.genutils.trees.NodeCorrespondence method) (polymerist.genutils.trees.treebase.NodeCorrespondence method) NAMED_COLORS (in module polymerist.graphics.colors) named_phys_consts (in module polymerist.unitutils.physconsts) natural_order (polymerist.maths.combinatorics.permutations.Permutation property) NDArraySerializer (class in polymerist.genutils.fileutils.jsonio.serialize) nearest_int_coord_along_normal() (in module polymerist.maths.lattices.integral) NIHCACTUSQueryStrategy (class in polymerist.smileslib.chemdbqueries) node_idx (polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister attribute) node_stack (polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister attribute) (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) node_successors (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister property) NodeCorrespondence (class in polymerist.genutils.trees) (class in polymerist.genutils.trees.treebase) NoIntermonomerBondsFound NOSE_HOOVER (polymerist.mdtools.openmmtools.thermo.Thermostat attribute)

NOSEHOOVER (polymerist.mdtools.openmmtools.thermo.Thermostat attribute) NPHEnsembleUnsupported NPT (polymerist.mdtools.openmmtools.thermo.Ensemble attribute) NULL (polymerist.genutils.sequences.similarity.edits.EditOperation attribute) NullPropertyResponse Num (in module polymerist.maths.lattices.coordinates) num (polymerist.maths.fractions.ratios.Ratio attribute) (polymerist.maths.fractions.ratios.Rational attribute) num_ascents (polymerist.maths.combinatorics.permutations.Permutation property) num_automorphisms() (in module polymerist.rdutils.substructures) num_chains (polymerist.polymers.monographs.MonomerGraph property) num_descents (polymerist.maths.combinatorics.permutations.Permutation property) num_from_factorization() (in module polymerist.maths.primes) num_inversions (polymerist.maths.combinatorics.permutations.Permutation property) num_mid_and_term (polymerist.polymers.monomers.MonomerGroup property) (polymerist.polymers.monomers.repr.MonomerGroup property) num_mols_in_box() (in module polymerist.mdtools.openfftools.physprops) num_monomers (polymerist.polymers.monographs.MonomerGraph property) num_samples (polymerist.mdtools.openmmtools.parameters.IntegratorParameters attribute) num_steps (polymerist.mdtools.openmmtools.parameters.IntegratorParameters property) (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) num_substruct_queries() (in module polymerist.rdutils.substructures) num_substruct_queries_distinct() (in module polymerist.rdutils.substructures) num_type_name (in module polymerist.genutils.typetools.numpytypes) number_density() (in module polymerist.mdtools.openfftools.physprops) number_of_bins (polymerist.genutils.sequences.discernment.inventory.SymbolInventory property) (polymerist.genutils.sequences.discernment.SymbolInventory property) number_of_symbols (polymerist.genutils.sequences.discernment.inventory.SymbolInventory property) (polymerist.genutils.sequences.discernment.SymbolInventory property) NVE (polymerist.mdtools.openmmtools.thermo.Ensemble attribute) NVT (polymerist.mdtools.openmmtools.thermo.Ensemble attribute)

O

object_alias (polymerist.genutils.importutils.pyimports.ImportedObjectInfo attribute) object_name (polymerist.genutils.importutils.pyimports.ImportedObjectInfo attribute) occurence_matrix (polymerist.genutils.sequences.discernment.inventory.SymbolInventory property) (polymerist.genutils.sequences.discernment.SymbolInventory property) odd_even_idxs (polymerist.maths.lattices.integral.CubicIntegerLattice property) odd_idxs (polymerist.maths.lattices.integral.CubicIntegerLattice property) odd_points (polymerist.maths.lattices.integral.CubicIntegerLattice attribute) odd_sublattice (polymerist.maths.lattices.integral.CubicIntegerLattice property) offmol (in module polymerist.mdtools.openfftools.solvation.solvents) offmol_mass() (in module polymerist.mdtools.openfftools.physprops)

offsets (polymerist.genutils.sequences.similarity.edits.EditOperation attribute) offtop_mass() (in module polymerist.mdtools.openfftools.physprops) OpenMMUnitLike (in module polymerist.unitutils.dimensions) optional_in_place() (in module polymerist.genutils.decorators.functional) order (polymerist.maths.combinatorics.permutations.Permutation property) ordinal_from_int() (in module polymerist.genutils.textual.ordinals) ordinal_suffix_from_int() (in module polymerist.genutils.textual.ordinals) ordinal_suffix_from_int_alt() (in module polymerist.genutils.textual.ordinals) outgoing_flavor (polymerist.polymers.smidgelib.MonomerGraphBondInfo attribute) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo attribute)

P

P (in module polymerist.genutils.sequences.discernment.strategies) (in module polymerist.rdutils.reactions.fragment) (in module polymerist.rdutils.sanitization) pack_topology_with_solvent() (in module polymerist.mdtools.openfftools.solvation.packing) package_atom_metadata() (in module polymerist.mdtools.openfftools.topology) pad_box_vectors() (in module polymerist.mdtools.openfftools.boxvectors) pad_box_vectors_uniform() (in module polymerist.mdtools.openfftools.boxvectors) pad_sequence() (in module polymerist.genutils.sequences) (in module polymerist.genutils.sequences.seqops) parameters_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) Params (in module polymerist.genutils.decorators.functional) (in module polymerist.genutils.decorators.meta) (in module polymerist.genutils.fileutils.pathutils) (in module polymerist.genutils.importutils.dependencies) parent (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler attribute) parent_module (polymerist.genutils.importutils.pyimports.ImportedObjectInfo attribute) parity (polymerist.maths.combinatorics.permutations.Permutation attribute) parse_pdb_atom_record() (in module polymerist.molfiles.pdb.pdbatoms) parse_str_dict() (polymerist.polymers.smidgelib.MonomerGraphBondInfo static method) (polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo static method) parse_within_delimiters() (in module polymerist.genutils.textual.delimiters) PartialBlockSequence partition() (in module polymerist.mdtools.openfftools.partition) pascal() (in module polymerist) (in module polymerist.maths.combinatorics.tables) paths_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) PathSerializer (class in polymerist.genutils.fileutils.jsonio) (class in polymerist.genutils.fileutils.jsonio.serialize) PathToNodeCorrespondence (class in polymerist.genutils.fileutils.filetree) PDB_ATOM_RECORD_TOKENS (in module polymerist.molfiles.pdb.pdbatoms) PE_FRAGMENTS (in module polymerist.polymers.monomers) (in module polymerist.polymers.monomers.fragments) PEG_PLGA_FRAGMENTS (in module polymerist.polymers.monomers) (in module polymerist.polymers.monomers.fragments) pentagonal() (in module polymerist.maths.combinatorics.numbers) percent (in module polymerist.unitutils.extraunits) percent_base_unit (in module polymerist.unitutils.extraunits) period (polymerist.polymers.building.sequencing.LinearCopolymerSequencer attribute) Permutation (class in polymerist.maths.combinatorics.permutations) personal_logger (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler attribute) PHYS_CONSTS_WITH_UNITS (in module polymerist.unitutils.physconsts) PINPRICS() (in module polymerist.rdutils.rdcoords.piercing) PintUnitLike (in module polymerist.unitutils.dimensions) places (polymerist.maths.numbersys.positional.PositionalNumberingSystem property) plot_df_props() (in module polymerist.graphics.plotutils) plot_image_with_colorbar() (in module polymerist.graphics.plotutils) points (polymerist.maths.lattices.coordinates.Coordinates attribute) poise (in module polymerist.unitutils.extraunits) poise_base_unit (in module polymerist.unitutils.extraunits) polymerist module polymerist.genutils module polymerist.genutils.attrs module polymerist.genutils.bits module polymerist.genutils.containers module polymerist.genutils.decorators module polymerist.genutils.decorators.classmod module polymerist.genutils.decorators.functional module polymerist.genutils.decorators.meta module polymerist.genutils.decorators.signatures module polymerist.genutils.duration module polymerist.genutils.fileutils module polymerist.genutils.fileutils.extensions module polymerist.genutils.fileutils.filetree module polymerist.genutils.fileutils.jsonio module polymerist.genutils.fileutils.jsonio.jsonify module polymerist.genutils.fileutils.jsonio.serialize module polymerist.genutils.fileutils.jsonio.update module polymerist.genutils.fileutils.pathutils module polymerist.genutils.filters module polymerist.genutils.importutils module polymerist.genutils.importutils.dependencies module polymerist.genutils.importutils.pkginspect module polymerist.genutils.importutils.pkgiter module polymerist.genutils.importutils.pyimports module polymerist.genutils.iteration module polymerist.genutils.logutils module polymerist.genutils.logutils.IOHandlers module polymerist.genutils.logutils.timestamps module polymerist.genutils.sequences module polymerist.genutils.sequences.discernment module polymerist.genutils.sequences.discernment.enumeration module polymerist.genutils.sequences.discernment.examples module polymerist.genutils.sequences.discernment.inventory module polymerist.genutils.sequences.discernment.strategies module polymerist.genutils.sequences.seqops module polymerist.genutils.sequences.similarity module polymerist.genutils.sequences.similarity.distances module polymerist.genutils.sequences.similarity.edits module polymerist.genutils.textual module polymerist.genutils.textual.casing module polymerist.genutils.textual.delimiters module polymerist.genutils.textual.encoding module polymerist.genutils.textual.interpolation module polymerist.genutils.textual.ordinals module polymerist.genutils.textual.prettyprint module polymerist.genutils.textual.substrings module polymerist.genutils.trees module polymerist.genutils.trees.treebase module polymerist.genutils.trees.treecopy module polymerist.genutils.trees.treeviz module polymerist.genutils.typetools module polymerist.genutils.typetools.categorical module polymerist.genutils.typetools.interfaces module polymerist.genutils.typetools.numpytypes module polymerist.graphics module polymerist.graphics.colors module polymerist.graphics.imageutils module polymerist.graphics.plotutils module polymerist.maths module polymerist.maths.combinatorics module polymerist.maths.combinatorics.numbers module polymerist.maths.combinatorics.partitions module polymerist.maths.combinatorics.permutations module polymerist.maths.combinatorics.tables module polymerist.maths.fractions module polymerist.maths.fractions.continued module polymerist.maths.fractions.ratios module polymerist.maths.greek module polymerist.maths.greek.alphabet module polymerist.maths.greek.prefixes module polymerist.maths.lattices module polymerist.maths.lattices.bravais module polymerist.maths.lattices.coordinates module polymerist.maths.lattices.integral module polymerist.maths.linearalg module polymerist.maths.linearalg.affine module polymerist.maths.linearalg.decomposition module polymerist.maths.numbersys module polymerist.maths.numbersys.commonbases module polymerist.maths.numbersys.positional module polymerist.maths.primes module polymerist.mdtools module polymerist.mdtools.lammpstools module polymerist.mdtools.lammpstools.lammpseval module polymerist.mdtools.lammpstools.unitstyles module polymerist.mdtools.openfftools module polymerist.mdtools.openfftools.boxvectors module

polymerist.mdtools.openfftools.partialcharge module polymerist.mdtools.openfftools.partialcharge.molchargers module polymerist.mdtools.openfftools.partialcharge.rescharge module polymerist.mdtools.openfftools.partialcharge.rescharge.calculation module polymerist.mdtools.openfftools.partialcharge.rescharge.interface module polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes module polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution module polymerist.mdtools.openfftools.partition module polymerist.mdtools.openfftools.physprops module polymerist.mdtools.openfftools.solvation module polymerist.mdtools.openfftools.solvation.packing module polymerist.mdtools.openfftools.solvation.solvents module polymerist.mdtools.openfftools.topology module polymerist.mdtools.openfftools.unitsys module polymerist.mdtools.openmmtools module polymerist.mdtools.openmmtools.evaluation module polymerist.mdtools.openmmtools.execution module polymerist.mdtools.openmmtools.forces module polymerist.mdtools.openmmtools.parameters module polymerist.mdtools.openmmtools.preparation module polymerist.mdtools.openmmtools.reporters module polymerist.mdtools.openmmtools.serialization module polymerist.mdtools.openmmtools.serialization.paths module polymerist.mdtools.openmmtools.serialization.state module polymerist.mdtools.openmmtools.serialization.system module polymerist.mdtools.openmmtools.serialization.topology module polymerist.mdtools.openmmtools.thermo module polymerist.molfiles module polymerist.molfiles.pdb module polymerist.molfiles.pdb.pdbatoms module polymerist.polymerist module polymerist.polymers module polymerist.polymers.building module polymerist.polymers.building.linear module polymerist.polymers.building.mbconvert module polymerist.polymers.building.sequencing module polymerist.polymers.estimation module polymerist.polymers.exceptions module polymerist.polymers.monographs module polymerist.polymers.monomers module polymerist.polymers.monomers.fragments module polymerist.polymers.monomers.repr module polymerist.polymers.monomers.specification module polymerist.polymers.smidgelib module polymerist.polymers.smidgelib.smidgebonds module polymerist.polymers.smidgelib.smidgeread module polymerist.polymers.smidgelib.smidgewrite module polymerist.rdutils module polymerist.rdutils.bonding module polymerist.rdutils.bonding.dissolution module polymerist.rdutils.bonding.formation module polymerist.rdutils.bonding.identification module polymerist.rdutils.bonding.permutation module polymerist.rdutils.bonding.portlib module polymerist.rdutils.bonding.substitution module polymerist.rdutils.chemlabel module polymerist.rdutils.rdcoords module polymerist.rdutils.rdcoords.piercing module polymerist.rdutils.rdcoords.tiling module polymerist.rdutils.rdgraphs module polymerist.rdutils.rdkdraw module polymerist.rdutils.rdprops module polymerist.rdutils.rdprops.atomprops module polymerist.rdutils.rdprops.bijection module polymerist.rdutils.rdprops.bondprops module polymerist.rdutils.reactions module polymerist.rdutils.reactions.assembly module polymerist.rdutils.reactions.fragment module polymerist.rdutils.reactions.reactexc module polymerist.rdutils.reactions.reactinfo module polymerist.rdutils.reactions.reactions module polymerist.rdutils.reactions.reactors module polymerist.rdutils.sanitization module polymerist.rdutils.selection module polymerist.rdutils.substructures module polymerist.smileslib module polymerist.smileslib.chemdbqueries module polymerist.smileslib.cleanup module polymerist.smileslib.functgroups module polymerist.smileslib.primitives module polymerist.smileslib.special module polymerist.unitutils module polymerist.unitutils.dimensions module polymerist.unitutils.extraunits module polymerist.unitutils.physconsts module polymerist.unitutils.unitstr module POLYMERIST_TOOLKIT_REGISTRY (in module polymerist.mdtools.openfftools) PolymerizationReactor (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.reactors) pop() (polymerist.genutils.containers.UnorderedRegistry method) Port (class in polymerist.rdutils.bonding.portlib) PORT_QUERY (in module polymerist.rdutils.bonding.portlib) PORT_SCHEMA (in module polymerist.rdutils.bonding.portlib) POSITIONAL_PARAMETER_TYPES (in module polymerist.genutils.decorators.signatures) PositionalNumberingSystem (class in polymerist.maths.numbersys.positional) powerset() (in module polymerist.genutils.iteration) predecessors (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) PREMATURE_CLOSURE (polymerist.genutils.textual.delimiters.DelimiterBalanceState attribute) prepare_reporters() (polymerist.mdtools.openmmtools.reporters.ReporterParameters method) prepend_parent() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.pathutils) presize_subplots() (in module polymerist.graphics.plotutils) pressure (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) (polymerist.mdtools.openmmtools.thermo.BarostatParameters attribute) prev_idx (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister property) prime_factorization() (in module polymerist.maths.primes) proc_name (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler attribute) procrustean_alignment() (polymerist.polymers.building.sequencing.LinearCopolymerSequencer method) procrustean_string() (in module polymerist.genutils.textual.prettyprint) produce_fragments() (polymerist.rdutils.reactions.fragment.IntermonomerBondIdentificationStrategy method) (polymerist.rdutils.reactions.IntermonomerBondIdentificationStrategy method) product() (in module polymerist.genutils.iteration) product_atom_idx (polymerist.rdutils.reactions.AtomTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.AtomTraceInfo attribute) product_bond_idx (polymerist.rdutils.reactions.BondTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.BondTraceInfo attribute) product_idx (polymerist.rdutils.reactions.AtomTraceInfo attribute) (polymerist.rdutils.reactions.BondTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.AtomTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.BondTraceInfo attribute) products() (polymerist.rdutils.reactions.assembly.ReactionAssembler method) (polymerist.rdutils.reactions.ReactionAssembler method) products_by_importance() (polymerist.rdutils.reactions.assembly.ReactionAssembler method) (polymerist.rdutils.reactions.ReactionAssembler method) ProductTemplateMismatch propagate() (polymerist.rdutils.reactions.PolymerizationReactor method) (polymerist.rdutils.reactions.reactors.PolymerizationReactor method) propagate_pooled() (polymerist.rdutils.reactions.PolymerizationReactor method) (polymerist.rdutils.reactions.reactors.PolymerizationReactor method) propogate_msg() (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler method) pubchempy_error (in module polymerist.smileslib.chemdbqueries) PubChemQueryStrategy (class in polymerist.smileslib.chemdbqueries) PushNodeSuccessor (class in polymerist.polymers.smidgelib.smidgewrite) python_type (polymerist.genutils.fileutils.jsonio.serialize.TypeSerializer attribute) (polymerist.genutils.fileutils.jsonio.TypeSerializer attribute)

Q

quantities_approx_equal() (in module polymerist.unitutils) (in module polymerist.unitutils.dimensions) Quantity (in module polymerist.unitutils.dimensions) QuantitySerializer (class in polymerist.genutils.fileutils.jsonio) (class in polymerist.genutils.fileutils.jsonio.serialize) query_atom (in module polymerist.smileslib.special)

queryable_namespaces() (polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy class method) (polymerist.smileslib.chemdbqueries.NIHCACTUSQueryStrategy class method) (polymerist.smileslib.chemdbqueries.PubChemQueryStrategy class method) queryable_properties() (polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy class method) (polymerist.smileslib.chemdbqueries.NIHCACTUSQueryStrategy class method) (polymerist.smileslib.chemdbqueries.PubChemQueryStrategy class method)

R

radices (polymerist.maths.numbersys.commonbases.FactorialNumberSystem property) (polymerist.maths.numbersys.commonbases.FixedRadixNumberSystem property) (polymerist.maths.numbersys.FactorialNumberSystem property) (polymerist.maths.numbersys.FixedRadixNumberSystem property) (polymerist.maths.numbersys.positional.PositionalNumberingSystem property) radix (polymerist.maths.numbersys.commonbases.FixedRadixNumberSystem property) (polymerist.maths.numbersys.FixedRadixNumberSystem property) randomize_points() (polymerist.maths.lattices.coordinates.Coordinates method) randRot() (in module polymerist.maths.linearalg.affine) Ratio (class in polymerist.maths.fractions.ratios) Rational (class in polymerist.maths.fractions.ratios) rational_approxes() (in module polymerist.maths.fractions.continued) RDATOM_MAGIC_PROPS (in module polymerist.rdutils.rdprops) rdmol_effective_radius() (in module polymerist.rdutils.rdcoords.tiling) RDMOL_MAGIC_PROPS (in module polymerist.rdutils.rdprops) rdmol_prop_heatmap() (in module polymerist.rdutils.rdkdraw) rdmol_prop_heatmap_colorscaled() (in module polymerist.rdutils.rdkdraw) rdmol_to_networkx() (in module polymerist.rdutils.rdgraphs) rdmols() (polymerist.polymers.monomers.MonomerGroup method) (polymerist.polymers.monomers.repr.MonomerGroup method) RDPROP_GETTERS (in module polymerist.rdutils.rdprops) RDPROP_SETTERS (in module polymerist.rdutils.rdprops) react() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) reactant_atom_idx (polymerist.rdutils.reactions.AtomTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.AtomTraceInfo attribute) reactant_idx (polymerist.rdutils.reactions.AtomTraceInfo attribute) (polymerist.rdutils.reactions.reactinfo.AtomTraceInfo attribute) REACTANT_INDEX_PROPNAME (in module polymerist.rdutils.reactions.reactinfo) reactants (polymerist.rdutils.reactions.assembly.ReactionAssembler property) (polymerist.rdutils.reactions.ReactionAssembler property) reactants_are_compatible() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) ReactantTemplateMismatch ReactionAssembler (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.assembly) reactive_atom_info (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) reactive_groups (polymerist.rdutils.reactions.assembly.ReactionAssembler attribute) (polymerist.rdutils.reactions.ReactionAssembler attribute) read_smidge() (polymerist.polymers.smidgelib.smidgeread.SMIDGEReader method) Real (in module polymerist.maths.fractions.continued) real_to_continued_fraction_coeffs() (in module polymerist.maths.fractions.continued) reciprocal (polymerist.maths.fractions.ratios.Ratio property) RecursiveDict (class in polymerist.genutils.containers) redistributed_charges() (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargeRedistributionStrategy method) (polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution.ChargeRedistributionStrategy method) reduce() (polymerist.maths.fractions.ratios.Rational method) (polymerist.polymers.building.sequencing.LinearCopolymerSequencer method) reduce_angles() (polymerist.maths.lattices.bravais.LatticeParameters method) reduced (polymerist.maths.fractions.ratios.Rational property) reduced() (polymerist.polymers.building.sequencing.LinearCopolymerSequencer method) regex (polymerist.genutils.logutils.timestamps.Timestamp attribute)

register_abstract_class_attrs() (in module polymerist.genutils.decorators.classmod) register_logger() (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler method) register_loggers() (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler method) register_subclasses() (in module polymerist.genutils.decorators.classmod) register_submodules() (in module polymerist.genutils.importutils.pkgiter) relabel_map_nums() (in module polymerist.rdutils.chemlabel) relative_module_name() (in module polymerist.genutils.importutils.pkginspect) RENDER_STYLE_MAP (in module polymerist.genutils.trees.treeviz) rep_configs (polymerist.mdtools.openmmtools.reporters.ReporterParameters property) repeat_string_to_length() (in module polymerist.genutils.textual.substrings) report_checkpoint (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) report_duration (polymerist.mdtools.openmmtools.parameters.IntegratorParameters property) report_interval (polymerist.mdtools.openmmtools.parameters.IntegratorParameters property) report_state (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) report_state_data (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) report_trajectory (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) Reporter (in module polymerist.mdtools.openmmtools.reporters) reporter_dict (polymerist.mdtools.openmmtools.reporters.ReporterConfig attribute) reporter_params (polymerist.mdtools.openmmtools.parameters.SimulationParameters attribute) reporter_paths (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) ReporterConfig (class in polymerist.mdtools.openmmtools.reporters) ReporterInitializer (in module polymerist.mdtools.openmmtools.reporters) ReporterParameters (class in polymerist.mdtools.openmmtools.reporters) representable_as_int() (in module polymerist.genutils.textual.encoding) requires_modules() (in module polymerist.genutils.importutils.dependencies) ReseparateRGroups (class in polymerist.rdutils.reactions) (class in polymerist.rdutils.reactions.fragment) reset() (polymerist.genutils.containers.UnorderedRegistry method) residual (polymerist.polymers.building.sequencing.LinearCopolymerSequencer attribute) residue_name (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargedResidue attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargedResidue attribute) ReturnType (in module polymerist.genutils.decorators.meta) (in module polymerist.genutils.importutils.dependencies) (in module polymerist.genutils.typetools.interfaces) (in module polymerist.mdtools.openfftools.unitsys) reverse (polymerist.maths.combinatorics.permutations.Permutation property) RGB (in module polymerist.graphics.colors) RGBA (in module polymerist.graphics.colors) RIGHT (polymerist.genutils.textual.prettyprint.Justification attribute) ring_piercing_idxs (in module polymerist.rdutils.rdcoords.piercing) run_simulation_schedule() (in module polymerist.mdtools.openmmtools.execution) rxn_name (polymerist.rdutils.reactions.assembly.ReactionAssembler attribute) (polymerist.rdutils.reactions.ReactionAssembler attribute) rxn_schema (polymerist.rdutils.reactions.PolymerizationReactor attribute) (polymerist.rdutils.reactions.reactors.PolymerizationReactor attribute) rxnname (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) rxnname_from_rxnfile() (polymerist.rdutils.reactions.AnnotatedReaction class method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction class method) RXNNAME_LINE_NO (polymerist.rdutils.reactions.AnnotatedReaction attribute) (polymerist.rdutils.reactions.reactions.AnnotatedReaction attribute) RXNNAME_RE (polymerist.rdutils.reactions.AnnotatedReaction attribute) (polymerist.rdutils.reactions.reactions.AnnotatedReaction attribute)

S

S (in module polymerist.genutils.sequences) (in module polymerist.genutils.sequences.seqops) sanitizable_mol_outputs() (in module polymerist.rdutils.sanitization) sanitize_mol() (in module polymerist.rdutils.sanitization) saturate_ports() (in module polymerist.rdutils.bonding.substitution) save_molecule() (in module polymerist.mdtools.openfftools.topology) scatter_3D() (in module polymerist.graphics.plotutils) scrape_SMARTS() (in module polymerist.smileslib.functgroups) second (polymerist.genutils.duration.Duration attribute) SECONDS_PER_INTERVAL (in module polymerist.genutils.duration) SECONDS_PER_INTERVAL_ORDERED (in module polymerist.genutils.duration) sequence_kernel (polymerist.polymers.building.sequencing.LinearCopolymerSequencer attribute) sequence_residual (polymerist.polymers.building.sequencing.LinearCopolymerSequencer property) SerialAtomLabeller (class in polymerist.molfiles.pdb) (class in polymerist.molfiles.pdb.pdbatoms) serialize_openmm_pdb() (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.topology) serialize_state_from_context() (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.state) serialize_system() (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.system) serialize_topology_from_simulation() (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.topology) service_name (polymerist.smileslib.chemdbqueries.NIHCACTUSQueryStrategy attribute) (polymerist.smileslib.chemdbqueries.PubChemQueryStrategy attribute) set_rdkdraw_size() (in module polymerist.rdutils) (in module polymerist.rdutils.rdkdraw) sgnmag() (in module polymerist.maths.fractions.ratios) Shape (in module polymerist.genutils.typetools.numpytypes) shortest_repeating_substring() (in module polymerist.genutils.textual.substrings) sign (polymerist.maths.combinatorics.permutations.Permutation property) simplifed (polymerist.maths.fractions.ratios.Rational attribute) simplify (polymerist.maths.fractions.ratios.Rational attribute) simulation_from_thermo() (in module polymerist.mdtools.openmmtools.preparation) SimulationParameters (class in polymerist.mdtools.openmmtools.parameters) SimulationPaths (class in polymerist.mdtools.openmmtools.serialization) (class in polymerist.mdtools.openmmtools.serialization.paths) skin (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) sliding_window() (in module polymerist.genutils.iteration) Smarts (in module polymerist.smileslib) (in module polymerist.smileslib.cleanup) SMARTS (polymerist.mdtools.openfftools.partialcharge.rescharge.ChargedResidue attribute) (polymerist.mdtools.openfftools.partialcharge.rescharge.rctypes.ChargedResidue attribute) (polymerist.polymers.monomers.MonomerGroup property) (polymerist.polymers.monomers.repr.MonomerGroup property) smarts (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) SMARTS (polymerist.smileslib.functgroups.FnGroupSMARTSEntry attribute) SMARTS_desc (polymerist.smileslib.functgroups.FnGroupSMARTSEntry attribute) SMIDGEReader (class in polymerist.polymers.smidgelib.smidgeread) SMIDGEReaderRegister (class in polymerist.polymers.smidgelib.smidgeread) SMIDGEReadState (class in polymerist.polymers.smidgelib.smidgeread) SMIDGEWriter (class in polymerist.polymers.smidgelib.smidgewrite) SMIDGEWriterRegister (class in polymerist.polymers.smidgelib.smidgewrite) SMIDGEWriterState (class in polymerist.polymers.smidgelib.smidgewrite) Smiles (in module polymerist.smileslib) (in module polymerist.smileslib.cleanup) smiles (polymerist.rdutils.reactions.AnnotatedReaction property) (polymerist.rdutils.reactions.reactions.AnnotatedReaction property) snake_case_to_camel_case() (in module polymerist.genutils.textual.casing) solutions (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample attribute) sort_dict_by_keys() (in module polymerist.genutils.iteration) sort_dict_by_values() (in module polymerist.genutils.iteration) source_file (polymerist.genutils.importutils.pyimports.ImportedObjectInfo attribute) spatial_data_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) SPECIAL_QUERY_ATOMS (in module polymerist.smileslib.special) SPECIAL_QUERY_MOLS (in module polymerist.smileslib.special) SPECIAL_QUERY_SMARTS (in module polymerist.smileslib.special)

splice_atoms() (in module polymerist.rdutils.bonding.substitution) start_time (polymerist.genutils.duration.Timer attribute) startfile() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.filetree) starting_from_index() (polymerist.maths.combinatorics.permutations.Cycle method) statcoulomb (in module polymerist.unitutils.extraunits) statcoulomb_base_unit (in module polymerist.unitutils.extraunits) state (polymerist.polymers.smidgelib.smidgeread.SMIDGEReader attribute) (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriter attribute) state_action() (polymerist.polymers.smidgelib.smidgeread.Accumulate method) (polymerist.polymers.smidgelib.smidgeread.BondEnd method) (polymerist.polymers.smidgelib.smidgeread.BondStart method) (polymerist.polymers.smidgelib.smidgeread.BranchEnd method) (polymerist.polymers.smidgelib.smidgeread.BranchStart method) (polymerist.polymers.smidgelib.smidgeread.ChainNew method) (polymerist.polymers.smidgelib.smidgeread.MonomerEnd method) (polymerist.polymers.smidgelib.smidgeread.MonomerStart method) (polymerist.polymers.smidgelib.smidgeread.SMIDGEReadState method) (polymerist.polymers.smidgelib.smidgewrite.BranchEnd method) (polymerist.polymers.smidgelib.smidgewrite.BranchStart method) (polymerist.polymers.smidgelib.smidgewrite.CheckIsVisitedNode method) (polymerist.polymers.smidgelib.smidgewrite.PushNodeSuccessor method) (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterState method) (polymerist.polymers.smidgelib.smidgewrite.UpdateNodeSuccessors method) (polymerist.polymers.smidgelib.smidgewrite.VisitNode method) (polymerist.polymers.smidgelib.smidgewrite.WriteEdge method) (polymerist.polymers.smidgelib.smidgewrite.WriteNode method) STATE_DAT_REPORTERS (in module polymerist.mdtools.openmmtools.reporters) state_data (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) state_data_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) state_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) StateLike (in module polymerist.mdtools.openmmtools.serialization) (in module polymerist.mdtools.openmmtools.serialization.state) StateReporter (class in polymerist.mdtools.openmmtools.reporters) statvolt (in module polymerist.unitutils.extraunits) statvolt_base_unit (in module polymerist.unitutils.extraunits) stirling_first() (in module polymerist.maths.combinatorics.numbers) stirling_second() (in module polymerist.maths.combinatorics.numbers) str_buffer (polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister attribute) strategy (polymerist.genutils.sequences.discernment.DISCERNMENTSolver attribute) (polymerist.genutils.sequences.discernment.enumeration.DISCERNMENTSolver attribute) stringify_dict() (in module polymerist.genutils.textual.prettyprint) strip_units() (in module polymerist.unitutils) (in module polymerist.unitutils.dimensions) STYLE_NAME (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) subhandler() (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler method) submodule_loggers() (in module polymerist.genutils.logutils.IOHandlers) SUBSTITUTION (polymerist.genutils.sequences.similarity.edits.EditOperation attribute) SubstructMatchFailedError successors (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) sum (polymerist.mdtools.openfftools.partialcharge.rescharge.calculation.Accumulator attribute) summarize_ring_piercing() (in module polymerist.rdutils.rdcoords.piercing) support (polymerist.maths.combinatorics.permutations.Permutation property) support_size (polymerist.maths.combinatorics.permutations.Permutation property) SUPPRESS_LAMMPS_STDOUT (in module polymerist.mdtools.lammpstools.lammpseval) suppress_rdkit_errors() (in module polymerist.smileslib.cleanup) surrounds() (polymerist.maths.lattices.coordinates.BoundingBox method) swap_bonds() (in module polymerist.rdutils.bonding.permutation) symbol_index_map (polymerist.genutils.sequences.discernment.inventory.SymbolInventory property) (polymerist.genutils.sequences.discernment.SymbolInventory property) symbol_inventory (polymerist.genutils.sequences.discernment.DISCERNMENTSolver property) (polymerist.genutils.sequences.discernment.enumeration.DISCERNMENTSolver property) SymbolInventory (class in polymerist.genutils.sequences.discernment) (class in polymerist.genutils.sequences.discernment.inventory) symmetric_group() (polymerist.maths.combinatorics.permutations.Permutation class method) system_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute)

T

T (in module polymerist.genutils.containers) (in module polymerist.genutils.decorators.functional) (in module polymerist.genutils.fileutils.jsonio.serialize) (in module polymerist.genutils.fileutils.pathutils) (in module polymerist.genutils.filters) (in module polymerist.genutils.iteration) (in module polymerist.genutils.sequences) (in module polymerist.genutils.sequences.discernment.examples) (in module polymerist.genutils.sequences.discernment.inventory) (in module polymerist.genutils.sequences.seqops) (in module polymerist.genutils.sequences.similarity.distances) (in module polymerist.genutils.sequences.similarity.edits) (in module polymerist.genutils.trees.treebase) (in module polymerist.maths.combinatorics.permutations) (in module polymerist.rdutils.rdprops.atomprops) (in module polymerist.rdutils.rdprops.bondprops) (in module polymerist.smileslib.cleanup) (in module polymerist.unitutils.dimensions) T1 (in module polymerist.genutils.iteration) T2 (in module polymerist.genutils.iteration) tanimoto_distance (in module polymerist.genutils.sequences.similarity.distances) target_word (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample attribute) TCall (in module polymerist.genutils.importutils.dependencies) temperature (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) (polymerist.mdtools.openmmtools.thermo.BarostatParameters attribute) (polymerist.mdtools.openmmtools.thermo.ThermostatParameters attribute) temporary_cd() (in module polymerist.genutils.fileutils) (in module polymerist.genutils.fileutils.filetree) term_orient (polymerist.polymers.monomers.MonomerGroup attribute) (polymerist.polymers.monomers.repr.MonomerGroup attribute) terminal_monomers (polymerist.polymers.monographs.MonomerGraph property) thermo_params (polymerist.mdtools.openmmtools.parameters.SimulationParameters attribute) ThermoParameters (class in polymerist.mdtools.openmmtools.thermo) Thermostat (class in polymerist.mdtools.openmmtools.thermo) thermostat (polymerist.mdtools.openmmtools.thermo.ThermostatParameters attribute) thermostat_params (polymerist.mdtools.openmmtools.thermo.ThermoParameters attribute) ThermostatParameters (class in polymerist.mdtools.openmmtools.thermo) ThermostatSerializer (in module polymerist.mdtools.openmmtools.thermo) tight_norm_for_rdmol_prop() (in module polymerist.rdutils.rdkdraw) tile_lattice_with_rdmol() (in module polymerist.rdutils.rdcoords.tiling) time (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) time_data_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) time_points (polymerist.mdtools.openmmtools.parameters.IntegratorParameters property) time_step (polymerist.mdtools.openmmtools.parameters.IntegratorParameters attribute) time_taken (polymerist.genutils.duration.Timer attribute) Timeable (in module polymerist.genutils.duration) Timer (class in polymerist.genutils.duration) timescale (polymerist.mdtools.openmmtools.thermo.ThermostatParameters attribute) Timestamp (class in polymerist.genutils.logutils.timestamps) TIMESTAMP_FMT (in module polymerist.genutils.logutils.timestamps) TIMESTAMP_LOG (in module polymerist.genutils.logutils.timestamps)

timestamp_now() (polymerist.genutils.logutils.timestamps.Timestamp method) TIMESTAMP_RE (in module polymerist.genutils.logutils.timestamps) TimeTemplate (class in polymerist.genutils.duration) TKWRAPPER_TYPES (in module polymerist.mdtools.openfftools) TKWRAPPERS (in module polymerist.mdtools.openfftools) to_cycles() (polymerist.maths.combinatorics.permutations.Permutation method) to_file() (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample method) to_json() (polymerist.genutils.sequences.discernment.examples.DISCERNMENTExample method) to_latex() (polymerist.maths.fractions.ratios.Ratio method) to_lattice_vectors() (polymerist.maths.lattices.bravais.LatticeParameters method) to_lehmer_code() (polymerist.maths.combinatorics.permutations.Permutation method) to_matrix() (polymerist.maths.combinatorics.permutations.Permutation method) to_rdkit_with_metadata() (in module polymerist.mdtools.openfftools.topology) to_rxnfile() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) to_seconds() (polymerist.genutils.duration.Duration method) to_smarts() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) to_smidge_string() (polymerist.polymers.monographs.MonomerGraph method) to_smiles() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) to_word() (polymerist.maths.combinatorics.permutations.Permutation method) tokens (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) TOOLKITS_BY_CHARGE_METHOD (in module polymerist.mdtools.openfftools) (in module polymerist.mdtools.openfftools.partialcharge) topology_from_molecule_onto_lattice() (in module polymerist.mdtools.openfftools.topology) topology_from_sdf() (in module polymerist.mdtools.openfftools.topology) topology_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) topology_to_sdf() (in module polymerist.mdtools.openfftools.topology) torque (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute) total_seconds (polymerist.genutils.duration.Duration property) total_time (polymerist.mdtools.openmmtools.parameters.IntegratorParameters attribute) traj_ext (polymerist.mdtools.openmmtools.reporters.ReporterParameters attribute) TRAJ_REPORTERS (in module polymerist.mdtools.openmmtools.reporters) trajectory_path (polymerist.mdtools.openmmtools.serialization.paths.SimulationPaths attribute) (polymerist.mdtools.openmmtools.serialization.SimulationPaths attribute) TrajectoryReporter (in module polymerist.mdtools.openmmtools.reporters) transition() (polymerist.polymers.smidgelib.smidgeread.SMIDGEReadState method) (polymerist.polymers.smidgelib.smidgewrite.BranchEnd method) (polymerist.polymers.smidgelib.smidgewrite.BranchStart method) (polymerist.polymers.smidgelib.smidgewrite.CheckIsVisitedNode method) (polymerist.polymers.smidgelib.smidgewrite.DetermineNodeSuccessors method) (polymerist.polymers.smidgelib.smidgewrite.PushNodeSuccessor method) (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterState method) (polymerist.polymers.smidgelib.smidgewrite.UpdateNodeSuccessors method) (polymerist.polymers.smidgelib.smidgewrite.VisitNode method) (polymerist.polymers.smidgelib.smidgewrite.WriteEdge method) (polymerist.polymers.smidgelib.smidgewrite.WriteNode method) translate() (polymerist.maths.lattices.coordinates.Coordinates method) traverse_wf_matrix() (in module polymerist.genutils.sequences.similarity.edits) tree_to_networkx() (in module polymerist.genutils.trees) (in module polymerist.genutils.trees.treecopy) treestr() (in module polymerist.genutils.trees) (in module polymerist.genutils.trees.treeviz) (in module polymerist.mdtools.openfftools) type_sers (polymerist.genutils.fileutils.jsonio.MultiTypeSerializer property) (polymerist.genutils.fileutils.jsonio.serialize.MultiTypeSerializer property) TypeSerializer (class in polymerist.genutils.fileutils.jsonio) (class in polymerist.genutils.fileutils.jsonio.serialize)

U

U (in module polymerist.genutils.typetools.categorical) UNCHANGED (polymerist.rdutils.reactions.BondChange attribute) (polymerist.rdutils.reactions.reactinfo.BondChange attribute) UNCLOSED_OPENING (polymerist.genutils.textual.delimiters.DelimiterBalanceState attribute) UniformDistributionStrategy (class in polymerist.mdtools.openfftools.partialcharge.rescharge) (class in polymerist.mdtools.openfftools.partialcharge.rescharge.redistribution) unique_monomer_names (polymerist.polymers.monographs.MonomerGraph property) unique_string() (in module polymerist.genutils.textual.substrings) uniquify_force_groups() (in module polymerist.mdtools.openmmtools.forces)

Unit (in module polymerist.unitutils.dimensions) unit_from_unit_str() (in module polymerist.unitutils.unitstr) UNITS_BY_NAME (in module polymerist.unitutils.unitstr) UNITS_BY_SYMBOL (in module polymerist.unitutils.unitstr) UnorderedRegistry (class in polymerist.genutils.containers) unpackage_atom_metadata() (in module polymerist.mdtools.openfftools.topology) unregister_logger() (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler method) unregister_loggers() (polymerist.genutils.logutils.IOHandlers.MultiStreamFileHandler method) update_frequency (polymerist.mdtools.openmmtools.thermo.BarostatParameters attribute) UpdateNodeSuccessors (class in polymerist.polymers.smidgelib.smidgewrite)

V

V (in module polymerist.genutils.iteration) valid_reactant_ordering() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) validate_braces (in module polymerist.genutils.textual.delimiters) validate_common_delimiters() (in module polymerist.genutils.textual.delimiters) validate_point() (polymerist.maths.lattices.coordinates.Coordinates method) validate_property() (polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy method) validate_reactants() (polymerist.rdutils.reactions.AnnotatedReaction method) (polymerist.rdutils.reactions.reactions.AnnotatedReaction method) Vector (in module polymerist.mdtools.openfftools.boxvectors) VectorQuantity (in module polymerist.mdtools.openfftools.boxvectors) velocity (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyle attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleCGS attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleElectron attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMetal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleMicro attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleNano attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleReal attribute) (polymerist.mdtools.lammpstools.unitstyles.LAMMPSUnitStyleSI attribute)

vertices (polymerist.maths.lattices.coordinates.BoundingBox property) visited (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister attribute) VisitNode (class in polymerist.polymers.smidgelib.smidgewrite) visualize (polymerist.polymers.monographs.MonomerGraph attribute) volume (polymerist.maths.lattices.bravais.LatticeParameters property)

W

water (in module polymerist.mdtools.openfftools.solvation.solvents) weighted_centroid() (polymerist.maths.lattices.coordinates.Coordinates method) write_smidge() (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriter method)

write_smidge_connected_component() (polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriter method) WriteEdge (class in polymerist.polymers.smidgelib.smidgewrite) WriteNode (class in polymerist.polymers.smidgelib.smidgewrite)

X

xRot() (in module polymerist.maths.linearalg.affine) xyz_to_box_vectors() (in module polymerist.mdtools.openfftools.boxvectors)

xyzScale() (in module polymerist.maths.linearalg.affine) xyzTrans() (in module polymerist.maths.linearalg.affine)

Y

year (polymerist.genutils.duration.Duration attribute)

yRot() (in module polymerist.maths.linearalg.affine)

Z

zRot() (in module polymerist.maths.linearalg.affine)