diff --git a/reference/external/logparser/base.html b/reference/external/logparser/base.html index e4e85a7b..72a72de9 100644 --- a/reference/external/logparser/base.html +++ b/reference/external/logparser/base.html @@ -748,7 +748,7 @@
-interact_irc(sanitize: bool = False, converged: bool = True, backend: str = 'openbabel', continuous_update: bool = False) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7fa8ca212bc0>#
+interact_irc(sanitize: bool = False, converged: bool = True, backend: str = 'openbabel', continuous_update: bool = False) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7f387e0f24d0>#

Create a IPython interactive widget to investigate the IRC results.

Parameters:
@@ -767,7 +767,7 @@
-interact_opt(sanitize: bool = True, backend: str = 'openbabel', continuous_update: bool = False) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7fa8ca212bc0>#
+interact_opt(sanitize: bool = True, backend: str = 'openbabel', continuous_update: bool = False) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7f387e0f24d0>#

Create a IPython interactive widget to investigate the optimization convergence.

Parameters:
@@ -904,7 +904,7 @@
-view_freq(mode_idx: int = 0, frames: int = 10, amplitude: float = 1.0, *args, **kwargs) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7fa8ca212bc0>#
+view_freq(mode_idx: int = 0, frames: int = 10, amplitude: float = 1.0, *args, **kwargs) → <ipywidgets.widgets.interaction._InteractFactory object at 0x7f387e0f24d0>#

Create a Py3DMol viewer for the frequency mode.

Parameters:
diff --git a/searchindex.js b/searchindex.js index bda3e028..d62550e2 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["index", "reference/cite", "reference/conf", "reference/conformer_generation/embedding_geometries/align", "reference/conformer_generation/embedding_geometries/embedders", "reference/conformer_generation/embedding_geometries/index", "reference/conformer_generation/embedding_geometries/ts_guessers", "reference/conformer_generation/geometry_optimization/index", "reference/conformer_generation/geometry_optimization/optimizers", "reference/conformer_generation/geometry_optimization/ts_optimizers", "reference/conformer_generation/index", "reference/conformer_generation/postprocessing/index", "reference/conformer_generation/postprocessing/pruners", "reference/conformer_generation/postprocessing/solvation", "reference/conformer_generation/postprocessing/ts_verifiers", "reference/conformer_generation/postprocessing/verifiers", 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"rdmc.external.logparser.base.BaseLog.auto_update_prop"]], "cclib_results (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.cclib_results"]], "charge (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.charge"]], "converged_geometries (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.converged_geometries"]], "finished (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.finished"]], "freqs (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.freqs"]], "get_best_opt_geom() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_best_opt_geom"]], "get_converged_geom_idx() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_converged_geom_idx"]], "get_irc_midpoint() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_irc_midpoint"]], "get_lowest_e_geometry() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_lowest_e_geometry"]], "get_mol() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_mol"]], "get_scannames() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_scannames"]], "get_scanparams() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_scanparams"]], "get_scf_energies() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_scf_energies"]], "get_xyzs() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.get_xyzs"]], "guess_rxn_from_irc() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.guess_rxn_from_irc"]], "guess_rxn_from_normal_mode() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.guess_rxn_from_normal_mode"]], "initial_geometry (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.initial_geometry"]], "interact_freq() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_freq"]], "interact_irc() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_irc"]], "interact_opt() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_opt"]], "interact_scan() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.interact_scan"]], "is_ts (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.is_ts"]], "job_type (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.job_type"]], "multiplicity (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.multiplicity"]], "neg_freqs (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.neg_freqs"]], "num_all_geoms (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.num_all_geoms"]], "num_converged_geoms (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.num_converged_geoms"]], "num_neg_freqs (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.num_neg_freqs"]], "opt_convergence (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.opt_convergence"]], "opt_criteria (rdmc.external.logparser.base.baselog attribute)": [[29, "rdmc.external.logparser.base.BaseLog.opt_criteria"]], "optstatus (rdmc.external.logparser.base.ccliblog property)": [[29, "rdmc.external.logparser.base.CclibLog.optstatus"]], "plot_irc_energies() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.plot_irc_energies"]], "plot_opt_convergence() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.plot_opt_convergence"]], "plot_scan_energies() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.plot_scan_energies"]], "rdmc.external.logparser.base": [[29, "module-rdmc.external.logparser.base"]], "require_job_type() (rdmc.external.logparser.base.baselog method)": [[29, "rdmc.external.logparser.base.BaseLog.require_job_type"]], "require_ts() (rdmc.external.logparser.base.baselog method)": [[29, "rdmc.external.logparser.base.BaseLog.require_ts"]], "schemes (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.schemes"]], "success (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.success"]], "termination_time (rdmc.external.logparser.base.baselog property)": [[29, "rdmc.external.logparser.base.BaseLog.termination_time"]], "time_regex (rdmc.external.logparser.base.baselog attribute)": [[29, "rdmc.external.logparser.base.BaseLog.time_regex"]], "view_freq() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.view_freq"]], "view_mol() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.view_mol"]], "view_traj() (rdmc.external.logparser.base.ccliblog method)": [[29, "rdmc.external.logparser.base.CclibLog.view_traj"]], "gaussianlog (class in rdmc.external.logparser.gaussian)": [[30, "rdmc.external.logparser.gaussian.GaussianLog"]], "opt_criteria (rdmc.external.logparser.gaussian.gaussianlog attribute)": [[30, "rdmc.external.logparser.gaussian.GaussianLog.opt_criteria"]], "rdmc.external.logparser.gaussian": [[30, "module-rdmc.external.logparser.gaussian"]], "time_regex (rdmc.external.logparser.gaussian.gaussianlog attribute)": [[30, "rdmc.external.logparser.gaussian.GaussianLog.time_regex"]], "rdmc.external.logparser": [[31, "module-rdmc.external.logparser"]], "orcalog (class in rdmc.external.logparser.orca)": [[32, "rdmc.external.logparser.orca.ORCALog"]], "multiplicity (rdmc.external.logparser.orca.orcalog property)": [[32, "rdmc.external.logparser.orca.ORCALog.multiplicity"]], "opt_criteria (rdmc.external.logparser.orca.orcalog attribute)": [[32, "rdmc.external.logparser.orca.ORCALog.opt_criteria"]], "rdmc.external.logparser.orca": [[32, "module-rdmc.external.logparser.orca"]], "time_regex (rdmc.external.logparser.orca.orcalog attribute)": [[32, "rdmc.external.logparser.orca.ORCALog.time_regex"]], "qchemlog (class in rdmc.external.logparser.qchem)": [[33, "rdmc.external.logparser.qchem.QChemLog"]], "get_mol() (rdmc.external.logparser.qchem.qchemlog method)": [[33, "rdmc.external.logparser.qchem.QChemLog.get_mol"]], "get_scf_energies() (rdmc.external.logparser.qchem.qchemlog method)": [[33, "rdmc.external.logparser.qchem.QChemLog.get_scf_energies"]], "opt_critieria (rdmc.external.logparser.qchem.qchemlog attribute)": [[33, "rdmc.external.logparser.qchem.QChemLog.opt_critieria"]], "rdmc.external.logparser.qchem": [[33, "module-rdmc.external.logparser.qchem"]], "time_regex (rdmc.external.logparser.qchem.qchemlog attribute)": [[33, "rdmc.external.logparser.qchem.QChemLog.time_regex"]], "rdmc.external.logparser.utils": [[34, "module-rdmc.external.logparser.utils"]], "scheme_to_dict() (in module rdmc.external.logparser.utils)": [[34, "rdmc.external.logparser.utils.scheme_to_dict"]], "check_isomorphic_molecules() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.check_isomorphic_molecules"]], "find_reaction_family() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.find_reaction_family"]], "from_rdkit_mol() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.from_rdkit_mol"]], "generate_reaction_complex() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.generate_reaction_complex"]], "load_rmg_database() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.load_rmg_database"]], "load_rxn_family_database() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.load_rxn_family_database"]], "rdmc.external.rmg": [[35, "module-rdmc.external.rmg"]], "openbabelff (class in rdmc.forcefield)": [[36, "rdmc.forcefield.OpenBabelFF"]], "rdkitff (class in rdmc.forcefield)": [[36, "rdmc.forcefield.RDKitFF"]], "add_angle_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_angle_constraint"]], "add_angle_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_angle_constraint"]], "add_distance_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_distance_constraint"]], "add_distance_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_distance_constraint"]], "add_torsion_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_torsion_constraint"]], "add_torsion_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_torsion_constraint"]], "available_force_field (rdmc.forcefield.openbabelff attribute)": [[36, "rdmc.forcefield.OpenBabelFF.available_force_field"]], "available_force_field (rdmc.forcefield.rdkitff attribute)": [[36, "rdmc.forcefield.RDKitFF.available_force_field"]], "available_solver (rdmc.forcefield.openbabelff attribute)": [[36, "rdmc.forcefield.OpenBabelFF.available_solver"]], "fix_atom() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.fix_atom"]], "fix_atom() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.fix_atom"]], "get_conformer_energies() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_conformer_energies"]], "get_energy() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_energy"]], "get_optimized_mol() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.get_optimized_mol"]], "get_optimized_mol() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_optimized_mol"]], "get_roo_radical_atoms() (in module rdmc.forcefield)": [[36, "rdmc.forcefield.get_roo_radical_atoms"]], "is_optimizable() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.is_optimizable"]], "is_optimizable() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.is_optimizable"]], "make_optimizable() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.make_optimizable"]], "mol (rdmc.forcefield.openbabelff property)": [[36, "rdmc.forcefield.OpenBabelFF.mol"]], "mol (rdmc.forcefield.rdkitff property)": [[36, "rdmc.forcefield.RDKitFF.mol"]], "optimize() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.optimize"]], "optimize() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.optimize"]], "optimize_confs() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.optimize_confs"]], "optimize_mol() (in module rdmc.forcefield)": [[36, "rdmc.forcefield.optimize_mol"]], "rdmc.forcefield": [[36, "module-rdmc.forcefield"]], "recover_mol() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.recover_mol"]], "set_solver() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.set_solver"]], "setup() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.setup"]], "setup() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.setup"]], "torsional_scan_1d() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.torsional_scan_1d"]], "type (rdmc.forcefield.openbabelff property)": [[36, "rdmc.forcefield.OpenBabelFF.type"]], "type (rdmc.forcefield.rdkitff property)": [[36, "rdmc.forcefield.RDKitFF.type"]], "update_atom_idx() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.update_atom_idx"]], "update_atom_idx() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.update_atom_idx"]], "fourierseries1d (class in rdmc.mathlib.curvefit)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D"]], "fit() (rdmc.mathlib.curvefit.fourierseries1d method)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.fit"]], "max_num_term (rdmc.mathlib.curvefit.fourierseries1d attribute)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.max_num_term"]], "predict() (rdmc.mathlib.curvefit.fourierseries1d method)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.predict"]], "rdmc.mathlib.curvefit": [[38, "module-rdmc.mathlib.curvefit"]], "get_centroid() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_centroid"]], "get_distances_from_a_point() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_distances_from_a_point"]], "get_mass_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_mass_center"]], "get_max_distance_from_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_max_distance_from_center"]], "get_weighted_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_weighted_center"]], "rdmc.mathlib.geom": [[39, "module-rdmc.mathlib.geom"]], "rotate() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.rotate"]], "translate() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.translate"]], "translate_centroid() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.translate_centroid"]], "compare_to_adjacent_point() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.compare_to_adjacent_point"]], "get_energy() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.get_energy"]], "get_step_to_adjacent_points() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.get_step_to_adjacent_points"]], "rdmc.mathlib.greedymin": [[40, "module-rdmc.mathlib.greedymin"]], "search_for_a_minimum() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.search_for_a_minimum"]], "search_minimum() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.search_minimum"]], "rdmc.mathlib": [[41, "module-rdmc.mathlib"]], "addnullconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AddNullConformer"]], "addredundantbonds() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AddRedundantBonds"]], "alignmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AlignMol"]], "assignstereochemistryfrom3d() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AssignStereochemistryFrom3D"]], "calcrmsd() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.CalcRMSD"]], "combinemol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.CombineMol"]], "copy() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Copy"]], "embedconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedConformer"]], "embedmultipleconfs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedMultipleConfs"]], "embedmultiplenullconfs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedMultipleNullConfs"]], "embednullconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedNullConformer"]], "fromfile() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromFile"]], "frominchi() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromInchi"]], "frommol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromMol"]], "fromobmol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromOBMol"]], "fromrmgmol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromRMGMol"]], "fromsdf() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSDF"]], "fromsmarts() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSmarts"]], "fromsmiles() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSmiles"]], "fromxyz() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromXYZ"]], "getadjacencymatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAdjacencyMatrix"]], "getallconformers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAllConformers"]], "getatommapnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomMapNumbers"]], "getatommasses() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomMasses"]], "getatomicnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomicNumbers"]], "getbestalign() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetBestAlign"]], "getbondsastuples() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetBondsAsTuples"]], "getconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetConformer"]], "getconformers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetConformers"]], "getdistancematrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetDistanceMatrix"]], "getelementsymbols() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetElementSymbols"]], "getformalcharge() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetFormalCharge"]], "getinternalcoordinates() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetInternalCoordinates"]], "getmolfrags() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetMolFrags"]], "getpositions() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetPositions"]], "getspinmultiplicity() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSpinMultiplicity"]], "getsubstructmatch() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSubstructMatch"]], "getsubstructmatches() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSubstructMatches"]], "getsymmsssr() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSymmSSSR"]], "gettorsiontops() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetTorsionTops"]], "gettorsionalmodes() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetTorsionalModes"]], "getvdwmatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetVdwMatrix"]], "hascollidingatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.HasCollidingAtoms"]], "hassameconnectivity() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.HasSameConnectivity"]], "kekulize() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Kekulize"]], "prepareoutputmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.PrepareOutputMol"]], "rdkitmol (class in rdmc.mol)": [[42, "rdmc.mol.RDKitMol"]], "reflect() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Reflect"]], "removehs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.RemoveHs"]], "renumberatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.RenumberAtoms"]], "sanitize() 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rdmc.external.rmg)": [[35, "rdmc.external.rmg.find_reaction_family"]], "from_rdkit_mol() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.from_rdkit_mol"]], "generate_reaction_complex() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.generate_reaction_complex"]], "load_rmg_database() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.load_rmg_database"]], "load_rxn_family_database() (in module rdmc.external.rmg)": [[35, "rdmc.external.rmg.load_rxn_family_database"]], "rdmc.external.rmg": [[35, "module-rdmc.external.rmg"]], "openbabelff (class in rdmc.forcefield)": [[36, "rdmc.forcefield.OpenBabelFF"]], "rdkitff (class in rdmc.forcefield)": [[36, "rdmc.forcefield.RDKitFF"]], "add_angle_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_angle_constraint"]], "add_angle_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_angle_constraint"]], "add_distance_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_distance_constraint"]], "add_distance_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_distance_constraint"]], "add_torsion_constraint() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.add_torsion_constraint"]], "add_torsion_constraint() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.add_torsion_constraint"]], "available_force_field (rdmc.forcefield.openbabelff attribute)": [[36, "rdmc.forcefield.OpenBabelFF.available_force_field"]], "available_force_field (rdmc.forcefield.rdkitff attribute)": [[36, "rdmc.forcefield.RDKitFF.available_force_field"]], "available_solver (rdmc.forcefield.openbabelff attribute)": [[36, "rdmc.forcefield.OpenBabelFF.available_solver"]], "fix_atom() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.fix_atom"]], "fix_atom() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.fix_atom"]], "get_conformer_energies() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_conformer_energies"]], "get_energy() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_energy"]], "get_optimized_mol() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.get_optimized_mol"]], "get_optimized_mol() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.get_optimized_mol"]], "get_roo_radical_atoms() (in module rdmc.forcefield)": [[36, "rdmc.forcefield.get_roo_radical_atoms"]], "is_optimizable() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.is_optimizable"]], "is_optimizable() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.is_optimizable"]], "make_optimizable() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.make_optimizable"]], "mol (rdmc.forcefield.openbabelff property)": [[36, "rdmc.forcefield.OpenBabelFF.mol"]], "mol (rdmc.forcefield.rdkitff property)": [[36, "rdmc.forcefield.RDKitFF.mol"]], "optimize() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.optimize"]], "optimize() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.optimize"]], "optimize_confs() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.optimize_confs"]], "optimize_mol() (in module rdmc.forcefield)": [[36, "rdmc.forcefield.optimize_mol"]], "rdmc.forcefield": [[36, "module-rdmc.forcefield"]], "recover_mol() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.recover_mol"]], "set_solver() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.set_solver"]], "setup() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.setup"]], "setup() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.setup"]], "torsional_scan_1d() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.torsional_scan_1d"]], "type (rdmc.forcefield.openbabelff property)": [[36, "rdmc.forcefield.OpenBabelFF.type"]], "type (rdmc.forcefield.rdkitff property)": [[36, "rdmc.forcefield.RDKitFF.type"]], "update_atom_idx() (rdmc.forcefield.openbabelff method)": [[36, "rdmc.forcefield.OpenBabelFF.update_atom_idx"]], "update_atom_idx() (rdmc.forcefield.rdkitff method)": [[36, "rdmc.forcefield.RDKitFF.update_atom_idx"]], "fourierseries1d (class in rdmc.mathlib.curvefit)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D"]], "fit() (rdmc.mathlib.curvefit.fourierseries1d method)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.fit"]], "max_num_term (rdmc.mathlib.curvefit.fourierseries1d attribute)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.max_num_term"]], "predict() (rdmc.mathlib.curvefit.fourierseries1d method)": [[38, "rdmc.mathlib.curvefit.FourierSeries1D.predict"]], "rdmc.mathlib.curvefit": [[38, "module-rdmc.mathlib.curvefit"]], "get_centroid() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_centroid"]], "get_distances_from_a_point() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_distances_from_a_point"]], "get_mass_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_mass_center"]], "get_max_distance_from_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_max_distance_from_center"]], "get_weighted_center() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.get_weighted_center"]], "rdmc.mathlib.geom": [[39, "module-rdmc.mathlib.geom"]], "rotate() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.rotate"]], "translate() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.translate"]], "translate_centroid() (in module rdmc.mathlib.geom)": [[39, "rdmc.mathlib.geom.translate_centroid"]], "compare_to_adjacent_point() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.compare_to_adjacent_point"]], "get_energy() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.get_energy"]], "get_step_to_adjacent_points() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.get_step_to_adjacent_points"]], "rdmc.mathlib.greedymin": [[40, "module-rdmc.mathlib.greedymin"]], "search_for_a_minimum() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.search_for_a_minimum"]], "search_minimum() (in module rdmc.mathlib.greedymin)": [[40, "rdmc.mathlib.greedymin.search_minimum"]], "rdmc.mathlib": [[41, "module-rdmc.mathlib"]], "addnullconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AddNullConformer"]], "addredundantbonds() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AddRedundantBonds"]], "alignmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AlignMol"]], "assignstereochemistryfrom3d() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.AssignStereochemistryFrom3D"]], "calcrmsd() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.CalcRMSD"]], "combinemol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.CombineMol"]], "copy() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Copy"]], "embedconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedConformer"]], "embedmultipleconfs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedMultipleConfs"]], "embedmultiplenullconfs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedMultipleNullConfs"]], "embednullconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.EmbedNullConformer"]], "fromfile() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromFile"]], "frominchi() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromInchi"]], "frommol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromMol"]], "fromobmol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromOBMol"]], "fromrmgmol() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromRMGMol"]], "fromsdf() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSDF"]], "fromsmarts() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSmarts"]], "fromsmiles() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromSmiles"]], "fromxyz() (rdmc.mol.rdkitmol class method)": [[42, "rdmc.mol.RDKitMol.FromXYZ"]], "getadjacencymatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAdjacencyMatrix"]], "getallconformers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAllConformers"]], "getatommapnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomMapNumbers"]], "getatommasses() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomMasses"]], "getatomicnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetAtomicNumbers"]], "getbestalign() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetBestAlign"]], "getbondsastuples() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetBondsAsTuples"]], "getconformer() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetConformer"]], "getconformers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetConformers"]], "getdistancematrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetDistanceMatrix"]], "getelementsymbols() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetElementSymbols"]], "getformalcharge() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetFormalCharge"]], "getinternalcoordinates() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetInternalCoordinates"]], "getmolfrags() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetMolFrags"]], "getpositions() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetPositions"]], "getspinmultiplicity() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSpinMultiplicity"]], "getsubstructmatch() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSubstructMatch"]], "getsubstructmatches() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSubstructMatches"]], "getsymmsssr() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetSymmSSSR"]], "gettorsiontops() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetTorsionTops"]], "gettorsionalmodes() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetTorsionalModes"]], "getvdwmatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.GetVdwMatrix"]], "hascollidingatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.HasCollidingAtoms"]], "hassameconnectivity() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.HasSameConnectivity"]], "kekulize() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Kekulize"]], "prepareoutputmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.PrepareOutputMol"]], "rdkitmol (class in rdmc.mol)": [[42, "rdmc.mol.RDKitMol"]], "reflect() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Reflect"]], "removehs() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.RemoveHs"]], "renumberatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.RenumberAtoms"]], "sanitize() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.Sanitize"]], "saturatebiradicalsites12() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateBiradicalSites12"]], "saturatebiradicalsitescdb() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateBiradicalSitesCDB"]], "saturatecarbene() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateCarbene"]], "saturatemol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SaturateMol"]], "setatommapnumbers() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SetAtomMapNumbers"]], "setpositions() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SetPositions"]], "setvdwmatrix() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.SetVdwMatrix"]], "toatoms() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToAtoms"]], "tograph() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToGraph"]], "toinchi() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToInchi"]], "tomolblock() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToMolBlock"]], "toobmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToOBMol"]], "torwmol() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToRWMol"]], "tosdffile() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToSDFFile"]], "tosmiles() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToSmiles"]], "toxyz() (rdmc.mol.rdkitmol method)": [[42, "rdmc.mol.RDKitMol.ToXYZ"]], "generate_radical_resonance_structures() (in module rdmc.mol)": [[42, "rdmc.mol.generate_radical_resonance_structures"]], "generate_vdw_mat() (in module rdmc.mol)": [[42, "rdmc.mol.generate_vdw_mat"]], "get_unique_mols() (in module rdmc.mol)": [[42, "rdmc.mol.get_unique_mols"]], "has_matched_mol() (in module rdmc.mol)": [[42, "rdmc.mol.has_matched_mol"]], "parse_xyz_or_smiles_list() (in module rdmc.mol)": [[42, "rdmc.mol.parse_xyz_or_smiles_list"]], "rdmc.mol": [[42, "module-rdmc.mol"]], "rdmc": [[43, "module-rdmc"]], "reaction (class in rdmc.reaction)": [[44, "rdmc.reaction.Reaction"]], "active_atoms (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.active_atoms"]], "active_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.active_bonds"]], "apply_resonance_correction() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.apply_resonance_correction"]], "bond_analysis() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.bond_analysis"]], "broken_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.broken_bonds"]], "changed_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.changed_bonds"]], "draw_2d() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.draw_2d"]], "formed_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.formed_bonds"]], "from_reactant_and_product_smiles() (rdmc.reaction.reaction class method)": [[44, "rdmc.reaction.Reaction.from_reactant_and_product_smiles"]], "from_reaction_smiles() (rdmc.reaction.reaction class method)": [[44, "rdmc.reaction.Reaction.from_reaction_smiles"]], "get_reverse_reaction() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.get_reverse_reaction"]], "init_reactant_product() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.init_reactant_product"]], "involved_atoms (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.involved_atoms"]], "involved_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.involved_bonds"]], "is_charge_balanced (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.is_charge_balanced"]], "is_element_balanced (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.is_element_balanced"]], "is_mult_equal (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.is_mult_equal"]], "is_num_atoms_balanced (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.is_num_atoms_balanced"]], "make_ts() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.make_ts"]], "num_atoms (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.num_atoms"]], "num_broken_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.num_broken_bonds"]], "num_changed_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.num_changed_bonds"]], "num_formed_bonds (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.num_formed_bonds"]], "num_products (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.num_products"]], "num_reactants (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.num_reactants"]], "rdmc.reaction": [[44, "module-rdmc.reaction"]], "require_bond_analysis() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.require_bond_analysis"]], "to_rdkit_reaction() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.to_rdkit_reaction"]], "to_smiles() (rdmc.reaction.reaction method)": [[44, "rdmc.reaction.Reaction.to_smiles"]], "ts (rdmc.reaction.reaction property)": [[44, "rdmc.reaction.Reaction.ts"]], "clean_ts() (in module rdmc.ts)": [[45, "rdmc.ts.clean_ts"]], "examine_normal_mode() (in module rdmc.ts)": [[45, "rdmc.ts.examine_normal_mode"]], "get_all_changing_bonds() (in module rdmc.ts)": [[45, "rdmc.ts.get_all_changing_bonds"]], "get_broken_bonds() (in module rdmc.ts)": [[45, "rdmc.ts.get_broken_bonds"]], "get_formed_and_broken_bonds() (in module rdmc.ts)": [[45, "rdmc.ts.get_formed_and_broken_bonds"]], "get_formed_bonds() (in module rdmc.ts)": [[45, "rdmc.ts.get_formed_bonds"]], "guess_rxn_from_normal_mode() (in module rdmc.ts)": [[45, "rdmc.ts.guess_rxn_from_normal_mode"]], "is_da_rxn_endo() (in module rdmc.ts)": [[45, "rdmc.ts.is_DA_rxn_endo"]], "rdmc.ts": [[45, "module-rdmc.ts"]], "determine_smallest_atom_index_in_torsion() (in module rdmc.utils)": [[46, "rdmc.utils.determine_smallest_atom_index_in_torsion"]], "find_internal_torsions() (in module rdmc.utils)": [[46, "rdmc.utils.find_internal_torsions"]], "find_ring_torsions() (in module rdmc.utils)": [[46, "rdmc.utils.find_ring_torsions"]], "fix_co_openbabel() (in module rdmc.utils)": [[46, "rdmc.utils.fix_CO_openbabel"]], "get_atom_masses() (in module rdmc.utils)": [[46, "rdmc.utils.get_atom_masses"]], "get_element_symbols() (in module rdmc.utils)": [[46, "rdmc.utils.get_element_symbols"]], "get_internal_coords() (in module rdmc.utils)": [[46, "rdmc.utils.get_internal_coords"]], "get_obmol_coords() (in module rdmc.utils)": [[46, "rdmc.utils.get_obmol_coords"]], "openbabel_mol_to_rdkit_mol() (in module rdmc.utils)": [[46, "rdmc.utils.openbabel_mol_to_rdkit_mol"]], "parse_xyz_by_jensen() (in module rdmc.utils)": [[46, "rdmc.utils.parse_xyz_by_jensen"]], "parse_xyz_by_openbabel() (in module rdmc.utils)": [[46, "rdmc.utils.parse_xyz_by_openbabel"]], "rdkit_mol_to_openbabel_mol() (in module rdmc.utils)": [[46, "rdmc.utils.rdkit_mol_to_openbabel_mol"]], "rdkit_mol_to_openbabel_mol_manual() (in module rdmc.utils)": [[46, "rdmc.utils.rdkit_mol_to_openbabel_mol_manual"]], "rdmc.utils": [[46, "module-rdmc.utils"]], "reverse_map() (in module rdmc.utils)": [[46, "rdmc.utils.reverse_map"]], "rmg_mol_to_rdkit_mol() (in module rdmc.utils)": [[46, "rdmc.utils.rmg_mol_to_rdkit_mol"]], "set_obmol_coords() (in module rdmc.utils)": [[46, "rdmc.utils.set_obmol_coords"]], "set_rdconf_coordinates() (in module rdmc.utils)": [[46, "rdmc.utils.set_rdconf_coordinates"]], "conformer_viewer() (in module rdmc.view)": [[47, "rdmc.view.conformer_viewer"]], "freq_viewer() (in module rdmc.view)": [[47, "rdmc.view.freq_viewer"]], "grid_viewer() (in module rdmc.view)": [[47, "rdmc.view.grid_viewer"]], "interactive_conformer_viewer() (in module rdmc.view)": [[47, "rdmc.view.interactive_conformer_viewer"]], "mol_animation() (in module rdmc.view)": [[47, "rdmc.view.mol_animation"]], "mol_viewer() (in module rdmc.view)": [[47, "rdmc.view.mol_viewer"]], "rdmc.view": [[47, "module-rdmc.view"]], "ts_viewer() (in module rdmc.view)": [[47, "rdmc.view.ts_viewer"]]}}) \ No newline at end of file