RDMC APIs

• rdmc.external
  • rdmc.external.rmg
    • check_isomorphic_molecules()
    • find_reaction_family()
    • from_rdkit_mol()
    • generate_reaction_complex()
    • load_rmg_database()
    • load_rxn_family_database()
  • rdmc.external.inpwriter
    • rdmc.external.inpwriter.gaussian
      • write_gaussian_config()
      • write_gaussian_freq()
      • write_gaussian_gsm()
      • write_gaussian_inp()
      • write_gaussian_irc()
      • write_gaussian_opt()
    • rdmc.external.inpwriter.qchem
      • write_qchem_freq()
      • write_qchem_irc()
      • write_qchem_opt()
    • rdmc.external.inpwriter.orca
      • write_orca_freq()
      • write_orca_gsm()
      • write_orca_irc()
      • write_orca_opt()
    • rdmc.external.inpwriter.utils
  • rdmc.external.logparser
    • rdmc.external.logparser.base
    • rdmc.external.logparser.gaussian
    • rdmc.external.logparser.qchem
    • rdmc.external.logparser.orca
    • rdmc.external.logparser.utils
• rdmc.mathlib
  • rdmc.mathlib.geom
    • get_centroid()
    • get_distances_from_a_point()
    • get_mass_center()
    • get_max_distance_from_center()
    • get_weighted_center()
    • rotate()
    • translate()
    • translate_centroid()
  • rdmc.mathlib.curvefit
    • FourierSeries1D
      • FourierSeries1D.fit()
      • FourierSeries1D.max_num_term
      • FourierSeries1D.predict()
  • rdmc.mathlib.greedymin
    • compare_to_adjacent_point()
    • get_energy()
    • get_step_to_adjacent_points()
    • search_for_a_minimum()
    • search_minimum()
• rdmc.conformer_generation
  • Embedding Geometries
    • rdmc.conformer_generation.embedders
    • rdmc.conformer_generation.align
      • NaiveAlign
      • align_reactant_fragments()
      • prepare_mols()
      • reset_pmol()
    • rdmc.conformer_generation.ts_guessers
  • Geometry Optimization
    • rdmc.conformer_generation.optimizers
    • rdmc.conformer_generation.ts_optimizers
  • Postprocessing
    • rdmc.conformer_generation.verifiers
    • rdmc.conformer_generation.ts_verifiers
    • rdmc.conformer_generation.pruners
    • rdmc.conformer_generation.solvation
      • ConfSolv
      • Estimator
  • Workflow
    • rdmc.conformer_generation.generators
    • rdmc.conformer_generation.ts_generators
    • rdmc.conformer_generation.metrics
      • SCGMetric
    • rdmc.conformer_generation.sampler
  • Utils

• rdmc.mol
• rdmc.reaction
  • Reaction
    • Reaction.active_atoms
    • Reaction.active_bonds
    • Reaction.apply_resonance_correction()
    • Reaction.bond_analysis()
    • Reaction.broken_bonds
    • Reaction.changed_bonds
    • Reaction.draw_2d()
    • Reaction.draw_3d()
    • Reaction.formed_bonds
    • Reaction.from_reactant_and_product_smiles()
    • Reaction.from_reaction_smiles()
    • Reaction.get_fingerprint()
    • Reaction.get_reverse_reaction()
    • Reaction.has_same_products()
    • Reaction.has_same_reactants()
    • Reaction.init_reactant_product()
    • Reaction.involved_atoms
    • Reaction.involved_bonds
    • Reaction.is_charge_balanced
    • Reaction.is_element_balanced
    • Reaction.is_equivalent()
    • Reaction.is_mult_equal
    • Reaction.is_num_atoms_balanced
    • Reaction.is_resonance_corrected
    • Reaction.is_same_products()
    • Reaction.is_same_reactants()
    • Reaction.make_ts()
    • Reaction.map_h_atoms()
    • Reaction.num_atoms
    • Reaction.num_broken_bonds
    • Reaction.num_changed_bonds
    • Reaction.num_formed_bonds
    • Reaction.num_heavy_atoms
    • Reaction.num_products
    • Reaction.num_reactants
    • Reaction.product_element_count
    • Reaction.reactant_element_count
    • Reaction.require_bond_analysis()
    • Reaction.to_rdkit_reaction()
    • Reaction.to_smiles()
    • Reaction.ts
  • is_equivalent_reaction()
• rdmc.conf
  • EditableConformer
    • EditableConformer.Canonicalize()
    • EditableConformer.GetAllTorsionsDeg()
    • EditableConformer.GetAngleDeg()
    • EditableConformer.GetAngleRad()
    • EditableConformer.GetBondLength()
    • EditableConformer.GetCentroid()
    • EditableConformer.GetDistanceMatrix()
    • EditableConformer.GetOwningMol()
    • EditableConformer.GetPrincipalAxesAndMoments()
    • EditableConformer.GetTorsionDeg()
    • EditableConformer.GetTorsionalModes()
    • EditableConformer.HasCollidingAtoms()
    • EditableConformer.HasOwningMol()
    • EditableConformer.SetAllTorsionsDeg()
    • EditableConformer.SetAngleDeg()
    • EditableConformer.SetAngleRad()
    • EditableConformer.SetBondLength()
    • EditableConformer.SetOwningMol()
    • EditableConformer.SetPositions()
    • EditableConformer.SetTorsionDeg()
    • EditableConformer.SetTorsionalModes()
    • EditableConformer.ToConformer()
    • EditableConformer.ToMol()
• rdmc.forcefield
  • OpenBabelFF
    • OpenBabelFF.add_angle_constraint()
    • OpenBabelFF.add_distance_constraint()
    • OpenBabelFF.add_torsion_constraint()
    • OpenBabelFF.available_force_field
    • OpenBabelFF.available_solver
    • OpenBabelFF.fix_atom()
    • OpenBabelFF.get_optimized_mol()
    • OpenBabelFF.is_optimizable()
    • OpenBabelFF.mol
    • OpenBabelFF.optimize()
    • OpenBabelFF.set_solver()
    • OpenBabelFF.setup()
    • OpenBabelFF.type
    • OpenBabelFF.update_atom_idx()
  • RDKitFF
    • RDKitFF.add_angle_constraint()
    • RDKitFF.add_distance_constraint()
    • RDKitFF.add_torsion_constraint()
    • RDKitFF.available_force_field
    • RDKitFF.fix_atom()
    • RDKitFF.get_conformer_energies()
    • RDKitFF.get_energy()
    • RDKitFF.get_optimized_mol()
    • RDKitFF.is_optimizable()
    • RDKitFF.make_optimizable()
    • RDKitFF.mol
    • RDKitFF.optimize()
    • RDKitFF.optimize_confs()
    • RDKitFF.recover_mol()
    • RDKitFF.setup()
    • RDKitFF.torsional_scan_1d()
    • RDKitFF.type
    • RDKitFF.update_atom_idx()
  • get_roo_radical_atoms()
  • optimize_mol()
• rdmc.utils
  • filter_kwargs()