/**************************************************************************** * Copyright (C) 2009-2015 EPAM Systems * * This file is part of Indigo toolkit. * * This file may be distributed and/or modified under the terms of the * GNU General Public License version 3 as published by the Free Software * Foundation and appearing in the file LICENSE.GPL included in the * packaging of this file. * * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. ***************************************************************************/ #ifndef __molecule_standardize_options__ #define __molecule_standardize_options__ #ifdef _WIN32 #pragma warning(push) #pragma warning(disable:4251) #endif namespace indigo { class StandardizeOptions { public: StandardizeOptions (); void reset (); // Sets or repairs the stereo on a molecule to a standard form using the coordinates // as the guide. Default is false. bool standardize_stereo; // Sets the charges on a molecule to a standard form. Default is false. bool standardize_charges; // Translates a molecule so its geometric center lies at the origin. Default is false. bool center_molecule; // Removes fragments that consist of only a single heavy atom. Default is false. bool remove_single_atom_fragments; // Keeps only the smallest fragment in the molecule. Default is false. bool keep_smallest_fragment; // Keeps only the largest fragment in the molecule. Default is false. bool keep_largest_fragment; // Removes the largest fragment in the molecule. Default is false. bool remove_largest_fragment; // Converts all non-Hydrogen atoms atoms in the molecule to carbon. Default is false. bool make_non_h_atoms_c_atoms; // Converts all non-Hydrogen atoms in the molecule to the A query atom type. // Default is false. bool make_non_h_atoms_a_atoms; // Converts all non-Carbon, non-Hydrogen atoms in the molecule to the Q query atom type. // Default is false. bool make_non_c_h_atoms_q_atoms; // Converts all bonds in the molecule to single bonds. Default is false. bool make_all_bonds_single; // Sets all x, y, z coordinates to zero. Default is false. bool clear_coordinates; // Sets the coordinate dimension (0D, 2D, 3D) based on the atomic coordinates. // Default is false. bool fix_coordinate_dimension; // Finds atoms with triple bonds and non-linear geometry and fixes them // so that the bond angles are 180 degrees. Default is false. bool straighten_triple_bonds; // Finds atoms with two double-bonds and non-linear geometry and fixes them // so that the bond angles are 180 degrees.Default is false. bool straighten_allenes; // Deletes all atoms and bonds in the molecule, keeping the molecule object // in the data record. Default is false. bool clear_molecule; // Deletes the molecule object from the data record. Default is false. bool remove_molecule; // Sets all atoms and bonds to NoStereo. Default is false. bool clear_stereo; // Removes all relative stereo groupings. Default is false. bool clear_enhanced_stereo; // Sets all atoms and bonds marked UnknownStereo to NoStereo. Default is false. bool clear_unknown_stereo; // Sets all atoms marked UnknownStereo to NoStereo. Default is false. bool clear_unknown_atom_stereo; // Sets all bonds marked UnknownStereo to NoStereo. Default is false. bool clear_unknown_cis_trans_bond_stereo; // Sets all bonds marked CisStereo or TransStereo to UnknownStereo. Default is false. bool clear_cis_trans_bond_stereo; // Uses 2D coordinates and up/down bond markings (or 3D coordinates) to assign // the stereochemistry of the atoms or bonds. Default is false. bool set_stereo_from_coordinates; // Repositions the stereo bond markings in an attempt to find the best bond // to mark as a wedge bond for each stereo atom. Default is false. bool reposition_stereo_bonds; // Repositions the stereo bond markings for axial stereo centers // (allenes and atropisomers) in an attempt to find the best bond // to mark as a wedge bond for each center. Default is false. bool reposition_axial_stereo_bonds; // Checks the wedge bonds in the molecule to ensure that the wedge // is drawn with the stereo atom at the narrow end of the wedge. Default is false. bool fix_direction_of_wedge_bonds; // Sets all formal charges to zero. Default is false. bool clear_charges; // Clears any pi bonds and Pi systems from the molecule. Default is false. bool clear_pi_bonds; // Clears any highlight colors from atoms and bonds. Default is false. bool clear_highlight_colors; // Deletes all query information from atoms and bonds. Default is false. bool clear_query_info; // Clears labels from atoms. Default is false. bool clear_atom_labels; // Clears labels from bonds. Default is false. bool clear_bond_labels; // Converts directly bonded zwitterions (positively charged atom bonded // to negatively charged atom, A+B-) to the neutral representation (A=B). Default is false. bool neutralize_bonded_zwitterions; // Clears any atom valence query features and resets all implicit hydrogen // counts to their standard values. Default is false. bool clear_unusual_valence; // Clears all isotope markings from atoms. Default is false. bool clear_isotopes; // Clears all explicit zero-order coordination bonds of dative type (V3000 type-9 bonds). // Default is false. bool clear_dative_bonds; // Clears all explicit zero-order hydrogen bonds (V3000 type-10 bonds). Default is false. bool clear_hydrogen_bonds; // R atoms bonded to the centers of rings are converted to R atoms at all open // positions on the ring. Default is false. bool localize_markush_r_atoms_on_rings; // Create coordination bond (zero-order bond) instead of wrong co-valent bond // Default is false. bool create_coordination_bonds; // Create hydrogen bond (zero-order bond) instead of wrong co-valent bond // Default is false. bool create_hydrogen_bonds; }; } #ifdef _WIN32 #pragma warning(pop) #endif #endif // __molecule_standardize_options__