/**************************************************************************** * 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 __base_molecule__ #define __base_molecule__ #include "graph/graph.h" #include "base_cpp/red_black.h" #include "math/algebra.h" #include "molecule/molecule_stereocenters.h" #include "molecule/molecule_cis_trans.h" #include "molecule/molecule_allene_stereo.h" #include "base_cpp/obj_array.h" #include "molecule/molecule_sgroups.h" #include "molecule/molecule_rgroups.h" #include "molecule/molecule_tgroups.h" #include "molecule/molecule_arom.h" #include "molecule/molecule_standardize.h" #include "molecule/molecule_ionize.h" #ifdef _WIN32 #pragma warning(push) #pragma warning(disable:4251) #endif namespace indigo { enum { CHARGE_UNKNOWN = -100 }; enum { ATOM_AROMATIC = 1, ATOM_ALIPHATIC = 2 }; enum { BOND_ZERO = 0, BOND_SINGLE = 1, BOND_DOUBLE = 2, BOND_TRIPLE = 3, BOND_AROMATIC = 4 }; enum { BOND_UP = 1, BOND_DOWN = 2, BOND_EITHER = 3 }; // Flags that disables copying information in making submolecule, // merging with molecule and cloning procedures enum { SKIP_ALL = -1, SKIP_CIS_TRANS = 0x01, SKIP_STEREOCENTERS = 0x02, SKIP_XYZ = 0x04, SKIP_RGROUP_FRAGMENTS = 0x08, SKIP_ATTACHMENT_POINTS = 0x16, SKIP_TGROUPS = 0x32, SKIP_TEMPLATE_ATTACHMENT_POINTS = 0x64 }; class Molecule; class QueryMolecule; class DLLEXPORT BaseMolecule : public Graph { public: typedef RedBlackMap Mapping; BaseMolecule (); virtual ~BaseMolecule (); // Casting methods. Invalid casting throws exceptions. virtual Molecule& asMolecule (); virtual QueryMolecule& asQueryMolecule (); virtual bool isQueryMolecule (); virtual void clear (); // 'neu' means 'new' in German virtual BaseMolecule * neu () = 0; virtual int getAtomNumber (int idx) = 0; // > 0 -- ELEM_***, 0 -- pseudo-atom, -1 -- not sure virtual int getAtomCharge (int idx) = 0; // charge or CHARGE_UNKNOWN if not sure virtual int getAtomIsotope (int idx) = 0; // > 0 -- isotope, -1 -- not sure virtual int getAtomRadical (int idx) = 0; // > 0 -- RADICAL_***, -1 -- not sure virtual int getAtomAromaticity (int idx) = 0; // ATOM_AROMATIC, ATOM_ALIPHATIC, or -1 -- not sure virtual int getExplicitValence (int idx) = 0; // explicit valence or -1 if not set virtual int getAtomValence (int idx) = 0; // >= 0 -- valence, -1 is not set explicitly virtual int getAtomSubstCount (int idx) = 0; virtual int getAtomRingBondsCount (int idx) = 0; // >= 0 -- ring bonds count, -1 -- not sure int getAtomRadical_NoThrow (int idx, int fallback); int getAtomValence_NoThrow (int idx, int fallback); virtual int getAtomMaxH (int idx) = 0; virtual int getAtomMinH (int idx) = 0; virtual int getAtomTotalH (int idx) = 0; int possibleAtomTotalH (int idx, int hcount); virtual bool isPseudoAtom (int idx) = 0; virtual const char * getPseudoAtom (int idx) = 0; virtual bool isTemplateAtom (int idx) = 0; virtual const char * getTemplateAtom (int idx) = 0; virtual const int getTemplateAtomSeqid (int idx) = 0; virtual const char * getTemplateAtomClass (int idx) = 0; virtual const int getTemplateAtomDisplayOption (int idx) = 0; int countRSites (); int countSGroups (); static void collapse (BaseMolecule& bm, int id, Mapping& mapAtom, Mapping& mapBondInv); static void collapse (BaseMolecule& bm, int id); static void collapse (BaseMolecule& bm); int transformSCSRtoFullCTAB (); int transformFullCTABtoSCSR (ObjArray &templates); virtual bool isRSite (int atom_idx) = 0; virtual dword getRSiteBits (int atom_idx) = 0; virtual void allowRGroupOnRSite (int atom_idx, int rg_idx) = 0; void getAllowedRGroups (int atom_idx, Array &rgroup_list); int getSingleAllowedRGroup (int atom_idx); int getRSiteAttachmentPointByOrder (int idx, int order) const; void setRSiteAttachmentOrder (int atom_idx, int att_atom_idx, int order); void setTemplateAtomAttachmentOrder (int atom_idx, int att_atom_idx, const char *att_id); int getTemplateAtomAttachmentPoint (int atom_idx, int order); void getTemplateAtomAttachmentPointId (int atom_idx, int order, Array &apid); int getTemplateAtomAttachmentPointsCount (int atom_idx); int getTemplateAtomAttachmentPointById (int atom_idx, Array &att_id); void addAttachmentPoint (int order, int atom_index); int getAttachmentPoint (int order, int index) const; void removeAttachmentPointsFromAtom (int atom_index); int attachmentPointCount () const; void removeAttachmentPoints (); void getAttachmentIndicesForAtom (int atom_idx, Array &res); virtual bool isSaturatedAtom (int idx) = 0; virtual int getBondOrder (int idx) = 0; // > 0 -- BOND_***, -1 -- not sure virtual int getBondTopology (int idx) = 0; // > 0 -- TOPOLOGY_***, -1 -- not sure // true if the atom number belongs to the given list, false otherwise virtual bool atomNumberBelongs (int idx, const int *numbers, int count) = 0; // true if the atom can have that number, false otherwise virtual bool possibleAtomNumber (int idx, int number) = 0; // true if the atom can have that number and that charge, false otherwise virtual bool possibleAtomNumberAndCharge (int idx, int number, int charge) = 0; // true if the atom can have that number and that charge, false otherwise virtual bool possibleAtomNumberAndIsotope (int idx, int number, int isotope) = 0; // true if the atom can have that isotope index, false otherwise virtual bool possibleAtomIsotope (int idx, int isotope) = 0; // true if the atom can have that isotope index, false otherwise virtual bool possibleAtomCharge (int idx, int charge) = 0; // human-readable atom and bond desciptions for diagnostic purposes virtual void getAtomDescription (int idx, Array &description) = 0; virtual void getBondDescription (int idx, Array &description) = 0; // true if the bond can be that order, false otherwise virtual bool possibleBondOrder (int idx, int order) = 0; // true if bond stereoconfiguration is important virtual bool bondStereoCare (int idx) = 0; // Returns true if some bonds were changed virtual bool aromatize (const AromaticityOptions &options) = 0; // Returns true if all bonds were dearomatized virtual bool dearomatize (const AromaticityOptions &options) = 0; enum { CHANGED_ATOM_NUMBER = 0x01, CHANGED_CONNECTIVITY = 0x02, CHANGED_ALL = 0xFF, }; virtual void invalidateAtom (int index, int mask); Vec3f & getAtomXyz (int idx); void setAtomXyz (int idx, float x, float y, float z); void setAtomXyz (int idx, const Vec3f& v); void clearXyz (); MoleculeStereocenters stereocenters; MoleculeCisTrans cis_trans; MoleculeAlleneStereo allene_stereo; bool have_xyz; bool isChrial (); struct TemplateAttPoint { int ap_occur_idx; int ap_aidx; Array ap_id; }; ObjPool template_attachment_points; MoleculeSGroups sgroups; MoleculeTGroups tgroups; MoleculeRGroups rgroups; StringPool custom_collections; Array name; static bool hasCoord (BaseMolecule &mol); static bool hasZCoord (BaseMolecule &mol); void mergeWithSubmolecule (BaseMolecule &mol, const Array &vertices, const Array *edges, Array *mapping_out, int skip_flags = 0); int mergeAtoms (int atom1, int atom2); void flipBond (int atom_parent, int atom_from, int atom_to); void makeSubmolecule (BaseMolecule &mol, const Array &vertices, Array *mapping_out, int skip_flags = 0); void makeSubmolecule (BaseMolecule &other, const Filter &filter, Array *mapping_out, Array *inv_mapping, int skip_flags = 0); void makeEdgeSubmolecule (BaseMolecule &mol, const Array &vertices, const Array &edges, Array *v_mapping, int skip_flags = 0); void clone (BaseMolecule &other, Array *mapping, Array *inv_mapping, int skip_flags = 0); // This is a bad hack for those who are too lazy to handle the mappings. // NEVER USE IT. void clone_KeepIndices (BaseMolecule &other, int skip_flags = 0); void mergeWithMolecule (BaseMolecule &other, Array *mapping, int skip_flags = 0); void removeAtoms (const Array &indices); void removeAtoms (const Filter &filter); void removeAtom (int idx); void removeBonds (const Array &indices); void removeBond (int idx); void removeSGroup (int idx); void removeSGroupWithBasis (int idx); void unhighlightAll (); void highlightAtom (int idx); void highlightBond (int idx); void highlightAtoms (const Filter &filter); void highlightBonds (const Filter &filter); void unhighlightAtom (int idx); void unhighlightBond (int idx); int countHighlightedAtoms (); int countHighlightedBonds (); bool hasHighlighting (); bool isAtomHighlighted (int idx); bool isBondHighlighted (int idx); void highlightSubmolecule (BaseMolecule &sub, const int *mapping, bool entire); static int getVacantPiOrbitals (int group, int charge, int radical, int conn, int *lonepairs_out); // Returns edit revision for this molecule. // Each time molecule is changed revision number is increased. // If revision number is the same then molecule hasn't been changed. int getEditRevision (); // Manually update edit revision. This is required when molecule is changed // directly without calling molecule methods (for example mol.cis_trans.clear() and etc.) void updateEditRevision (); void clearBondDirections (); int getBondDirection (int idx) const; void setBondDirection (int idx, int dir); int getBondDirection2 (int center_idx, int nei_idx); void mergeSGroupsWithSubmolecule (BaseMolecule &mol, Array &mapping); void mergeSGroupsWithSubmolecule (BaseMolecule &mol, Array &mapping, Array &edge_mapping); void clearSGroups(); void getSGroupAtomsCenterPoint (SGroup &sgroup, Vec2f &res); void getAtomsCenterPoint (Array &atoms, Vec2f &res); void getAtomSymbol (int v, Array &output); DECL_ERROR; protected: void _mergeWithSubmolecule_Sub (BaseMolecule &mol, const Array &vertices, const Array *edges, Array &mapping, Array &edge_mapping, int skip_flags); void _flipSGroupBond(SGroup &sgroup, int src_bond_idx, int new_bond_idx); void _flipSuperatomBond(Superatom &sa, int src_bond_idx, int new_bond_idx); void _flipTemplateAtomAttachmentPoint(int idx, int atom_from, int atom_to); virtual void _mergeWithSubmolecule (BaseMolecule &mol, const Array &vertices, const Array *edges, const Array &mapping, int skip_flags) = 0; virtual void _postMergeWithSubmolecule (BaseMolecule &mol, const Array &vertices, const Array *edges, const Array &mapping, int skip_flags); virtual void _flipBond (int atom_parent, int atom_from, int atom_to); virtual void _removeAtoms (const Array &indices, const int *mapping); virtual void _removeBonds (const Array &indices); int _addBaseAtom (); int _addBaseBond (int beg, int end); void _removeAtomsFromSGroup (SGroup &sgroup, Array &mapping); void _removeAtomsFromMultipleGroup (MultipleGroup &mg, Array &mapping); void _removeAtomsFromSuperatom (Superatom &sa, Array &mapping); void _removeBondsFromSGroup (SGroup &sgroup, Array &mapping); void _removeBondsFromSuperatom (Superatom &sa, Array &mapping); bool _mergeSGroupWithSubmolecule (SGroup &sgroup, SGroup &super, BaseMolecule &supermol, Array &mapping, Array &edge_mapping); void _checkSgroupHierarchy(int pidx, int oidx); int _transformTGroupToSGroup (int idx); int _addTemplate (TGroup &tgroup); Array _hl_atoms; Array _hl_bonds; Array _bond_directions; Array _xyz; ObjArray< Array > _rsite_attachment_points; bool _rGroupFragment; ObjArray< Array > _attachment_index; // When molecule gets edited then edit revision is increased. // If edit revision is the same then molecule wasn't edited int _edit_revision; }; } #ifdef _WIN32 #pragma warning(pop) #endif #endif