12 #ifndef _RD_MOL_OPS_H_
13 #define _RD_MOL_OPS_H_
19 #include <boost/smart_ptr.hpp>
20 #include <boost/dynamic_bitset.hpp>
71 std::vector<int> &mapping);
84 const ROMol &mol, std::vector<std::vector<int>> &frags);
105 const ROMol &mol,
bool sanitizeFrags =
true,
106 std::vector<int> *frags =
nullptr,
107 std::vector<std::vector<int>> *fragsMolAtomMapping =
nullptr,
108 bool copyConformers =
true);
124 template <
typename T>
127 bool sanitizeFrags =
true,
128 const std::vector<T> *whiteList =
nullptr,
129 bool negateList =
false);
154 const ROMol &mol,
bool useBO =
true,
bool force =
false,
155 const std::vector<int> *bondPath =
nullptr,
bool cacheIt =
true);
185 bool addCoords =
false,
187 bool addResidueInfo =
false);
191 bool addCoords =
false,
193 bool addResidueInfo =
false);
228 bool implicitOnly =
false,
229 bool updateExplicitCount =
false,
230 bool sanitize =
true);
234 bool updateExplicitCount =
false,
235 bool sanitize =
true);
237 bool removeDegreeZero =
false;
238 bool removeHigherDegrees =
false;
239 bool removeOnlyHNeighbors =
241 bool removeIsotopes =
false;
242 bool removeAndTrackIsotopes =
false;
246 bool removeDummyNeighbors =
248 bool removeDefiningBondStereo =
250 bool removeWithWedgedBond =
true;
251 bool removeWithQuery =
false;
252 bool removeMapped =
true;
253 bool removeInSGroups =
false;
254 bool showWarnings =
true;
255 bool removeNonimplicit =
true;
256 bool updateExplicitCount =
258 bool removeHydrides =
true;
263 bool sanitize =
true);
268 bool sanitize =
true);
275 bool sanitize =
true);
303 bool mergeUnmappedOnly =
false);
307 bool mergeUnmappedOnly =
false);
329 bool adjustDegree =
true;
332 bool adjustRingCount =
false;
333 std::uint32_t adjustRingCountFlags =
336 bool makeDummiesQueries =
true;
339 bool aromatizeIfPossible =
true;
341 bool makeBondsGeneric =
345 bool makeAtomsGeneric =
349 bool adjustHeavyDegree =
false;
351 std::uint32_t adjustHeavyDegreeFlags =
354 bool adjustRingChain =
false;
357 bool useStereoCareForBonds =
361 bool adjustConjugatedFiveRings =
365 bool setMDLFiveRingAromaticity =
369 bool adjustSingleBondsToDegreeOneNeighbors =
373 bool adjustSingleBondsBetweenAromaticAtoms =
422 const ROMol &mol,
const std::vector<unsigned int> &newOrder);
480 unsigned int &operationThatFailed,
559 int (*func)(
RWMol &) =
nullptr);
625 unsigned int maxBackTracks = 100);
682 std::vector<std::vector<int>> &res);
685 const ROMol &mol, std::vector<std::vector<int>> *res =
nullptr);
723 std::vector<std::vector<int>> &res);
750 const ROMol &mol,
bool useBO =
false,
int emptyVal = 0,
bool force =
false,
751 const char *propNamePrefix =
nullptr,
752 const boost::dynamic_bitset<> *bondsToUse =
nullptr);
777 const ROMol &mol,
bool useBO =
false,
bool useAtomWts =
false,
778 bool force =
false,
const char *propNamePrefix =
nullptr);
804 const ROMol &mol,
const std::vector<int> &activeAtoms,
805 const std::vector<const Bond *> &bonds,
bool useBO =
false,
806 bool useAtomWts =
false);
830 const ROMol &mol,
int confId = -1,
bool useAtomWts =
false,
831 bool force =
false,
const char *propNamePrefix =
nullptr);
880 bool includeChirality=
true,
881 bool includeIsotopes=
true,
882 std::vector<std::vector<int> > *rankHistory=0);
907 const boost::dynamic_bitset<> &atomsToUse,
908 const boost::dynamic_bitset<> &bondsToUse,
909 const std::vector<std::string> *atomSymbols=0,
910 const std::vector<std::string> *bondSymbols=0,
912 std::vector<std::vector<int> > *rankHistory=0);
932 ROMol &mol,
int confId = -1,
bool replaceExistingTags =
true);
946 ROMol &mol,
int confId = -1,
bool replaceExistingTags =
true);
958 ROMol &mol,
int confId = -1,
bool replaceExistingTags =
true);
997 ROMol &mol,
bool cleanIt =
false,
bool force =
false,
998 bool flagPossibleStereoCenters =
false);
1030 bool cleanIt =
false);
1041 ROMol &mol,
bool replaceExistingTags =
true);
1045 const ROMol &mol, std::string prop);
RDKIT_GRAPHMOL_EXPORT const int ci_LOCAL_INF
The class for representing atoms.
RWMol is a molecule class that is intended to be edited.
#define RDKIT_GRAPHMOL_EXPORT
RDKIT_GRAPHMOL_EXPORT double * get3DDistanceMat(const ROMol &mol, int confId=-1, bool useAtomWts=false, bool force=false, const char *propNamePrefix=nullptr)
Computes the molecule's 3D distance matrix.
RDKIT_GRAPHMOL_EXPORT void cleanUp(RWMol &mol)
Designed to be called by the sanitizer to handle special cases before.
RDKIT_GRAPHMOL_EXPORT void assignStereochemistry(ROMol &mol, bool cleanIt=false, bool force=false, bool flagPossibleStereoCenters=false)
Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E)
RDKIT_GRAPHMOL_EXPORT std::vector< std::unique_ptr< MolSanitizeException > > detectChemistryProblems(const ROMol &mol, unsigned int sanitizeOps=SANITIZE_ALL)
Identifies chemistry problems (things that don't make chemical sense) in a molecule.
RDKIT_GRAPHMOL_EXPORT double * getAdjacencyMatrix(const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=nullptr, const boost::dynamic_bitset<> *bondsToUse=nullptr)
returns a molecule's adjacency matrix
RDKIT_GRAPHMOL_EXPORT ROMol * mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false)
RDKIT_GRAPHMOL_EXPORT void assignChiralTypesFromBondDirs(ROMol &mol, int confId=-1, bool replaceExistingTags=true)
Use bond directions to assign ChiralTypes to a molecule's atoms and stereo flags to its bonds.
RDKIT_GRAPHMOL_EXPORT int setAromaticity(RWMol &mol, AromaticityModel model=AROMATICITY_DEFAULT, int(*func)(RWMol &)=nullptr)
Sets up the aromaticity for a molecule.
RDKIT_GRAPHMOL_EXPORT void findRingFamilies(const ROMol &mol)
RDKIT_GRAPHMOL_EXPORT void fastFindRings(const ROMol &mol)
use a DFS algorithm to identify ring bonds and atoms in a molecule
RDKIT_GRAPHMOL_EXPORT double * getDistanceMat(const ROMol &mol, bool useBO=false, bool useAtomWts=false, bool force=false, const char *propNamePrefix=nullptr)
Computes the molecule's topological distance matrix.
RDKIT_GRAPHMOL_EXPORT int getFormalCharge(const ROMol &mol)
sums up all atomic formal charges and returns the result
AromaticityModel
Possible aromaticity models.
@ AROMATICITY_CUSTOM
use a function
@ AROMATICITY_DEFAULT
future proofing
RDKIT_GRAPHMOL_EXPORT std::map< T, boost::shared_ptr< ROMol > > getMolFragsWithQuery(const ROMol &mol, T(*query)(const ROMol &, const Atom *), bool sanitizeFrags=true, const std::vector< T > *whiteList=nullptr, bool negateList=false)
splits a molecule into pieces based on labels assigned using a query
RDKIT_GRAPHMOL_EXPORT void removeStereochemistry(ROMol &mol)
Removes all stereochemistry information from atoms (i.e. R/S) and bonds.
RDKIT_GRAPHMOL_EXPORT ROMol * addHs(const ROMol &mol, bool explicitOnly=false, bool addCoords=false, const UINT_VECT *onlyOnAtoms=nullptr, bool addResidueInfo=false)
returns a copy of a molecule with hydrogens added in as explicit Atoms
RDKIT_GRAPHMOL_EXPORT double computeBalabanJ(const ROMol &mol, bool useBO=true, bool force=false, const std::vector< int > *bondPath=nullptr, bool cacheIt=true)
calculates Balaban's J index for the molecule
RDKIT_GRAPHMOL_EXPORT void assignChiralTypesFromMolParity(ROMol &mol, bool replaceExistingTags=true)
Uses the molParity atom property to assign ChiralType to a molecule's atoms.
RDKIT_GRAPHMOL_EXPORT unsigned int getMolFrags(const ROMol &mol, std::vector< int > &mapping)
find fragments (disconnected components of the molecular graph)
RDKIT_GRAPHMOL_EXPORT void adjustHs(RWMol &mol)
adjust the number of implicit and explicit Hs for special cases
RDKIT_GRAPHMOL_EXPORT void assignStereochemistryFrom3D(ROMol &mol, int confId=-1, bool replaceExistingTags=true)
Uses a conformer to assign ChiralTypes to a molecule's atoms and stereo flags to its bonds.
@ SANITIZE_SETAROMATICITY
@ SANITIZE_SETCONJUGATION
@ SANITIZE_CLEANUPCHIRALITY
@ SANITIZE_SETHYBRIDIZATION
RDKIT_GRAPHMOL_EXPORT int countAtomElec(const Atom *at)
return the number of electrons available on an atom to donate for
RDKIT_GRAPHMOL_EXPORT void detectBondStereochemistry(ROMol &mol, int confId=-1)
RDKIT_GRAPHMOL_EXPORT void sanitizeMol(RWMol &mol, unsigned int &operationThatFailed, unsigned int sanitizeOps=SANITIZE_ALL)
carries out a collection of tasks for cleaning up a molecule and
RDKIT_GRAPHMOL_EXPORT ROMol * removeHs(const ROMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true)
returns a copy of a molecule with hydrogens removed
RDKIT_GRAPHMOL_EXPORT void parseAdjustQueryParametersFromJSON(MolOps::AdjustQueryParameters &p, const std::string &json)
updates an AdjustQueryParameters object from a JSON string
RDKIT_GRAPHMOL_EXPORT void removeAllHs(RWMol &mol, bool sanitize=true)
removes all Hs from a molecule
RDKIT_GRAPHMOL_EXPORT ROMol * adjustQueryProperties(const ROMol &mol, const AdjustQueryParameters *params=nullptr)
returns a copy of a molecule with query properties adjusted
RDKIT_GRAPHMOL_EXPORT void setBondStereoFromDirections(ROMol &mol)
Assign CIS/TRANS bond stereochemistry tags based on neighboring directions.
RDKIT_GRAPHMOL_EXPORT ROMol * renumberAtoms(const ROMol &mol, const std::vector< unsigned int > &newOrder)
returns a copy of a molecule with the atoms renumbered
RDKIT_GRAPHMOL_EXPORT int findSSSR(const ROMol &mol, std::vector< std::vector< int >> &res)
finds a molecule's Smallest Set of Smallest Rings
RDKIT_GRAPHMOL_EXPORT bool atomHasConjugatedBond(const Atom *at)
returns whether or not the given Atom is involved in a conjugated bond
RDKIT_GRAPHMOL_EXPORT void cleanupChirality(RWMol &mol)
removes bogus chirality markers (those on non-sp3 centers):
RDKIT_GRAPHMOL_EXPORT void Kekulize(RWMol &mol, bool markAtomsBonds=true, unsigned int maxBackTracks=100)
Kekulizes the molecule.
RDKIT_GRAPHMOL_EXPORT void assignRadicals(RWMol &mol)
Called by the sanitizer to assign radical counts to atoms.
RDKIT_GRAPHMOL_EXPORT void findPotentialStereoBonds(ROMol &mol, bool cleanIt=false)
finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREOANY.
RDKIT_GRAPHMOL_EXPORT void setHybridization(ROMol &mol)
calculates and sets the hybridization of all a molecule's Stoms
RDKIT_GRAPHMOL_EXPORT std::list< int > getShortestPath(const ROMol &mol, int aid1, int aid2)
Find the shortest path between two atoms.
RDKIT_GRAPHMOL_EXPORT unsigned getNumAtomsWithDistinctProperty(const ROMol &mol, std::string prop)
returns the number of atoms which have a particular property set
RDKIT_GRAPHMOL_EXPORT void assignChiralTypesFrom3D(ROMol &mol, int confId=-1, bool replaceExistingTags=true)
Uses a conformer to assign ChiralType to a molecule's atoms.
RDKIT_GRAPHMOL_EXPORT int symmetrizeSSSR(ROMol &mol, std::vector< std::vector< int >> &res)
symmetrize the molecule's Smallest Set of Smallest Rings
RDKIT_GRAPHMOL_EXPORT void setConjugation(ROMol &mol)
flags the molecule's conjugated bonds
RDKIT_GRAPHMOL_EXPORT void setDoubleBondNeighborDirections(ROMol &mol, const Conformer *conf=nullptr)
Sets bond directions based on double bond stereochemistry.
@ ADJUST_IGNORENONDUMMIES
std::vector< double > INVAR_VECT
INVAR_VECT::iterator INVAR_VECT_I
INVAR_VECT::const_iterator INVAR_VECT_CI
std::vector< UINT > UINT_VECT
Parameters controlling the behavior of MolOps::adjustQueryProperties.
static AdjustQueryParameters noAdjustments()
returns an AdjustQueryParameters object with all adjustments disabled