rdkit.Chem.rdmolops

Package rdkit :: Package Chem :: Module rdmolops |
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# Module rdmolops

    Module containing RDKit functionality for manipulating molecules.

Classes | [hide private]
| AdjustQueryParameters Parameters controlling which components of the query atoms are adjusted.
| AdjustQueryWhichFlags
| AromaticityModel
| SanitizeFlags

Functions | [hide private]
AddHs(...) AddHs( (Mol)mol [, (bool)explicitOnly=False [, (bool)addCoords=False [, (AtomPairsParameters)onlyOnAtoms=None]]]) -> Mol : Adds hydrogens to the graph of a molecule. |
AddRecursiveQuery(...) AddRecursiveQuery( (Mol)mol, (Mol)query, (int)atomIdx [, (bool)preserveExistingQuery=True]) -> None : Adds a recursive query to an atom |
AdjustQueryProperties(...) AdjustQueryProperties( (Mol)mol [, (AtomPairsParameters)params=None]) -> Mol : Returns a new molecule where the query properties of atoms have been modified. |
AssignAtomChiralTagsFromStructure(...) AssignAtomChiralTagsFromStructure( (Mol)mol [, (int)confId=-1 [, (bool)replaceExistingTags=True]]) -> None : Sets the chiral tags on a molecule's atoms based on a 3D conformation. |
AssignRadicals(...) AssignRadicals( (Mol)mol) -> None : Assigns radical counts to atoms |
AssignStereochemistry(...) AssignStereochemistry( (Mol)mol [, (bool)cleanIt=False [, (bool)force=False [, (bool)flagPossibleStereoCenters=False]]]) -> None : Does the CIP stereochemistry assignment for the molecule's atoms (R/S) and double bond (Z/E). |
Cleanup(...) Cleanup( (Mol)mol) -> None : cleans up certain common bad functionalities in the molecule |
CombineMols(...) CombineMols( (Mol)mol1, (Mol)mol2 [, (Point3D)offset=<rdkit.Geometry.rdGeometry.Point3D object at 0x7fc444bf9380>]) -> Mol : Combine the atoms from two molecules to produce a third |
DeleteSubstructs(...) DeleteSubstructs( (Mol)mol, (Mol)query [, (bool)onlyFrags=False [, (bool)useChirality=False]]) -> Mol : Removes atoms matching a substructure query from a molecule |
DetectBondStereoChemistry(...) DetectBondStereoChemistry( (Mol)mol, (Conformer)conformer) -> None : Assign stereochemistry to bonds based on coordinates and a conformer. |
DetectBondStereochemistry(...) DetectBondStereochemistry( (Mol)mol [, (int)confId=-1]) -> None : Assign stereochemistry to bonds based on coordinates. |
FastFindRings(...) FastFindRings( (Mol)arg1) -> None : Does a non-SSSR ring finding for a molecule. |
FindAllPathsOfLengthN(...) FindAllPathsOfLengthN( (Mol)mol, (int)length [, (bool)useBonds=True [, (bool)useHs=False [, (int)rootedAtAtom=-1]]]) -> _listSt6vectorIiSaIiEE : Finds all paths of a particular length in a molecule |
FindAllSubgraphsOfLengthMToN(...) FindAllSubgraphsOfLengthMToN( (Mol)mol, (int)min, (int)max [, (bool)useHs=False [, (int)rootedAtAtom=-1]]) -> object : Finds all subgraphs of a particular length in a molecule See documentation for FindAllSubgraphsOfLengthN for definitions |
FindAllSubgraphsOfLengthN(...) FindAllSubgraphsOfLengthN( (Mol)mol, (int)length [, (bool)useHs=False [, (int)rootedAtAtom=-1]]) -> _listSt6vectorIiSaIiEE : Finds all subgraphs of a particular length in a molecule |
FindAtomEnvironmentOfRadiusN(...) FindAtomEnvironmentOfRadiusN( (Mol)mol, (int)radius, (int)rootedAtAtom [, (bool)useHs=False]) -> _vecti : Finds the bonds within a certain radius of an atom in a molecule |
FindPotentialStereoBonds(...) FindPotentialStereoBonds( (Mol)mol [, (bool)cleanIt=False]) -> None : Find bonds than can be cis/trans in a molecule and mark them as 'any'. |
FindUniqueSubgraphsOfLengthN(...) FindUniqueSubgraphsOfLengthN( (Mol)mol, (int)length [, (bool)useHs=False [, (bool)useBO=True [, (int)rootedAtAtom=-1]]]) -> _listSt6vectorIiSaIiEE : Finds unique subgraphs of a particular length in a molecule |
FragmentOnBRICSBonds(...) FragmentOnBRICSBonds( (Mol)mol) -> Mol : Return a new molecule with all BRICS bonds broken |
FragmentOnBonds(...) FragmentOnBonds( (Mol)mol, (AtomPairsParameters)bondIndices [, (bool)addDummies=True [, (AtomPairsParameters)dummyLabels=None [, (AtomPairsParameters)bondTypes=None [, (list)cutsPerAtom=[]]]]]) -> Mol : Return a new molecule with all specified bonds broken |
FragmentOnSomeBonds(...) FragmentOnSomeBonds( (Mol)mol, (AtomPairsParameters)bondIndices [, (int)numToBreak=1 [, (bool)addDummies=True [, (AtomPairsParameters)dummyLabels=None [, (AtomPairsParameters)bondTypes=None [, (bool)returnCutsPerAtom=False]]]]]) -> tuple : fragment on some bonds |
Get3DDistanceMatrix(...) Get3DDistanceMatrix( (Mol)mol [, (int)confId=-1 [, (bool)useAtomWts=False [, (bool)force=False [, (str)prefix='']]]]) -> object : Returns the molecule's 3D distance matrix. |
GetAdjacencyMatrix(...) GetAdjacencyMatrix( (Mol)mol [, (bool)useBO=False [, (int)emptyVal=0 [, (bool)force=False [, (str)prefix='']]]]) -> object : Returns the molecule's adjacency matrix. |
GetDistanceMatrix(...) GetDistanceMatrix( (Mol)mol [, (bool)useBO=False [, (bool)useAtomWts=False [, (bool)force=False [, (str)prefix='']]]]) -> object : Returns the molecule's topological distance matrix. |
GetFormalCharge(...) GetFormalCharge( (Mol)arg1) -> int : Returns the formal charge for the molecule. |
GetMolFrags(...) GetMolFrags( (Mol)mol [, (bool)asMols=False [, (bool)sanitizeFrags=True]]) -> tuple : Finds the disconnected fragments from a molecule. |
GetSSSR(...) GetSSSR( (Mol)arg1) -> int : Get the smallest set of simple rings for a molecule. |
GetShortestPath(...) GetShortestPath( (Mol)arg1, (int)arg2, (int)arg3) -> tuple : Find the shortest path between two atoms using the Bellman-Ford algorithm. |
GetSymmSSSR(...) GetSymmSSSR( (Mol)arg1) -> _vectSt6vectorIiSaIiEE : Get a symmetrized SSSR for a molecule. |
Kekulize(...) Kekulize( (Mol)mol [, (bool)clearAromaticFlags=False]) -> None : Kekulizes the molecule |
LayeredFingerprint(...) LayeredFingerprint( (Mol)mol [, (int)layerFlags=4294967295 [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (list)atomCounts=[] [, (ExplicitBitVect)setOnlyBits=None [, (bool)branchedPaths=True [, (AtomPairsParameters)fromAtoms=0]]]]]]]]) -> ExplicitBitVect : Returns a layered fingerprint for a molecule |
MergeQueryHs(...) MergeQueryHs( (Mol)mol [, (bool)mergeUnmappedOnly=False]) -> Mol : merges hydrogens into their neighboring atoms as queries |
MolAddRecursiveQueries(...) MolAddRecursiveQueries( (Mol)mol, (dict)queries, (str)propName) -> None : Adds named recursive queries to atoms |
MolToSVG(...) MolToSVG( (Mol)arg1, (int)mol [, (int)width=300 [, (AtomPairsParameters)height=300 [, (bool)highlightAtoms=None [, (int)kekulize=True [, (int)lineWidthMult=1 [, (bool)fontSize=12 [, (int)includeAtomCircles=True]]]]]]]) -> str : Returns svg for a molecule |
MurckoDecompose(...) MurckoDecompose( (Mol)mol) -> Mol : Do a Murcko decomposition and return the scaffold |
ParseMolQueryDefFile(...) ParseMolQueryDefFile( (AtomPairsParameters)fileobj [, (bool)standardize=True [, (str)delimiter='\t' [, (str)comment='//' [, (int)nameColumn=0 [, (int)smartsColumn=1]]]]]) -> dict : reads query definitions from a simply formatted file |
PathToSubmol(...) PathToSubmol( (Mol)mol, (AtomPairsParameters)path [, (bool)useQuery=False [, (AtomPairsParameters)atomMap=None]]) -> Mol : |
PatternFingerprint(...) PatternFingerprint( (Mol)mol [, (int)fpSize=2048 [, (list)atomCounts=[] [, (ExplicitBitVect)setOnlyBits=None]]]) -> ExplicitBitVect : A fingerprint using SMARTS patterns |
RDKFingerprint(...) RDKFingerprint( (Mol)mol [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (int)nBitsPerHash=2 [, (bool)useHs=True [, (float)tgtDensity=0.0 [, (int)minSize=128 [, (bool)branchedPaths=True [, (bool)useBondOrder=True [, (AtomPairsParameters)atomInvariants=0 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)atomBits=None [, (AtomPairsParameters)bitInfo=None]]]]]]]]]]]]]) -> ExplicitBitVect : Returns an RDKit topological fingerprint for a molecule |
RemoveHs(...) RemoveHs( (Mol)mol [, (bool)implicitOnly=False [, (bool)updateExplicitCount=False [, (bool)sanitize=True]]]) -> Mol : Removes any hydrogens from the graph of a molecule. |
RemoveStereochemistry(...) RemoveStereochemistry( (Mol)mol) -> None : Removes all stereochemistry info from the molecule. |
RenumberAtoms(...) RenumberAtoms( (Mol)mol, (AtomPairsParameters)newOrder) -> Mol : Returns a copy of a molecule with renumbered atoms |
ReplaceCore(...) ReplaceCore( (Mol)mol, (Mol)core, (AtomPairsParameters)matches [, (bool)replaceDummies=True [, (bool)labelByIndex=False [, (bool)requireDummyMatch=False]]]) -> Mol : Removes the core of a molecule and labels the sidechains with dummy atoms based on The matches indices given in the matching vector matches. |
ReplaceSidechains(...) ReplaceSidechains( (Mol)mol, (Mol)coreQuery [, (bool)useChirality=False]) -> Mol : Replaces sidechains in a molecule with dummy atoms for their attachment points. |
ReplaceSubstructs(...) ReplaceSubstructs( (Mol)mol, (Mol)query, (Mol)replacement [, (bool)replaceAll=False [, (int)replacementConnectionPoint=0 [, (bool)useChirality=False]]]) -> object : Replaces atoms matching a substructure query in a molecule |
SanitizeMol(...) SanitizeMol( (Mol)mol [, (int)sanitizeOps=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL [, (bool)catchErrors=False]]) -> SanitizeFlags : Kekulize, check valencies, set aromaticity, conjugation and hybridization |
SetAromaticity(...) SetAromaticity( (Mol)mol [, (AromaticityModel)model=rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT]) -> None : does aromaticity perception |
SetConjugation(...) SetConjugation( (Mol)mol) -> None : finds conjugated bonds |
SetHybridization(...) SetHybridization( (Mol)mol) -> None : Assigns hybridization states to atoms |
SplitMolByPDBChainId(...) SplitMolByPDBChainId( (Mol)mol [, (AtomPairsParameters)whiteList=None [, (bool)negateList=False]]) -> dict : Splits a molecule into pieces based on PDB chain information. |
SplitMolByPDBResidues(...) SplitMolByPDBResidues( (Mol)mol [, (AtomPairsParameters)whiteList=None [, (bool)negateList=False]]) -> dict : Splits a molecule into pieces based on PDB residue information. |
UnfoldedRDKFingerprintCountBased(...) UnfoldedRDKFingerprintCountBased( (Mol)mol [, (int)minPath=1 [, (int)maxPath=7 [, (bool)useHs=True [, (bool)branchedPaths=True [, (bool)useBondOrder=True [, (AtomPairsParameters)atomInvariants=0 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)atomBits=None [, (AtomPairsParameters)bitInfo=None]]]]]]]]]) -> ULongSparseIntVect : Returns an unfolded count-based version of the RDKit fingerprint for a molecule |
WedgeMolBonds(...) WedgeMolBonds( (Mol)arg1, (Conformer)arg2) -> None : Set the wedging on single bonds in a molecule. |

Variables | [hide private]
| ADJUST_IGNOREALL = `rdkit.Chem.rdmolops.AdjustQueryWhichFlags.A`...``
| ADJUST_IGNORECHAINS = `rdkit.Chem.rdmolops.AdjustQueryWhichFlag`...``
| ADJUST_IGNOREDUMMIES = `rdkit.Chem.rdmolops.AdjustQueryWhichFla`...``
| ADJUST_IGNORENONDUMMIES = `rdkit.Chem.rdmolops.AdjustQueryWhich`...``
| ADJUST_IGNORENONE = `rdkit.Chem.rdmolops.AdjustQueryWhichFlags.`...``
| ADJUST_IGNORERINGS = `rdkit.Chem.rdmolops.AdjustQueryWhichFlags`...``
| AROMATICITY_CUSTOM = `rdkit.Chem.rdmolops.AromaticityModel.AROM`...``
| AROMATICITY_DEFAULT = `rdkit.Chem.rdmolops.AromaticityModel.ARO`...``
| AROMATICITY_RDKIT = `rdkit.Chem.rdmolops.AromaticityModel.AROMA`...``
| AROMATICITY_SIMPLE = `rdkit.Chem.rdmolops.AromaticityModel.AROM`...``
| LayeredFingerprint_substructLayers = `7`
| SANITIZE_ADJUSTHS = `rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE`...``
| SANITIZE_ALL = `rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL`
| SANITIZE_CLEANUP = `rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_`...``
| SANITIZE_CLEANUPCHIRALITY = `rdkit.Chem.rdmolops.SanitizeFlags.`...``
| SANITIZE_FINDRADICALS = `rdkit.Chem.rdmolops.SanitizeFlags.SANI`...``
| SANITIZE_KEKULIZE = `rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE`...``
| SANITIZE_NONE = `rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE`
| SANITIZE_PROPERTIES = `rdkit.Chem.rdmolops.SanitizeFlags.SANITI`...``
| SANITIZE_SETAROMATICITY = `rdkit.Chem.rdmolops.SanitizeFlags.SA`...``
| SANITIZE_SETCONJUGATION = `rdkit.Chem.rdmolops.SanitizeFlags.SA`...``
| SANITIZE_SETHYBRIDIZATION = `rdkit.Chem.rdmolops.SanitizeFlags.`...``
| SANITIZE_SYMMRINGS = `rdkit.Chem.rdmolops.SanitizeFlags.SANITIZ`...``
| _LayeredFingerprint_version = ``'``0.7.0``'``
| _RDKFingerprint_version = ``'``2.0.0``'``
| __package__ = `None` hash(x)

Function Details | [hide private]

### AddHs(...) |
    AddHs( (Mol)mol [, (bool)explicitOnly=False [, (bool)addCoords=False [, (AtomPairsParameters)onlyOnAtoms=None]]]) -> Mol :
        Adds hydrogens to the graph of a molecule.

          ARGUMENTS:

            - mol: the molecule to be modified

            - explicitOnly: (optional) if this toggle is set, only explicit Hs will
              be added to the molecule.  Default value is 0 (add implicit and explicit Hs).

            - addCoords: (optional) if this toggle is set, The Hs will have 3D coordinates
              set.  Default value is 0 (no 3D coords).

            - onlyOnHs: (optional) if this sequence is provided, only these atoms will be
              considered to have Hs added to them

          RETURNS: a new molecule with added Hs

          NOTES:

            - The original molecule is *not* modified.

            - Much of the code assumes that Hs are not included in the molecular
              topology, so be *very* careful with the molecule that comes back from
              this function.

        C++ signature :
            RDKit::ROMol* AddHs(RDKit::ROMol [,bool=False [,bool=False [,boost::python::api::object=None]]])

### AddRecursiveQuery(...) |
    AddRecursiveQuery( (Mol)mol, (Mol)query, (int)atomIdx [, (bool)preserveExistingQuery=True]) -> None :
        Adds a recursive query to an atom

          ARGUMENTS:

            - mol: the molecule to be modified

            - query: the molecule to be used as the recursive query (this will be copied)

            - atomIdx: the atom to modify

            - preserveExistingQuery: (optional) if this is set, existing query information on the atom will be preserved

          RETURNS: None

        C++ signature :
            void AddRecursiveQuery(RDKit::ROMol {lvalue},RDKit::ROMol,unsigned int [,bool=True])

### AdjustQueryProperties(...) |
    AdjustQueryProperties( (Mol)mol [, (AtomPairsParameters)params=None]) -> Mol :
        Returns a new molecule where the query properties of atoms have been modified.

        C++ signature :
            RDKit::ROMol* AdjustQueryProperties(RDKit::ROMol [,boost::python::api::object=None])

### AssignAtomChiralTagsFromStructure(...) |
    AssignAtomChiralTagsFromStructure( (Mol)mol [, (int)confId=-1 [, (bool)replaceExistingTags=True]]) -> None :
        Sets the chiral tags on a molecule's atoms based on
          a 3D conformation.

          ARGUMENTS:

            - mol: the molecule to use
            - confId: the conformer id to use, -1 for the default
            - replaceExistingTags: if True, existing stereochemistry information will be cleared
                                   before running the calculation.

        C++ signature :
            void AssignAtomChiralTagsFromStructure(RDKit::ROMol {lvalue} [,int=-1 [,bool=True]])

### AssignRadicals(...) |
    AssignRadicals( (Mol)mol) -> None :
        Assigns radical counts to atoms

          ARGUMENTS:

            - mol: the molecule to use

          NOTES:

            - The molecule is modified in place.

        C++ signature :
            void AssignRadicals(RDKit::ROMol {lvalue})

### AssignStereochemistry(...) |
    AssignStereochemistry( (Mol)mol [, (bool)cleanIt=False [, (bool)force=False [, (bool)flagPossibleStereoCenters=False]]]) -> None :
        Does the CIP stereochemistry assignment
          for the molecule's atoms (R/S) and double bond (Z/E).
          Chiral atoms will have a property '_CIPCode' indicating
          their chiral code.

          ARGUMENTS:

            - mol: the molecule to use
            - cleanIt: (optional) if provided, atoms with a chiral specifier that aren't
              actually chiral (e.g. atoms with duplicate substituents or only 2 substituents,
              etc.) will have their chiral code set to CHI_UNSPECIFIED
            - force: (optional) causes the calculation to be repeated, even if it has already
              been done
            - flagPossibleStereoCenters (optional)   set the _ChiralityPossible property on
              atoms that are possible stereocenters

        C++ signature :
            void AssignStereochemistry(RDKit::ROMol {lvalue} [,bool=False [,bool=False [,bool=False]]])

### Cleanup(...) |
    Cleanup( (Mol)mol) -> None :
        cleans up certain common bad functionalities in the molecule

          ARGUMENTS:

            - mol: the molecule to use

          NOTES:

            - The molecule is modified in place.

        C++ signature :
            void Cleanup(RDKit::ROMol {lvalue})

### CombineMols(...) |
    CombineMols( (Mol)mol1, (Mol)mol2 [, (Point3D)offset=<rdkit.Geometry.rdGeometry.Point3D object at 0x7fc444bf9380>]) -> Mol :
        Combine the atoms from two molecules to produce a third

        C++ signature :
            RDKit::ROMol* CombineMols(RDKit::ROMol,RDKit::ROMol [,RDGeom::Point3D=<rdkit.Geometry.rdGeometry.Point3D object at 0x7fc444bf9380>])

### DeleteSubstructs(...) |
    DeleteSubstructs( (Mol)mol, (Mol)query [, (bool)onlyFrags=False [, (bool)useChirality=False]]) -> Mol :
        Removes atoms matching a substructure query from a molecule

          ARGUMENTS:

            - mol: the molecule to be modified

            - query: the molecule to be used as a substructure query

            - onlyFrags: (optional) if this toggle is set, atoms will only be removed if
              the entire fragment in which they are found is matched by the query.
              See below for examples.
              Default value is 0 (remove the atoms whether or not the entire fragment matches)

            - useChirality: (optional) match the substructure query using chirality

          RETURNS: a new molecule with the substructure removed

          NOTES:

            - The original molecule is *not* modified.

          EXAMPLES:

           The following examples substitute SMILES/SMARTS strings for molecules, you'd have
           to actually use molecules:

            - DeleteSubstructs('CCOC','OC') -> 'CC'

            - DeleteSubstructs('CCOC','OC',1) -> 'CCOC'

            - DeleteSubstructs('CCOCCl.Cl','Cl',1) -> 'CCOCCl'

            - DeleteSubstructs('CCOCCl.Cl','Cl') -> 'CCOC'

        C++ signature :
            RDKit::ROMol* DeleteSubstructs(RDKit::ROMol,RDKit::ROMol [,bool=False [,bool=False]])

### DetectBondStereoChemistry(...) |
    DetectBondStereoChemistry( (Mol)mol, (Conformer)conformer) -> None :
        Assign stereochemistry to bonds based on coordinates and a conformer.
                DEPRECATED: Please use the version that takes a conformer ID instead.

          ARGUMENTS:

            - mol: the molecule to be modified
            - conformer: Conformer providing the coordinates

        C++ signature :
            void DetectBondStereoChemistry(RDKit::ROMol {lvalue},RDKit::Conformer const*)

### DetectBondStereochemistry(...) |
    DetectBondStereochemistry( (Mol)mol [, (int)confId=-1]) -> None :
        Assign stereochemistry to bonds based on coordinates.

          ARGUMENTS:

            - mol: the molecule to be modified
            - confId: Conformer to use for the coordinates

        C++ signature :
            void DetectBondStereochemistry(RDKit::ROMol {lvalue} [,int=-1])

### FastFindRings(...) |
    FastFindRings( (Mol)arg1) -> None :
        Does a non-SSSR ring finding for a molecule.

          ARGUMENTS:

            - mol: the molecule to use.

          RETURNS: Nothing

        C++ signature :
            void FastFindRings(RDKit::ROMol)

### FindAllPathsOfLengthN(...) |
    FindAllPathsOfLengthN( (Mol)mol, (int)length [, (bool)useBonds=True [, (bool)useHs=False [, (int)rootedAtAtom=-1]]]) -> _listSt6vectorIiSaIiEE :
        Finds all paths of a particular length in a molecule

          ARGUMENTS:

            - mol: the molecule to use

            - length: an integer with the target length for the paths.

            - useBonds: (optional) toggles the use of bond indices in the paths.
              Otherwise atom indices are used.  *Note* this behavior is different
              from that for subgraphs.
              Defaults to 1.

            - rootedAtAtom: (optional) if nonzero, only paths from the specified
              atom will be returned.

          RETURNS: a tuple of tuples with IDs for the bonds.

          NOTES:

           - Difference between _subgraphs_ and _paths_ ::

               Subgraphs are potentially branched, whereas paths (in our
               terminology at least) cannot be.  So, the following graph:

                    C--0--C--1--C--3--C
                          |
                          2
                          |
                          C

               has 3 _subgraphs_ of length 3: (0,1,2),(0,1,3),(2,1,3)
               but only 2 _paths_ of length 3: (0,1,3),(2,1,3)

        C++ signature :
            std::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > FindAllPathsOfLengthN(RDKit::ROMol,unsigned int [,bool=True [,bool=False [,int=-1]]])

### FindAllSubgraphsOfLengthMToN(...) |
    FindAllSubgraphsOfLengthMToN( (Mol)mol, (int)min, (int)max [, (bool)useHs=False [, (int)rootedAtAtom=-1]]) -> object :
        Finds all subgraphs of a particular length in a molecule
          See documentation for FindAllSubgraphsOfLengthN for definitions

        C++ signature :
            boost::python::api::object FindAllSubgraphsOfLengthMToN(RDKit::ROMol,unsigned int,unsigned int [,bool=False [,int=-1]])

### FindAllSubgraphsOfLengthN(...) |
    FindAllSubgraphsOfLengthN( (Mol)mol, (int)length [, (bool)useHs=False [, (int)rootedAtAtom=-1]]) -> _listSt6vectorIiSaIiEE :
        Finds all subgraphs of a particular length in a molecule

          ARGUMENTS:

            - mol: the molecule to use

            - length: an integer with the target number of bonds for the subgraphs.

            - useHs: (optional) toggles whether or not bonds to Hs that are part of the graph
              should be included in the results.
              Defaults to 0.

            - rootedAtAtom: (optional) if nonzero, only subgraphs from the specified
              atom will be returned.

          RETURNS: a tuple of 2-tuples with bond IDs

          NOTES:

           - Difference between _subgraphs_ and _paths_ ::

               Subgraphs are potentially branched, whereas paths (in our
               terminology at least) cannot be.  So, the following graph:

                    C--0--C--1--C--3--C
                          |
                          2
                          |
                          C
          has 3 _subgraphs_ of length 3: (0,1,2),(0,1,3),(2,1,3)
          but only 2 _paths_ of length 3: (0,1,3),(2,1,3)

        C++ signature :
            std::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > FindAllSubgraphsOfLengthN(RDKit::ROMol,unsigned int [,bool=False [,int=-1]])

### FindAtomEnvironmentOfRadiusN(...) |
    FindAtomEnvironmentOfRadiusN( (Mol)mol, (int)radius, (int)rootedAtAtom [, (bool)useHs=False]) -> _vecti :
        Finds the bonds within a certain radius of an atom in a molecule

          ARGUMENTS:

            - mol: the molecule to use

            - radius: an integer with the target radius for the environment.

            - rootedAtAtom: the atom to consider

            - useHs: (optional) toggles whether or not bonds to Hs that are part of the graph
              should be included in the results.
              Defaults to 0.

          RETURNS: a vector of bond IDs

        C++ signature :
            std::vector<int, std::allocator<int> > FindAtomEnvironmentOfRadiusN(RDKit::ROMol,unsigned int,unsigned int [,bool=False])

### FindPotentialStereoBonds(...) |
    FindPotentialStereoBonds( (Mol)mol [, (bool)cleanIt=False]) -> None :
        Find bonds than can be cis/trans in a molecule and mark them as 'any'.
                 This function finds any double bonds that can potentially be part
                 of a cis/trans system. No attempt is made here to mark them cis or trans

          ARGUMENTS:

            - mol: the molecule to use
            - cleanIt: (optional) if this option is set to true, any previous marking of _CIPCode
                       on the bond is cleared - otherwise it is left untouched

        C++ signature :
            void FindPotentialStereoBonds(RDKit::ROMol {lvalue} [,bool=False])

### FindUniqueSubgraphsOfLengthN(...) |
    FindUniqueSubgraphsOfLengthN( (Mol)mol, (int)length [, (bool)useHs=False [, (bool)useBO=True [, (int)rootedAtAtom=-1]]]) -> _listSt6vectorIiSaIiEE :
        Finds unique subgraphs of a particular length in a molecule

          ARGUMENTS:

            - mol: the molecule to use

            - length: an integer with the target number of bonds for the subgraphs.

            - useHs: (optional) toggles whether or not bonds to Hs that are part of the graph
              should be included in the results.
              Defaults to 0.

            - useBO: (optional) Toggles use of bond orders in distinguishing one subgraph from
              another.
              Defaults to 1.

            - rootedAtAtom: (optional) if nonzero, only subgraphs from the specified
              atom will be returned.

          RETURNS: a tuple of tuples with bond IDs

        C++ signature :
            std::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > FindUniqueSubgraphsOfLengthN(RDKit::ROMol,unsigned int [,bool=False [,bool=True [,int=-1]]])

### FragmentOnBRICSBonds(...) |
    FragmentOnBRICSBonds( (Mol)mol) -> Mol :
        Return a new molecule with all BRICS bonds broken

        C++ signature :
            RDKit::ROMol* FragmentOnBRICSBonds(RDKit::ROMol)

### FragmentOnBonds(...) |
    FragmentOnBonds( (Mol)mol, (AtomPairsParameters)bondIndices [, (bool)addDummies=True [, (AtomPairsParameters)dummyLabels=None [, (AtomPairsParameters)bondTypes=None [, (list)cutsPerAtom=[]]]]]) -> Mol :
        Return a new molecule with all specified bonds broken

          ARGUMENTS:

              - mol            - the molecule to be modified
              - bondIndices    - indices of the bonds to be broken
              - addDummies  - toggles addition of dummy atoms to indicate where
                  bonds were broken
              - dummyLabels - used to provide the labels to be used for the dummies.
                  the first element in each pair is the label for the dummy
                  that replaces the bond's beginAtom, the second is for the
                  dummy that replaces the bond's endAtom. If not provided, the
                  dummies are labeled with atom indices.
              - bondTypes - used to provide the bond type to use between the
                  fragments and the dummy atoms. If not provided, defaults to single.
              - cutsPerAtom - used to return the number of cuts made at each atom.

          RETURNS:
              a new Mol with the modifications

        C++ signature :
            RDKit::ROMol* FragmentOnBonds(RDKit::ROMol,boost::python::api::object [,bool=True [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::list=[]]]]])

### FragmentOnSomeBonds(...) |
    FragmentOnSomeBonds( (Mol)mol, (AtomPairsParameters)bondIndices [, (int)numToBreak=1 [, (bool)addDummies=True [, (AtomPairsParameters)dummyLabels=None [, (AtomPairsParameters)bondTypes=None [, (bool)returnCutsPerAtom=False]]]]]) -> tuple :
        fragment on some bonds

        C++ signature :
            boost::python::tuple FragmentOnSomeBonds(RDKit::ROMol,boost::python::api::object [,unsigned int=1 [,bool=True [,boost::python::api::object=None [,boost::python::api::object=None [,bool=False]]]]])

### Get3DDistanceMatrix(...) |
    Get3DDistanceMatrix( (Mol)mol [, (int)confId=-1 [, (bool)useAtomWts=False [, (bool)force=False [, (str)prefix='']]]]) -> object :
        Returns the molecule's 3D distance matrix.

          ARGUMENTS:

            - mol: the molecule to use

            - confId: (optional) chooses the conformer Id to use
              Default value is -1.

            - useAtomWts: (optional) toggles using atom weights for the diagonal elements of the
              matrix (to return a "Balaban" distance matrix).
              Default value is 0.

            - force: (optional) forces the calculation to proceed, even if there is a cached value.
              Default value is 0.

            - prefix: (optional, internal use) sets the prefix used in the property cache
              Default value is .

          RETURNS: a Numeric array of floats with the distance matrix

        C++ signature :
            _object* Get3DDistanceMatrix(RDKit::ROMol {lvalue} [,int=-1 [,bool=False [,bool=False [,char const*='']]]])

### GetAdjacencyMatrix(...) |
    GetAdjacencyMatrix( (Mol)mol [, (bool)useBO=False [, (int)emptyVal=0 [, (bool)force=False [, (str)prefix='']]]]) -> object :
        Returns the molecule's adjacency matrix.

          ARGUMENTS:

            - mol: the molecule to use

            - useBO: (optional) toggles use of bond orders in calculating the matrix.
              Default value is 0.

            - emptyVal: (optional) sets the elements of the matrix between non-adjacent atoms
              Default value is 0.

            - force: (optional) forces the calculation to proceed, even if there is a cached value.
              Default value is 0.

            - prefix: (optional, internal use) sets the prefix used in the property cache
              Default value is .

          RETURNS: a Numeric array of floats containing the adjacency matrix

        C++ signature :
            _object* GetAdjacencyMatrix(RDKit::ROMol {lvalue} [,bool=False [,int=0 [,bool=False [,char const*='']]]])

### GetDistanceMatrix(...) |
    GetDistanceMatrix( (Mol)mol [, (bool)useBO=False [, (bool)useAtomWts=False [, (bool)force=False [, (str)prefix='']]]]) -> object :
        Returns the molecule's topological distance matrix.

          ARGUMENTS:

            - mol: the molecule to use

            - useBO: (optional) toggles use of bond orders in calculating the distance matrix.
              Default value is 0.

            - useAtomWts: (optional) toggles using atom weights for the diagonal elements of the
              matrix (to return a "Balaban" distance matrix).
              Default value is 0.

            - force: (optional) forces the calculation to proceed, even if there is a cached value.
              Default value is 0.

            - prefix: (optional, internal use) sets the prefix used in the property cache
              Default value is .

          RETURNS: a Numeric array of floats with the distance matrix

        C++ signature :
            _object* GetDistanceMatrix(RDKit::ROMol {lvalue} [,bool=False [,bool=False [,bool=False [,char const*='']]]])

### GetFormalCharge(...) |
    GetFormalCharge( (Mol)arg1) -> int :
        Returns the formal charge for the molecule.

          ARGUMENTS:

            - mol: the molecule to use

        C++ signature :
            int GetFormalCharge(RDKit::ROMol)

### GetMolFrags(...) |
    GetMolFrags( (Mol)mol [, (bool)asMols=False [, (bool)sanitizeFrags=True]]) -> tuple :
        Finds the disconnected fragments from a molecule.

          For example, for the molecule 'CC(=O)[O-].[NH3+]C' GetMolFrags() returns
          ((0, 1, 2, 3), (4, 5))

          ARGUMENTS:

            - mol: the molecule to use
            - asMols: (optional) if this is provided and true, the fragments
              will be returned as molecules instead of atom ids.
            - sanitizeFrags: (optional) if this is provided and true, the fragments
              molecules will be sanitized before returning them.

          RETURNS: a tuple of tuples with IDs for the atoms in each fragment
                   or a tuple of molecules.

        C++ signature :
            boost::python::tuple GetMolFrags(RDKit::ROMol [,bool=False [,bool=True]])

### GetSSSR(...) |
    GetSSSR( (Mol)arg1) -> int :
        Get the smallest set of simple rings for a molecule.

          ARGUMENTS:

            - mol: the molecule to use.

          RETURNS: a sequence of sequences containing the rings found as atom ids
                 The length of this will be equal to NumBonds-NumAtoms+1 for single-fragment molecules.

        C++ signature :
            int GetSSSR(RDKit::ROMol {lvalue})

### GetShortestPath(...) |
    GetShortestPath( (Mol)arg1, (int)arg2, (int)arg3) -> tuple :
        Find the shortest path between two atoms using the Bellman-Ford algorithm.

          ARGUMENTS:

            - mol: the molecule to use
            - idx1: index of the first atom
            - idx2: index of the second atom

        C++ signature :
            boost::python::tuple GetShortestPath(RDKit::ROMol,int,int)

### GetSymmSSSR(...) |
    GetSymmSSSR( (Mol)arg1) -> _vectSt6vectorIiSaIiEE :
        Get a symmetrized SSSR for a molecule.

          The symmetrized SSSR is at least as large as the SSSR for a molecule.
          In certain highly-symmetric cases (e.g. cubane), the symmetrized SSSR can be
          a bit larger (i.e. the number of symmetrized rings is >= NumBonds-NumAtoms+1).

          ARGUMENTS:

            - mol: the molecule to use.

          RETURNS: a sequence of sequences containing the rings found as atom ids

        C++ signature :
            std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > GetSymmSSSR(RDKit::ROMol {lvalue})

### Kekulize(...) |
    Kekulize( (Mol)mol [, (bool)clearAromaticFlags=False]) -> None :
        Kekulizes the molecule

          ARGUMENTS:

            - mol: the molecule to use

            - clearAromaticFlags: (optional) if this toggle is set, all atoms and bonds in the
              molecule will be marked non-aromatic following the kekulization.
              Default value is 0.

          NOTES:

            - The molecule is modified in place.

        C++ signature :
            void Kekulize(RDKit::ROMol {lvalue} [,bool=False])

### LayeredFingerprint(...) |
    LayeredFingerprint( (Mol)mol [, (int)layerFlags=4294967295 [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (list)atomCounts=[] [, (ExplicitBitVect)setOnlyBits=None [, (bool)branchedPaths=True [, (AtomPairsParameters)fromAtoms=0]]]]]]]]) -> ExplicitBitVect :
        Returns a layered fingerprint for a molecule

          NOTE: This function is experimental. The API or results may change from
            release to release.

          Explanation of the algorithm below.

          ARGUMENTS:

            - mol: the molecule to use

            - layerFlags: (optional) which layers to include in the fingerprint
              See below for definitions. Defaults to all.

            - minPath: (optional) minimum number of bonds to include in the subgraphs
              Defaults to 1.

            - maxPath: (optional) maximum number of bonds to include in the subgraphs
              Defaults to 7.

            - fpSize: (optional) number of bits in the fingerprint
              Defaults to 2048.

            - atomCounts: (optional)
                if provided, this should be a list at least as long as the number of atoms
                in the molecule. It will be used to provide the count of the number
                of paths that set bits each atom is involved in.
                NOTE: the list is not zeroed out here.

            - setOnlyBits: (optional)
                if provided, only bits that are set in this bit vector will be set
                in the result. This is essentially the same as doing:
                   res &= setOnlyBits
                but also has an impact on the atomCounts (if being used)

            - branchedPaths: (optional) if set both branched and unbranched paths will be
              used in the fingerprint.
              Defaults to True.

            - fromAtoms: (optional) a sequence of atom indices. If provided, only paths/subgraphs
              starting from these atoms will be used.
              Defaults to empty.

          RETURNS: a DataStructs.ExplicitBitVect with _fpSize_ bits

          Layer definitions:
             - 0x01: pure topology
             - 0x02: bond order
             - 0x04: atom types
             - 0x08: presence of rings
             - 0x10: ring sizes
             - 0x20: aromaticity

        C++ signature :
            ExplicitBitVect* LayeredFingerprint(RDKit::ROMol [,unsigned int=4294967295 [,unsigned int=1 [,unsigned int=7 [,unsigned int=2048 [,boost::python::list=[] [,ExplicitBitVect*=None [,bool=True [,boost::python::api::object=0]]]]]]]])

### MergeQueryHs(...) |
    MergeQueryHs( (Mol)mol [, (bool)mergeUnmappedOnly=False]) -> Mol :
        merges hydrogens into their neighboring atoms as queries

        C++ signature :
            RDKit::ROMol* MergeQueryHs(RDKit::ROMol [,bool=False])

### MolAddRecursiveQueries(...) |
    MolAddRecursiveQueries( (Mol)mol, (dict)queries, (str)propName) -> None :
        Adds named recursive queries to atoms

        C++ signature :
            void MolAddRecursiveQueries(RDKit::ROMol {lvalue},boost::python::dict,std::string)

### MolToSVG(...) |
    MolToSVG( (Mol)arg1, (int)mol [, (int)width=300 [, (AtomPairsParameters)height=300 [, (bool)highlightAtoms=None [, (int)kekulize=True [, (int)lineWidthMult=1 [, (bool)fontSize=12 [, (int)includeAtomCircles=True]]]]]]]) -> str :
        Returns svg for a molecule

        C++ signature :
            std::string MolToSVG(RDKit::ROMol,unsigned int [,unsigned int=300 [,boost::python::api::object=300 [,bool=None [,unsigned int=True [,unsigned int=1 [,bool=12 [,int=True]]]]]]])

### MurckoDecompose(...) |
    MurckoDecompose( (Mol)mol) -> Mol :
        Do a Murcko decomposition and return the scaffold

        C++ signature :
            RDKit::ROMol* MurckoDecompose(RDKit::ROMol)

### ParseMolQueryDefFile(...) |
    ParseMolQueryDefFile( (AtomPairsParameters)fileobj [, (bool)standardize=True [, (str)delimiter='\t' [, (str)comment='//' [, (int)nameColumn=0 [, (int)smartsColumn=1]]]]]) -> dict :
        reads query definitions from a simply formatted file

        C++ signature :
            boost::python::dict ParseMolQueryDefFile(boost::python::api::object {lvalue} [,bool=True [,std::string='\t' [,std::string='//' [,unsigned int=0 [,unsigned int=1]]]]])

### PathToSubmol(...) |
    PathToSubmol( (Mol)mol, (AtomPairsParameters)path [, (bool)useQuery=False [, (AtomPairsParameters)atomMap=None]]) -> Mol :

        C++ signature :
            RDKit::ROMol* PathToSubmol(RDKit::ROMol,boost::python::api::object {lvalue} [,bool=False [,boost::python::api::object=None]])

### PatternFingerprint(...) |
    PatternFingerprint( (Mol)mol [, (int)fpSize=2048 [, (list)atomCounts=[] [, (ExplicitBitVect)setOnlyBits=None]]]) -> ExplicitBitVect :
        A fingerprint using SMARTS patterns

          NOTE: This function is experimental. The API or results may change from
            release to release.

        C++ signature :
            ExplicitBitVect* PatternFingerprint(RDKit::ROMol [,unsigned int=2048 [,boost::python::list=[] [,ExplicitBitVect*=None]]])

### RDKFingerprint(...) |
    RDKFingerprint( (Mol)mol [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (int)nBitsPerHash=2 [, (bool)useHs=True [, (float)tgtDensity=0.0 [, (int)minSize=128 [, (bool)branchedPaths=True [, (bool)useBondOrder=True [, (AtomPairsParameters)atomInvariants=0 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)atomBits=None [, (AtomPairsParameters)bitInfo=None]]]]]]]]]]]]]) -> ExplicitBitVect :
        Returns an RDKit topological fingerprint for a molecule

          Explanation of the algorithm below.

          ARGUMENTS:

            - mol: the molecule to use

            - minPath: (optional) minimum number of bonds to include in the subgraphs
              Defaults to 1.

            - maxPath: (optional) maximum number of bonds to include in the subgraphs
              Defaults to 7.

            - fpSize: (optional) number of bits in the fingerprint
              Defaults to 2048.

            - nBitsPerHash: (optional) number of bits to set per path
              Defaults to 2.

            - useHs: (optional) include paths involving Hs in the fingerprint if the molecule
              has explicit Hs.
              Defaults to True.

            - tgtDensity: (optional) fold the fingerprint until this minimum density has
              been reached
              Defaults to 0.

            - minSize: (optional) the minimum size the fingerprint will be folded to when
              trying to reach tgtDensity
              Defaults to 128.

            - branchedPaths: (optional) if set both branched and unbranched paths will be
              used in the fingerprint.
              Defaults to True.

            - useBondOrder: (optional) if set both bond orders will be used in the path hashes
              Defaults to True.

            - atomInvariants: (optional) a sequence of atom invariants to use in the path hashes
              Defaults to empty.

            - fromAtoms: (optional) a sequence of atom indices. If provided, only paths/subgraphs
              starting from these atoms will be used.
              Defaults to empty.

            - atomBits: (optional) an empty list. If provided, the result will contain a list
              containing the bits each atom sets.
              Defaults to empty.

           - bitInfo: (optional) an empty dict. If provided, the result will contain a dict
             with bits as keys and corresponding bond paths as values.
             Defaults to empty.

          RETURNS: a DataStructs.ExplicitBitVect with _fpSize_ bits

          ALGORITHM:

           This algorithm functions by find all subgraphs between minPath and maxPath in
           length.  For each subgraph:

             1) A hash is calculated.

             2) The hash is used to seed a random-number generator

             3) _nBitsPerHash_ random numbers are generated and used to set the corresponding
                bits in the fingerprint

        C++ signature :
            ExplicitBitVect* RDKFingerprint(RDKit::ROMol [,unsigned int=1 [,unsigned int=7 [,unsigned int=2048 [,unsigned int=2 [,bool=True [,double=0.0 [,unsigned int=128 [,bool=True [,bool=True [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=None [,boost::python::api::object=None]]]]]]]]]]]]])

### RemoveHs(...) |
    RemoveHs( (Mol)mol [, (bool)implicitOnly=False [, (bool)updateExplicitCount=False [, (bool)sanitize=True]]]) -> Mol :
        Removes any hydrogens from the graph of a molecule.

          ARGUMENTS:

            - mol: the molecule to be modified

            - implicitOnly: (optional) if this toggle is set, only implicit Hs will
              be removed from the graph.  Default value is 0 (remove implicit and explicit Hs).

            - updateExplicitCount: (optional) if this toggle is set, the explicit H count on atoms with
              Hs will be updated. Default value is 0 (do not update explicit H count).

            - sanitize: (optional) if this toggle is set, the molecule will be sanitized after the Hs
              are removed. Default value is 1 (do sanitize).

          RETURNS: a new molecule with the Hs removed

          NOTES:

            - The original molecule is *not* modified.

        C++ signature :
            RDKit::ROMol* RemoveHs(RDKit::ROMol [,bool=False [,bool=False [,bool=True]]])

### RemoveStereochemistry(...) |
    RemoveStereochemistry( (Mol)mol) -> None :
        Removes all stereochemistry info from the molecule.

        C++ signature :
            void RemoveStereochemistry(RDKit::ROMol {lvalue})

### RenumberAtoms(...) |
    RenumberAtoms( (Mol)mol, (AtomPairsParameters)newOrder) -> Mol :
        Returns a copy of a molecule with renumbered atoms

          ARGUMENTS:

            - mol: the molecule to be modified

            - newOrder: the new ordering the atoms (should be numAtoms long)
                 for example: if newOrder is [3,2,0,1], then atom 3 in the original
                 molecule will be atom 0 in the new one

        C++ signature :
            RDKit::ROMol* RenumberAtoms(RDKit::ROMol,boost::python::api::object {lvalue})

### ReplaceCore(...) |
    ReplaceCore( (Mol)mol, (Mol)core, (AtomPairsParameters)matches [, (bool)replaceDummies=True [, (bool)labelByIndex=False [, (bool)requireDummyMatch=False]]]) -> Mol :
        Removes the core of a molecule and labels the sidechains with dummy atoms based on
        The matches indices given in the matching vector matches.
        Calling:
          ReplaceCore(mol,core,mol.GetSubstructMatch(core))

          ARGUMENTS:

            - mol: the molecule to be modified

            - coreQuery: the molecule to be used as a substructure query for recognizing the core

            - matches: a matching vector of the type returned by mol.GetSubstructMatch(...)

            - replaceDummies: toggles replacement of atoms that match dummies in the query

            - labelByIndex: toggles labeling the attachment point dummy atoms with
                            the index of the core atom they're attached to.

            - requireDummyMatch: if the molecule has side chains that attach at points not
                                 flagged with a dummy, it will be rejected (None is returned)

          RETURNS: a new molecule with the core removed

          NOTES:

            - The original molecule is *not* modified.
        EXAMPLES:
            >>> from rdkit.Chem import MolToSmiles, MolFromSmiles, ReplaceCore
            >>> mol = MolFromSmiles('C1ONNCC1')
            >>> core = MolFromSmiles('NN')

            Note: Using isomericSmiles is necessary to see the labels.
            >>> MolToSmiles(ReplaceCore(mol, core, mol.GetSubstructMatch(core)), isomericSmiles=True)
            '[1*]OCCC[2*]'

            Since NN is symmetric, we should actually get two matches here if we don't
            uniquify the matches.
            >>> [MolToSmiles(ReplaceCore(mol, core, match), isomericSmiles=True)
            ...     for match in mol.GetSubstructMatches(core, uniquify=False)]
            ['[1*]OCCC[2*]', '[1*]CCCO[2*]']

        C++ signature :
            RDKit::ROMol* ReplaceCore(RDKit::ROMol,RDKit::ROMol,boost::python::api::object [,bool=True [,bool=False [,bool=False]]])

    ReplaceCore( (Mol)mol, (Mol)coreQuery [, (bool)replaceDummies=True [, (bool)labelByIndex=False [, (bool)requireDummyMatch=False [, (bool)useChirality=False]]]]) -> Mol :
        Removes the core of a molecule and labels the sidechains with dummy atoms.

          ARGUMENTS:

            - mol: the molecule to be modified

            - coreQuery: the molecule to be used as a substructure query for recognizing the core

            - replaceDummies: toggles replacement of atoms that match dummies in the query

            - labelByIndex: toggles labeling the attachment point dummy atoms with
                            the index of the core atom they're attached to.

            - requireDummyMatch: if the molecule has side chains that attach at points not
                                 flagged with a dummy, it will be rejected (None is returned)

            - useChirality: use chirality matching in the coreQuery

          RETURNS: a new molecule with the core removed

          NOTES:

            - The original molecule is *not* modified.

          EXAMPLES:

           >>> from rdkit.Chem import MolToSmiles, MolFromSmiles, MolFromSmarts, ReplaceCore

           Basic usage: remove a core as specified by SMILES (or another molecule).
           To get the atom labels which are stored as an isotope of the matched atom,
           the output must be written as isomeric smiles.
           A small confusion is that atom isotopes of 0 aren't shown in smiles strings.

           Here we remove a ring and leave the decoration (r-group) behind.

           >>> MolToSmiles(ReplaceCore(MolFromSmiles('CCCC1CCC1'),MolFromSmiles('C1CCC1')),
           ...             isomericSmiles=True)
           '[1*]CCC'

           The isotope label by default is matched by the first connection found. In order to
           indicate which atom the decoration is attached in the core query, use labelByIndex=True.
           Here the attachment is from the third atom in the smiles string, which is indexed by 3
           in the core, like all good computer scientists expect, atoms indices start at 0.
           >>> MolToSmiles(ReplaceCore(MolFromSmiles('CCN1CCC1'),MolFromSmiles('C1CCN1'),
           ...                         labelByIndex=True),
           ...   isomericSmiles=True)
           '[3*]CC'

           Non-core matches just return None
           >>> ReplaceCore(MolFromSmiles('CCC1CC1'),MolFromSmiles('C1CCC1'))

           The bond between atoms are considered part of the core and are removed as well
           >>> MolToSmiles(ReplaceCore(MolFromSmiles('C1CC2C1CCC2'),MolFromSmiles('C1CCC1')),
           ...             isomericSmiles=True)
           '[1*]CCC[2*]'
           >>> MolToSmiles(ReplaceCore(MolFromSmiles('C1CNCC1'),MolFromSmiles('N')),
           ...             isomericSmiles=True)
           '[1*]CCCC[2*]'

           When using dummy atoms, cores should be read in as SMARTS.  When read as SMILES
           dummy atoms only match other dummy atoms.
           The replaceDummies flag indicates whether matches to the dummy atoms should be considered as part
           of the core or as part of the decoration (r-group)
           >>> MolToSmiles(ReplaceCore(MolFromSmiles('C1CNCC1'),MolFromSmarts('[*]N[*]'),
           ...                         replaceDummies=True),
           ...             isomericSmiles=True)
           '[1*]CC[2*]'
           >>> MolToSmiles(ReplaceCore(MolFromSmiles('C1CNCC1'),MolFromSmarts('[*]N[*]'),
           ...                         replaceDummies=False),
           ...             isomericSmiles=True)
           '[1*]CCCC[2*]'

           >>> MolToSmiles(ReplaceCore(MolFromSmiles('C1CCC1CN'),MolFromSmarts('C1CCC1[*]'),
           ...                         replaceDummies=False),
           ...             isomericSmiles=True)
           '[1*]CN'

        C++ signature :
            RDKit::ROMol* ReplaceCore(RDKit::ROMol,RDKit::ROMol [,bool=True [,bool=False [,bool=False [,bool=False]]]])

### ReplaceSidechains(...) |
    ReplaceSidechains( (Mol)mol, (Mol)coreQuery [, (bool)useChirality=False]) -> Mol :
        Replaces sidechains in a molecule with dummy atoms for their attachment points.

          ARGUMENTS:

            - mol: the molecule to be modified

            - coreQuery: the molecule to be used as a substructure query for recognizing the core

            - useChirality: (optional) match the substructure query using chirality

          RETURNS: a new molecule with the sidechains removed

          NOTES:

            - The original molecule is *not* modified.

          EXAMPLES:

           The following examples substitute SMILES/SMARTS strings for molecules, you'd have
           to actually use molecules:

            - ReplaceSidechains('CCC1CCC1','C1CCC1') -> '[Xa]C1CCC1'

            - ReplaceSidechains('CCC1CC1','C1CCC1') -> ''

            - ReplaceSidechains('C1CC2C1CCC2','C1CCC1') -> '[Xa]C1CCC1[Xb]'

        C++ signature :
            RDKit::ROMol* ReplaceSidechains(RDKit::ROMol,RDKit::ROMol [,bool=False])

### ReplaceSubstructs(...) |
    ReplaceSubstructs( (Mol)mol, (Mol)query, (Mol)replacement [, (bool)replaceAll=False [, (int)replacementConnectionPoint=0 [, (bool)useChirality=False]]]) -> object :
        Replaces atoms matching a substructure query in a molecule

          ARGUMENTS:

            - mol: the molecule to be modified

            - query: the molecule to be used as a substructure query

            - replacement: the molecule to be used as the replacement

            - replaceAll: (optional) if this toggle is set, all substructures matching
              the query will be replaced in a single result, otherwise each result will
              contain a separate replacement.
              Default value is False (return multiple replacements)
            - replacementConnectionPoint: (optional) index of the atom in the replacement that
              the bond should be made to.
            - useChirality: (optional) match the substructure query using chirality

          RETURNS: a tuple of new molecules with the substructures replaced removed

          NOTES:

            - The original molecule is *not* modified.

          EXAMPLES:

           The following examples substitute SMILES/SMARTS strings for molecules, you'd have
           to actually use molecules:

            - ReplaceSubstructs('CCOC','OC','NC') -> ('CCNC',)

            - ReplaceSubstructs('COCCOC','OC','NC') -> ('COCCNC','CNCCOC')

            - ReplaceSubstructs('COCCOC','OC','NC',True) -> ('CNCCNC',)

            - ReplaceSubstructs('COCCOC','OC','CN',True,1) -> ('CNCCNC',)

        C++ signature :
            _object* ReplaceSubstructs(RDKit::ROMol,RDKit::ROMol,RDKit::ROMol [,bool=False [,unsigned int=0 [,bool=False]]])

### SanitizeMol(...) |
    SanitizeMol( (Mol)mol [, (int)sanitizeOps=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL [, (bool)catchErrors=False]]) -> SanitizeFlags :
        Kekulize, check valencies, set aromaticity, conjugation and hybridization

            - The molecule is modified in place.

            - If sanitization fails, an exception will be thrown unless catchErrors is set

          ARGUMENTS:

            - mol: the molecule to be modified
            - sanitizeOps: (optional) sanitization operations to be carried out
                           these should be constructed by or'ing together the
                           operations in rdkit.Chem.SanitizeFlags
            - catchErrors: (optional) if provided, instead of raising an exception
                           when sanitization fails (the default behavior), the
                           first operation that failed (as defined in rdkit.Chem.SanitizeFlags)
                           is returned. Zero is returned on success.

        C++ signature :
            RDKit::MolOps::SanitizeFlags SanitizeMol(RDKit::ROMol {lvalue} [,unsigned long=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL [,bool=False]])

### SetAromaticity(...) |
    SetAromaticity( (Mol)mol [, (AromaticityModel)model=rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT]) -> None :
        does aromaticity perception

          ARGUMENTS:

            - mol: the molecule to use
            - model: the model to use

          NOTES:

            - The molecule is modified in place.

        C++ signature :
            void SetAromaticity(RDKit::ROMol {lvalue} [,RDKit::MolOps::AromaticityModel=rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT])

### SetConjugation(...) |
    SetConjugation( (Mol)mol) -> None :
        finds conjugated bonds

          ARGUMENTS:

            - mol: the molecule to use

          NOTES:

            - The molecule is modified in place.

        C++ signature :
            void SetConjugation(RDKit::ROMol {lvalue})

### SetHybridization(...) |
    SetHybridization( (Mol)mol) -> None :
        Assigns hybridization states to atoms

          ARGUMENTS:

            - mol: the molecule to use

          NOTES:

            - The molecule is modified in place.

        C++ signature :
            void SetHybridization(RDKit::ROMol {lvalue})

### SplitMolByPDBChainId(...) |
    SplitMolByPDBChainId( (Mol)mol [, (AtomPairsParameters)whiteList=None [, (bool)negateList=False]]) -> dict :
        Splits a molecule into pieces based on PDB chain information.

          ARGUMENTS:

            - mol: the molecule to use
            - whiteList: only residues in this list will be returned
            - negateList: if set, negates the white list inclusion logic

          RETURNS: a dictionary keyed by chain id with molecules as the values

        C++ signature :
            boost::python::dict SplitMolByPDBChainId(RDKit::ROMol [,boost::python::api::object=None [,bool=False]])

### SplitMolByPDBResidues(...) |
    SplitMolByPDBResidues( (Mol)mol [, (AtomPairsParameters)whiteList=None [, (bool)negateList=False]]) -> dict :
        Splits a molecule into pieces based on PDB residue information.

          ARGUMENTS:

            - mol: the molecule to use
            - whiteList: only residues in this list will be returned
            - negateList: if set, negates the white list inclusion logic

          RETURNS: a dictionary keyed by residue name with molecules as the values

        C++ signature :
            boost::python::dict SplitMolByPDBResidues(RDKit::ROMol [,boost::python::api::object=None [,bool=False]])

### UnfoldedRDKFingerprintCountBased(...) |
    UnfoldedRDKFingerprintCountBased( (Mol)mol [, (int)minPath=1 [, (int)maxPath=7 [, (bool)useHs=True [, (bool)branchedPaths=True [, (bool)useBondOrder=True [, (AtomPairsParameters)atomInvariants=0 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)atomBits=None [, (AtomPairsParameters)bitInfo=None]]]]]]]]]) -> ULongSparseIntVect :
        Returns an unfolded count-based version of the RDKit fingerprint for a molecule

        ARGUMENTS:

                - mol: the molecule to use

                - minPath: (optional) minimum number of bonds to include in the subgraphs
                  Defaults to 1.

                - maxPath: (optional) maximum number of bonds to include in the subgraphs
                  Defaults to 7.

                - useHs: (optional) include paths involving Hs in the fingerprint if the molecule
                  has explicit Hs.
                  Defaults to True.

                - branchedPaths: (optional) if set both branched and unbranched paths will be
                  used in the fingerprint.
                  Defaults to True.

                - useBondOrder: (optional) if set both bond orders will be used in the path hashes
                  Defaults to True.

                - atomInvariants: (optional) a sequence of atom invariants to use in the path hashes
                  Defaults to empty.

                - fromAtoms: (optional) a sequence of atom indices. If provided, only paths/subgraphs
                  starting from these atoms will be used.
                  Defaults to empty.

                - atomBits: (optional) an empty list. If provided, the result will contain a list
                  containing the bits each atom sets.
                  Defaults to empty.

               - bitInfo: (optional) an empty dict. If provided, the result will contain a dict
                 with bits as keys and corresponding bond paths as values.
                 Defaults to empty.

        C++ signature :
            RDKit::SparseIntVect<unsigned long>* UnfoldedRDKFingerprintCountBased(RDKit::ROMol [,unsigned int=1 [,unsigned int=7 [,bool=True [,bool=True [,bool=True [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=None [,boost::python::api::object=None]]]]]]]]])

### WedgeMolBonds(...) |
    WedgeMolBonds( (Mol)arg1, (Conformer)arg2) -> None :
        Set the wedging on single bonds in a molecule.
           The wedging scheme used is that from Mol files.

          ARGUMENTS:

            - molecule: the molecule to update

        C++ signature :
            void WedgeMolBonds(RDKit::ROMol {lvalue},RDKit::Conformer const*)

Variables Details | [hide private]

  ### ADJUST_IGNOREALL Value:
      rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREALL

  ### ADJUST_IGNORECHAINS Value:
      rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORECHAINS

  ### ADJUST_IGNOREDUMMIES Value:
      rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREDUMMIES

  ### ADJUST_IGNORENONDUMMIES Value:
      rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONDUMMIES

  ### ADJUST_IGNORENONE Value:
      rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONE

  ### ADJUST_IGNORERINGS Value:
      rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORERINGS

  ### AROMATICITY_CUSTOM Value:
      rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_CUSTOM

  ### AROMATICITY_DEFAULT Value:
      rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT

  ### AROMATICITY_RDKIT Value:
      rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_RDKIT

  ### AROMATICITY_SIMPLE Value:
      rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_SIMPLE

  ### SANITIZE_ADJUSTHS Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS

  ### SANITIZE_CLEANUP Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP

  ### SANITIZE_CLEANUPCHIRALITY Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPCHIRALITY

  ### SANITIZE_FINDRADICALS Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_FINDRADICALS

  ### SANITIZE_KEKULIZE Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE

  ### SANITIZE_PROPERTIES Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES

  ### SANITIZE_SETAROMATICITY Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETAROMATICITY

  ### SANITIZE_SETCONJUGATION Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETCONJUGATION

  ### SANITIZE_SETHYBRIDIZATION Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETHYBRIDIZATION

  ### SANITIZE_SYMMRINGS Value:
      rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SYMMRINGS