Chem.rdmolops

AddHs(...)

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).

  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:
    AddHs(RDKit::ROMol mol, bool explicitOnly=False, bool addCoords=False) -> RDKit::ROMol*

AssignAtomChiralCodes(...)

source code

Does the CIP chirality assignment (R/S) 
  for the molecule's atoms.
  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


C++ signature:
    AssignAtomChiralCodes(RDKit::ROMol {lvalue} mol, bool cleanIt=False, bool force=False) -> void*

AssignBondStereoCodes(...)

source code

Does the CIP stereochemistry assignment (Z/E)
   for the molecule's bonds .
  Qualifying bonds will have a property '_CIPCode' indicating
  their stereochemistry.

  ARGUMENTS:

    - mol: the molecule to use
    - cleanIt: (optional) ignored
    - force: (optional) causes the calculation to be repeated, even if it has already
      been done


C++ signature:
    AssignBondStereoCodes(RDKit::ROMol {lvalue} mol, bool cleanIt=False, bool force=False) -> void*

DaylightFingerprint(...)

source code

Returns a "Daylight"-type 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.

    - nBitsPerPath: (optional) number of bits to set per path
      Defaults to 4.

    - useHs: (optional) include information about number of Hs on each
      atom when calculating path hashes.
      Defaults to 1.

    - 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.

  RETURNS: a DataStructs.ExplicitBitVect with _fpSize_ bits

  ALGORITHM:

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

     1) The Balaban J value is calculated.

     2) The 32 bit Balaban J value is used to seed a random-number generator

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



C++ signature:
    DaylightFingerprint(RDKit::ROMol mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=4, bool useHs=True, double tgtDensity=0.0, unsigned int minSize=128) -> ExplicitBitVect*

DeleteSubstructs(...)

source code

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)

  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:
    DeleteSubstructs(RDKit::ROMol mol, RDKit::ROMol query, bool onlyFrags=False) -> RDKit::ROMol*

FindAllPathsOfLengthN(...)

source code

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.

  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:
    FindAllPathsOfLengthN(RDKit::ROMol mol, unsigned int length, bool useBonds=True, bool useHs=False) -> std::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >

FindAllSubgraphsOfLengthN(...)

source code

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.

    - verbose: (optional, internal use) toggles verbosity in the search algorithm.
      Defaults to 0.

  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:
    FindAllSubgraphsOfLengthN(RDKit::ROMol mol, unsigned int length, bool useHs=False) -> std::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >

FindUniqueSubgraphsOfLengthN(...)

source code

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.

  RETURNS: a tuple of tuples with bond IDs



C++ signature:
    FindUniqueSubgraphsOfLengthN(RDKit::ROMol mol, unsigned int length, bool useHs=False, bool useBO=True) -> std::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >

GetAdjacencyMatrix(...)

source code

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:
    GetAdjacencyMatrix(RDKit::ROMol {lvalue} mol, bool useBO=False, int emptyVal=0, bool force=False, char const* prefix='') -> _object*

GetDistanceMatrix(...)

source code

Returns the molecule's 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:
    GetDistanceMatrix(RDKit::ROMol {lvalue} mol, bool useBO=False, bool useAtomWts=False, bool force=False, char const* prefix='') -> _object*

GetMolFrags(...)

source code

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

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


C++ signature:
    GetMolFrags(RDKit::ROMol) -> std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >

GetSSSR(...)

source code

Get the smallest set of simple rings for a molecule.

  ARGUMENTS:

    - mol: the molecule to use.

  RETURNS: the number of rings found
         This will be equal to NumBonds-NumAtoms+1 for single-fragment molecules.


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

GetSymmSSSR(...)

source code

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: the number of rings found


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

Kekulize(...)

source code

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:
    Kekulize(RDKit::ROMol {lvalue} mol, bool clearAromaticFlags=False) -> void*

RDKFingerprint(...)

source code

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.

    - nBitsPerPath: (optional) number of bits to set per path
      Defaults to 4.

    - useHs: (optional) include information about number of Hs on each
      atom when calculating path hashes.
      Defaults to 1.

    - 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.

  RETURNS: a DataStructs.ExplicitBitVect with _fpSize_ bits

  ALGORITHM:

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

     1) A hash is calculated.

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

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



C++ signature:
    RDKFingerprint(RDKit::ROMol mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=4, bool useHs=True, double tgtDensity=0.0, unsigned int minSize=128) -> ExplicitBitVect*

RemoveHs(...)

source code

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).

  RETURNS: a new molecule with the Hs removed

  NOTES:

    - The original molecule is *not* modified.


C++ signature:
    RemoveHs(RDKit::ROMol mol, bool implicitOnly=False) -> RDKit::ROMol*

ReplaceCore(...)

source code

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

  RETURNS: a new molecule with the core 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:

    - ReplaceCore('CCC1CCC1','C1CCC1') -> 'CC[Xa]'

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

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

    - ReplaceCore('C1CNCC1','N') -> '[Xa]CCCC[Xb]'

    - ReplaceCore('C1CCC1CN','C1CCC1[*]',False) -> '[Xa]CN'


C++ signature:
    ReplaceCore(RDKit::ROMol mol, RDKit::ROMol coreQuery, bool replaceDummies=True) -> RDKit::ROMol*

ReplaceSidechains(...)

source code

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

  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:
    ReplaceSidechains(RDKit::ROMol mol, RDKit::ROMol coreQuery) -> RDKit::ROMol*

ReplaceSubstructs(...)

source code

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)

  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',)


C++ signature:
    ReplaceSubstructs(RDKit::ROMol mol, RDKit::ROMol query, RDKit::ROMol replacement, bool replaceAll=False) -> _object*

SanitizeMol(...)

source code

Kekulize, check valencies, set aromaticity, conjugation and hybridization

    - The molecule is modified in place.

    - If sanitization fails, an exception will be thrown

  ARGUMENTS:

    - mol: the molecule to be modified

  NOTES:


C++ signature:
    SanitizeMol(RDKit::ROMol {lvalue}) -> void*

WedgeMolBonds(...)

source code

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:
    WedgeMolBonds(RDKit::ROMol {lvalue}, RDKit::Conformer const*) -> void*

Module rdmolops

AddHs(...)

AssignAtomChiralCodes(...)

AssignBondStereoCodes(...)

DaylightFingerprint(...)

DeleteSubstructs(...)

FindAllPathsOfLengthN(...)

FindAllSubgraphsOfLengthN(...)

FindUniqueSubgraphsOfLengthN(...)

GetAdjacencyMatrix(...)

GetDistanceMatrix(...)

GetFormalCharge(...)

GetMolFrags(...)

GetSSSR(...)

GetSymmSSSR(...)

Kekulize(...)

RDKFingerprint(...)

RemoveHs(...)

ReplaceCore(...)

ReplaceSidechains(...)

ReplaceSubstructs(...)

SanitizeMol(...)

WedgeMolBonds(...)