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Module containing RDKit functionality for manipulating and querying molecules.
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AddHs( (Mol)mol [, (bool)explicitOnly=False [, (bool)addCoords=False]]) -> 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).
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]])
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AssignAtomChiralCodes( (Mol)mol [, (bool)cleanIt=False [, (bool)force=False]]) -> None :
DEPRECATED: use AssignStereochemistry() instead
C++ signature :
void AssignAtomChiralCodes(RDKit::ROMol {lvalue} [,bool=False [,bool=False]])
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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
- 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 :
void AssignAtomChiralTagsFromStructure(RDKit::ROMol {lvalue} [,int=-1 [,bool=True]])
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AssignBondStereoCodes( (Mol)mol [, (bool)cleanIt=False [, (bool)force=False]]) -> None :
DEPRECATED: use AssignStereochemistry() instead
C++ signature :
void AssignBondStereoCodes(RDKit::ROMol {lvalue} [,bool=False [,bool=False]])
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AssignStereochemistry( (Mol)mol [, (bool)cleanIt=False [, (bool)force=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
C++ signature :
void AssignStereochemistry(RDKit::ROMol {lvalue} [,bool=False [,bool=False]])
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DaylightFingerprint( (Mol)mol [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (int)nBitsPerHash=4 [, (bool)useHs=True [, (float)tgtDensity=0.0 [, (int)minSize=128]]]]]]]) -> ExplicitBitVect :
DEPRECATED: use RDKFingerprint() instead.
C++ signature :
ExplicitBitVect* DaylightFingerprint(RDKit::ROMol [,unsigned int=1 [,unsigned int=7 [,unsigned int=2048 [,unsigned int=4 [,bool=True [,double=0.0 [,unsigned int=128]]]]]]])
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DeleteSubstructs( (Mol)mol, (Mol)query [, (bool)onlyFrags=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)
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])
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FindAllPathsOfLengthN( (Mol)mol, (int)length [, (bool)useBonds=True [, (bool)useHs=False]]) -> _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.
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
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2
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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]])
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FindAllSubgraphsOfLengthN( (Mol)mol, (int)length [, (bool)useHs=False]) -> _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.
- 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
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2
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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])
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FindUniqueSubgraphsOfLengthN( (Mol)mol, (int)length [, (bool)useHs=False [, (bool)useBO=True]]) -> _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.
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]])
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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*='']]]])
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GetDistanceMatrix( (Mol)mol [, (bool)useBO=False [, (bool)useAtomWts=False [, (bool)force=False [, (str)prefix='']]]]) -> object :
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 :
_object* GetDistanceMatrix(RDKit::ROMol {lvalue} [,bool=False [,bool=False [,bool=False [,char const*='']]]])
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GetFormalCharge( (Mol)arg1) -> int :
Returns the formal charge for the molecule.
ARGUMENTS:
- mol: the molecule to use
C++ signature :
int GetFormalCharge(RDKit::ROMol)
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GetMolFrags( (Mol)mol [, (bool)asMols=False]) -> 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.
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])
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GetSSSR( (Mol)arg1) -> int :
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 :
int GetSSSR(RDKit::ROMol {lvalue})
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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: the number of rings found
C++ signature :
std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > GetSymmSSSR(RDKit::ROMol {lvalue})
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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])
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LayeredFingerprint( (Mol)mol [, (int)layerFlags=4294967295L [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (float)tgtDensity=0.0 [, (int)minSize=128]]]]]]) -> 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.
- 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
Layer definitions:
- 0x01: pure topology
- 0x02: bond order
- 0x04: atom types
- 0x08: presence of rings
- 0x10: ring sizes
C++ signature :
ExplicitBitVect* LayeredFingerprint(RDKit::ROMol [,unsigned int=4294967295L [,unsigned int=1 [,unsigned int=7 [,unsigned int=2048 [,double=0.0 [,unsigned int=128]]]]]])
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MergeQueryHs( (Mol)mol) -> Mol :
merges hydrogens into their neighboring atoms as queries
C++ signature :
RDKit::ROMol* MergeQueryHs(RDKit::ROMol)
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RDKFingerprint( (Mol)mol [, (int)minPath=1 [, (int)maxPath=7 [, (int)fpSize=2048 [, (int)nBitsPerHash=4 [, (bool)useHs=True [, (float)tgtDensity=0.0 [, (int)minSize=128]]]]]]]) -> 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.
- 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 :
ExplicitBitVect* RDKFingerprint(RDKit::ROMol [,unsigned int=1 [,unsigned int=7 [,unsigned int=2048 [,unsigned int=4 [,bool=True [,double=0.0 [,unsigned int=128]]]]]]])
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RemoveHs( (Mol)mol [, (bool)implicitOnly=False]) -> 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).
RETURNS: a new molecule with the Hs removed
NOTES:
- The original molecule is *not* modified.
C++ signature :
RDKit::ROMol* RemoveHs(RDKit::ROMol [,bool=False])
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RemoveStereochemistry( (Mol)mol) -> None :
Removes all stereochemistry info from the molecule.
C++ signature :
void RemoveStereochemistry(RDKit::ROMol {lvalue})
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ReplaceCore( (Mol)mol, (Mol)coreQuery [, (bool)replaceDummies=True [, (bool)labelByIndex=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
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 :
RDKit::ROMol* ReplaceCore(RDKit::ROMol,RDKit::ROMol [,bool=True [,bool=False]])
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ReplaceSidechains( (Mol)mol, (Mol)coreQuery) -> 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
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)
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ReplaceSubstructs( (Mol)mol, (Mol)query, (Mol)replacement [, (bool)replaceAll=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)
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 :
_object* ReplaceSubstructs(RDKit::ROMol,RDKit::ROMol,RDKit::ROMol [,bool=False])
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SanitizeMol( (Mol)arg1) -> None :
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 :
void SanitizeMol(RDKit::ROMol {lvalue})
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SetAromaticity( (Mol)mol) -> None :
does aromaticity perception
ARGUMENTS:
- mol: the molecule to use
NOTES:
- The molecule is modified in place.
C++ signature :
void SetAromaticity(RDKit::ROMol {lvalue})
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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*)
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