rdkit.Chem.rdmolops module — The RDKit 2025.09.6 documentation

# rdkit.Chem.rdmolops module

Module containing RDKit functionality for manipulating molecules.

rdkit.Chem.rdmolops.AddHs((rdkit.Chem.rdchem.Mol)mol, (AddHsParameters)params[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)onlyOnAtoms=None]) → rdkit.Chem.rdchem.Mol :

  Adds hydrogens to the graph of a molecule.

  > > ARGUMENTS:

  > > > - mol: the molecule to be modified

  > > > - params: AddHsParameters object controlling the addition.

  > > > - onlyOnAtoms: (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.n

  > C++ signature :

  >   RDKit::ROMol* AddHs(RDKit::ROMol,RDKit::MolOps::AddHsParameters [,boost::python::api::object=None])

  AddHs( (rdkit.Chem.rdchem.Mol)mol [, (bool)explicitOnly=False [, (bool)addCoords=False [, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)onlyOnAtoms=None [, (bool)addResidueInfo=False]]]]) -> rdkit.Chem.rdchem.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).

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

    > > - addResidueInfo: (optional) if this is true, add residue info to hydrogen atoms (useful for PDB files).

    > 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 [,bool=False]]]])

class rdkit.Chem.rdmolops.AddHsParameters((object)arg1) → None :

  Bases: `instance`

  Parameters controlling H addition.

  C++ signature :

    void __init__(_object*)

  property addCoords

    add coordinates for the Hs

  property addResidueInfo

    add residue info to the Hs

  property explicitOnly

    only add explict Hs

  property skipQueries

    do not add Hs to query atoms or atoms with query bonds

rdkit.Chem.rdmolops.AddRecursiveQuery((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.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])

rdkit.Chem.rdmolops.AddStereoAnnotations((rdkit.Chem.rdchem.Mol)mol[, (str)absLabel='abs ({cip})'[, (str)orLabel='or{id}'[, (str)andLabel='and{id}'[, (str)cipLabel='({cip})'[, (str)bondLabel='({cip})']]]]]) → None :

  add R/S, relative stereo, and E/Z annotations to atoms and bonds

  > > Arguments:

  > >   - mol: molecule to modify

  > >   - absLabel: label for atoms in an ABS stereo group

  > >   - orLabel: label for atoms in an OR stereo group

  > >   - andLabel: label for atoms in an AND stereo group

  > >   - cipLabel: label for chiral atoms that aren’t in a stereo group.

  > >   - bondLabel: label for CIP stereochemistry on bonds

  > If any label is empty, the corresponding annotations will not be added.

  > The labels can contain the following placeholders:

  >   - {id} - the stereo group’s index

  >   - {cip} - the atom or bond’s CIP stereochemistry

  > Note that CIP labels will only be added if CIP stereochemistry has been assigned to the molecule.

  C++ signature :

    void AddStereoAnnotations(RDKit::ROMol {lvalue} [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’abs ({cip})’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’or{id}’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’and{id}’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’({cip})’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’({cip})’]]]]])

rdkit.Chem.rdmolops.AddWavyBondsForStereoAny((rdkit.Chem.rdchem.Mol)mol[, (bool)clearDoubleBondFlags=True[, (int)addWhenImpossible=1000]]) → None :
  set wavy bonds around double bonds with STEREOANY stereo
    ARGUMENTS :

      - molecule : the molecule to updaten -

      - conformer : the conformer to use to determine wedge direction

  C++ signature :

    void AddWavyBondsForStereoAny(RDKit::ROMol {lvalue} [,bool=True [,unsigned int=1000]])

class rdkit.Chem.rdmolops.AdjustQueryParameters((object)arg1) → None :

  Bases: `instance`

  Parameters controlling which components of the query atoms/bonds are adjusted.

  Note that some of the options here are either directly contradictory or make

    no sense when combined with each other. We generally assume that client code is doing something sensible and don’t attempt to detect possible conflicts or problems.

  A note on the flags controlling which atoms/bonds are modified:

    These generally limit the set of atoms/bonds to be modified. For example:

    > - ADJUST_IGNORERINGS atoms/bonds in rings will not be modified.

    > - ADJUST_IGNORENONE causes all atoms/bonds to be modified

    > - ADJUST_IGNOREALL no atoms/bonds will be modified

    Some of the options obviously make no sense for bonds

  C++ signature :

    void __init__(_object*)

  static NoAdjustments() → AdjustQueryParameters :

    Returns an AdjustQueryParameters object with all parameters set to false

    C++ signature :

      RDKit::MolOps::AdjustQueryParameters NoAdjustments()

  property adjustConjugatedFiveRings

    set bond queries in conjugated five-rings to SINGLE|DOUBLE|AROMATIC

  property adjustDegree

    add degree queries

  property adjustDegreeFlags

    controls which atoms have their degree queries changed

  property adjustHeavyDegree

    adjust the heavy-atom degree

  property adjustHeavyDegreeFlags

    controls which atoms have their heavy-atom degree queries changed

  property adjustRingChain

    add ring-chain queries to atoms

  property adjustRingChainFlags

    controls which atoms have ring-chain queries added

  property adjustRingCount

    add ring-count queries

  property adjustRingCountFlags

    controls which atoms have ring-count queries added

  property adjustSingleBondsBetweenAromaticAtoms

    sets non-ring single bonds between two aromatic or conjugated atoms to SINGLE|AROMATIC

  property adjustSingleBondsToDegreeOneNeighbors

    set single bonds bewteen aromatic or conjugated atoms and degree-one neighbors to SINGLE|AROMATIC

  property aromatizeIfPossible

    perceive and set aromaticity

  property makeAtomsGeneric

    convert atoms to generic queries (any atoms)

  property makeAtomsGenericFlags

    controls which atoms are converted to generic queries

  property makeBondsGeneric

    converts bonds to generic queries (any bonds)

  property makeBondsGenericFlags

    controls which bonds are converted to generic queries

  property makeDummiesQueries

    convert dummy atoms without isotope labels to any-atom queries

  property setMDLFiveRingAromaticity

    uses the 5-ring aromaticity behavior of the (former) MDL software as documented in the Chemical Representation Guide

  property useStereoCareForBonds

    if this is set sterochemistry information will be removed from double bonds that do not have the stereoCare property set

rdkit.Chem.rdmolops.AdjustQueryProperties((rdkit.Chem.rdchem.Mol)mol[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)params=None]) → rdkit.Chem.rdchem.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])

rdkit.Chem.rdmolops.AdjustQueryPropertiesWithGenericGroups((rdkit.Chem.rdchem.Mol)mol[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)params=None]) → rdkit.Chem.rdchem.Mol :

  Returns a new molecule where the query properties of atoms have been modified and generic group queries have been prepared.

  C++ signature :

    RDKit::ROMol* AdjustQueryPropertiesWithGenericGroups(RDKit::ROMol [,boost::python::api::object=None])

class rdkit.Chem.rdmolops.AdjustQueryWhichFlags

  Bases: `enum`

  ADJUST_IGNOREALL = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREALL
  ADJUST_IGNORECHAINS = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORECHAINS
  ADJUST_IGNOREDUMMIES = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREDUMMIES
  ADJUST_IGNOREMAPPED = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREMAPPED
  ADJUST_IGNORENONDUMMIES = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONDUMMIES
  ADJUST_IGNORENONE = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONE
  ADJUST_IGNORERINGS = rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORERINGS
  names = {'ADJUST_IGNOREALL': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREALL, 'ADJUST_IGNORECHAINS': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORECHAINS, 'ADJUST_IGNOREDUMMIES': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREDUMMIES, 'ADJUST_IGNOREMAPPED': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREMAPPED, 'ADJUST_IGNORENONDUMMIES': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONDUMMIES, 'ADJUST_IGNORENONE': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONE, 'ADJUST_IGNORERINGS': rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORERINGS}
  values = {0: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONE, 1: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORECHAINS, 2: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREDUMMIES, 4: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORERINGS, 8: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNORENONDUMMIES, 16: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREMAPPED, 268435455: rdkit.Chem.rdmolops.AdjustQueryWhichFlags.ADJUST_IGNOREALL}

class rdkit.Chem.rdmolops.AromaticityModel

  Bases: `enum`

  AROMATICITY_CUSTOM = rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_CUSTOM
  AROMATICITY_DEFAULT = rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT
  AROMATICITY_MDL = rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_MDL
  AROMATICITY_MMFF94 = rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_MMFF94
  AROMATICITY_RDKIT = rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_RDKIT
  AROMATICITY_SIMPLE = rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_SIMPLE
  names = {'AROMATICITY_CUSTOM': rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_CUSTOM, 'AROMATICITY_DEFAULT': rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT, 'AROMATICITY_MDL': rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_MDL, 'AROMATICITY_MMFF94': rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_MMFF94, 'AROMATICITY_RDKIT': rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_RDKIT, 'AROMATICITY_SIMPLE': rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_SIMPLE}
  values = {0: rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_DEFAULT, 1: rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_RDKIT, 2: rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_SIMPLE, 4: rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_MDL, 8: rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_MMFF94, 268435455: rdkit.Chem.rdmolops.AromaticityModel.AROMATICITY_CUSTOM}

rdkit.Chem.rdmolops.AssignAtomChiralTagsFromMolParity((rdkit.Chem.rdchem.Mol)mol[, (bool)replaceExistingTags=True]) → None :
  Sets the chiral tags on a molecule’s atoms based on

    the molParity atom property.

    ARGUMENTS:

    > - mol: the molecule to use

    > - replaceExistingTags: if True, existing stereochemistry information will be cleared

    > before running the calculation.

  C++ signature :

    void AssignAtomChiralTagsFromMolParity(RDKit::ROMol {lvalue} [,bool=True])

rdkit.Chem.rdmolops.AssignAtomChiralTagsFromStructure((rdkit.Chem.rdchem.Mol)mol[, (int)confId=-1[, (bool)replaceExistingTags=True]]) → None :
  Sets the chiral tags on a molecule’s atoms based on

    a 3D conformation. NOTE that this does not check to see if atoms are chiral centers (i.e. all substituents are different), it merely sets the chiral type flags based on the coordinates and atom ordering. Use AssignStereochemistryFrom3D() if you want chiral flags only on actual stereocenters.

    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]])

rdkit.Chem.rdmolops.AssignChiralTypesFromBondDirs((rdkit.Chem.rdchem.Mol)mol[, (int)confId=-1[, (bool)replaceExistingTags=True]]) → None :

  Uses bond directions to assign ChiralTypes to a molecule’s atoms.

  > ARGUMENTS:

  > > - mol: the molecule to use

  > > - confId: (optional) the conformation to use

  > > - replaceExistingTags: (optional) replace any existing information about stereochemistry

  C++ signature :

    void AssignChiralTypesFromBondDirs(RDKit::ROMol {lvalue} [,int=-1 [,bool=True]])

rdkit.Chem.rdmolops.AssignRadicals((rdkit.Chem.rdchem.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})

rdkit.Chem.rdmolops.AssignStereochemistry((rdkit.Chem.rdchem.Mol)mol[, (bool)cleanIt=False[, (bool)force=False[, (bool)flagPossibleStereoCenters=False]]]) → None :
  Assign stereochemistry tags to atoms and bonds.

    If useLegacyStereoPerception is true, it also does the CIP stereochemistry assignment for the molecule’s atoms (R/S) and double bonds (Z/E). This assignment is based on legacy code which is fast, but is known to incorrectly assign CIP labels in some cases. instead, to assign CIP labels based on an accurate, though slower, implementation of the CIP rules, call CIPLabeler::assignCIPLabels(). Chiral atoms will have a property ‘_CIPCode’ indicating their chiral code.

    ARGUMENTS:

    > - mol: the molecule to use

    > - cleanIt: (optional) if provided, any existing values of the property _CIPCode

    >     will be cleared, 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. Bonds with STEREOCIS/STEREOTRANS specified that have duplicate substituents based upon the CIP atom ranks will be marked STEREONONE.

    > - 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]]])

rdkit.Chem.rdmolops.AssignStereochemistryFrom3D((rdkit.Chem.rdchem.Mol)mol[, (int)confId=-1[, (bool)replaceExistingTags=True]]) → None :
  Uses a conformer (should be 3D) to assign ChiralTypes to a molecule’s atoms

    > and stereo flags to its bonds

    ARGUMENTS:

    > - mol: the molecule to use

    > - confId: (optional) the conformation to use

    > - replaceExistingTags: (optional) replace any existing information about stereochemistry

  C++ signature :

    void AssignStereochemistryFrom3D(RDKit::ROMol {lvalue} [,int=-1 [,bool=True]])

rdkit.Chem.rdmolops.AtomHasConjugatedBond((rdkit.Chem.rdchem.Atom)atom) → bool :

  returns whether or not the atom is involved in a conjugated bond

  C++ signature :

    bool AtomHasConjugatedBond(RDKit::Atom const*)

class rdkit.Chem.rdmolops.BondWedgingParameters((object)arg1) → None :

  Bases: `instance`

  Parameters controlling how bond wedging is done.

  C++ signature :

    void __init__(_object*)

  property wedgeTwoBondsIfPossible

    If this is enabled then two bonds will be wedged at chiral centers subject to the following constraints:

    > 1. ring bonds will not be wedged

    > 2. bonds to chiral centers will not be wedged

    > 3. bonds separated by more than 120 degrees will not be

    >      wedged

class rdkit.Chem.rdmolops.BoolVector((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  append((BoolVector)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :
    C++ signature :

      void append(std::vector<bool, std::allocator<bool> > {lvalue},boost::python::api::object)

  extend((BoolVector)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :
    C++ signature :

      void extend(std::vector<bool, std::allocator<bool> > {lvalue},boost::python::api::object)

rdkit.Chem.rdmolops.CanonicalizeStereoGroups((rdkit.Chem.rdchem.Mol)mol[, (StereoGroupAbsOptions)outputAbsoluteGroups=rdkit.Chem.rdmolops.StereoGroupAbsOptions.OnlyIncludeWhenOtherGroupsExist[, (int)maxStereoGroups=12]]) → rdkit.Chem.rdchem.Mol :

  Rationalize Enhanced Stereo indications to a canonical form

  > ARGUMENTS:

  > > - molecule: the molecule to update

  > > -StereoGroupAbsOptions outputAbsoluteGroups: controls output of abs groups:

  > >   > one of: OnlyIncludeWhenOtherGroupsExist, NeverInclude, AlwaysInclude

  > >   maxStereoGroups: maximm number of OR or AND stereo groups to process (default is 12):

  C++ signature :

    RDKit::ROMol* CanonicalizeStereoGroups(RDKit::ROMol {lvalue} [,RDKit::StereoGroupAbsOptions=rdkit.Chem.rdmolops.StereoGroupAbsOptions.OnlyIncludeWhenOtherGroupsExist [,unsigned int=12]])

rdkit.Chem.rdmolops.Cleanup((rdkit.Chem.rdchem.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})

rdkit.Chem.rdmolops.CleanupAtropisomers((rdkit.Chem.rdchem.Mol)mol) → None :

  removes bogus atropisomeric markers (e.g. those without sp2 begin and end atoms)

  > ARGUMENTS:

  > > - mol: the molecule to use

  > NOTES:

  > > - The molecule is modified in place.

  C++ signature :

    void CleanupAtropisomers(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.CleanupChirality((rdkit.Chem.rdchem.Mol)mol) → None :

  removes bogus chirality markers (e.g. tetrahedral flags on non-sp3 centers)

  > ARGUMENTS:

  > > - mol: the molecule to use

  > NOTES:

  > > - The molecule is modified in place.

  C++ signature :

    void CleanupChirality(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.CleanupOrganometallics((rdkit.Chem.rdchem.Mol)mol) → None :

  cleans up certain common bad functionalities in the organometallic molecule

  > > Note that this function is experimental and may either change in behavior or be replaced with something else in future releases.

  > > > ARGUMENTS :

  > - mol : the molecule to use

  > NOTES :

  > - The molecule is modified in place.

  C++ signature :

    void CleanupOrganometallics(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.CleanupStereoGroups((rdkit.Chem.rdchem.Mol)mol) → None :

  removes atoms without specified chirality from stereo groups

  C++ signature :

    void CleanupStereoGroups(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.CollapseAttachmentPoints((rdkit.Chem.rdchem.Mol)mol[, (bool)markedOnly=True]) → None :

  dummy atoms in the graph are removed and replaced with attachment point annotations on the attached atoms

  > Arguments:

  >   - mol: molecule to be modified

  >   - markedOnly: if true, only dummy atoms with the _fromAttachPoint property will be collapsed

  > In order for a dummy atom to be considered for collapsing it must have:

  >   - degree 1 with a single or unspecified bond

  >   - the bond to it can not be wedged

  >   - either no query or be an AtomNullQuery

  C++ signature :

    void CollapseAttachmentPoints(RDKit::ROMol {lvalue} [,bool=True])

rdkit.Chem.rdmolops.CombineMols((rdkit.Chem.rdchem.Mol)mol1, (rdkit.Chem.rdchem.Mol)mol2[, (rdkit.Geometry.rdGeometry.Point3D)offset=<rdkit.Geometry.rdGeometry.Point3D object at 0x7b88d01c89c0>]) → rdkit.Chem.rdchem.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 0x7b88d01c89c0>])

rdkit.Chem.rdmolops.ComputeAtomCIPRanks((rdkit.Chem.rdchem.Mol)mol) → tuple :
  Computes the CIP ranks for the atoms in a molecule.

    The ranks are stored as an atom property ‘_CIPRank’ and returned as a tuple.

  C++ signature :

    boost::python::tuple ComputeAtomCIPRanks(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.ConvertGenericQueriesToSubstanceGroups((rdkit.Chem.rdchem.Mol)mol) → None :

  documentation

  C++ signature :

    void ConvertGenericQueriesToSubstanceGroups(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.CopyMolSubset((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomIndices, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondIndices[, (SubsetOptions)options=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc365fc0>]) → rdkit.Chem.rdchem.Mol :
  Extract a subgraph from an ROMol. Bonds, atoms, substance groups and

    stereo groups are only extracted to the subgraph if all participant entities are contained within the given atoms and bonds.

    ARGUMENTS:

      - mol - starting mol

      - atoms - indices atoms to extract

      - bonds - indices bonds to extract

      - subsetInfo - optional subsetInfo to record the atoms and bonds used

      - options - optional subset options, note the method is ignored since all the atoms and bonds are sp

    C++ signature :

      RDKit::ROMol* CopyMolSubset(RDKit::ROMol,boost::python::api::object,boost::python::api::object [,RDKit::SubsetOptions=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc365fc0>])

  CopyMolSubset( (rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomIndices, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondIndices, (SubsetInfo)subsetInfo [, (SubsetOptions)options=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc365f50>]) -> rdkit.Chem.rdchem.Mol :

    Extract a subgraph from an ROMol. Bonds, atoms, substance groups and stereo groups are only extracted to the subgraph if all participant entities are contained within the given atoms and bonds.

    ARGUMENTS:

      - mol - starting mol

      - atoms - indices atoms to extract

      - bonds - indices bonds to extract

      - subsetInfo - optional subsetInfo to record the atoms and bonds used

      - options - optional subset options, note the method is ignored since all the atoms and bonds are sp

    C++ signature :

      RDKit::ROMol* CopyMolSubset(RDKit::ROMol,boost::python::api::object,boost::python::api::object,RDKit::SubsetInfo {lvalue} [,RDKit::SubsetOptions=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc365f50>])

  CopyMolSubset( (rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)path [, (SubsetOptions)options=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc366030>]) -> rdkit.Chem.rdchem.Mol :

    copy a subset of a molecule

    C++ signature :

      RDKit::ROMol* CopyMolSubset(RDKit::ROMol,boost::python::api::object [,RDKit::SubsetOptions=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc366030>])

  CopyMolSubset( (rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)path, (SubsetInfo)subsetInfo [, (SubsetOptions)options=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc366180>]) -> rdkit.Chem.rdchem.Mol :

    copy a subset of a molecule

    C++ signature :

      RDKit::ROMol* CopyMolSubset(RDKit::ROMol,boost::python::api::object,RDKit::SubsetInfo {lvalue} [,RDKit::SubsetOptions=<rdkit.Chem.rdmolops.SubsetOptions object at 0x7b87fc366180>])

rdkit.Chem.rdmolops.CountAtomElec((rdkit.Chem.rdchem.Atom)atom) → int :

  returns the number of electrons available on an atom to donate for aromaticity

  C++ signature :

    int CountAtomElec(RDKit::Atom const*)

rdkit.Chem.rdmolops.DativeBondsToHaptic((rdkit.Chem.rdchem.Mol)mol) → rdkit.Chem.rdchem.Mol :

  Does the reverse of hapticBondsToDative. If there are multiple contiguous atoms attached by dative bonds to an atom (probably a metal atom), the dative bonds will be replaced by a dummy atom in their centre attached to the (metal) atom by a dative bond, which is labelled with ENDPTS of the atoms that had the original dative bonds.

  Parameters:

    mol (-) – the molecule to use

  Returns:

    a modified copy of the molecule

  C++ signature :

    RDKit::ROMol* DativeBondsToHaptic(RDKit::ROMol)

rdkit.Chem.rdmolops.DeleteSubstructs((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)query[, (bool)onlyFrags=False[, (bool)useChirality=False]]) → rdkit.Chem.rdchem.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]])

rdkit.Chem.rdmolops.DetectBondStereoChemistry((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Conformer)conformer) → None :
  Assign stereochemistry to bonds based on coordinates and a conformer.

    > DEPRECATED

    ARGUMENTS:

    > - mol: the molecule to be modified

    > - conformer: Conformer providing the coordinates

  C++ signature :

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

rdkit.Chem.rdmolops.DetectBondStereochemistry((rdkit.Chem.rdchem.Mol)mol[, (int)confId=-1]) → None :
  DEPRECATED

    - mol: the molecule to be modified

    - confId: Conformer to use for the coordinates

  C++ signature :

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

rdkit.Chem.rdmolops.DetectChemistryProblems((rdkit.Chem.rdchem.Mol)mol[, (int)sanitizeOps=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL]) → tuple :

  checks for chemistry problems

  C++ signature :

    boost::python::tuple DetectChemistryProblems(RDKit::ROMol [,unsigned int=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL])

rdkit.Chem.rdmolops.ExpandAttachmentPoints((rdkit.Chem.rdchem.Mol)mol[, (bool)addAsQueries=True[, (bool)addCoords=True]]) → None :

  attachment points encoded as attachPt properties are added to the graph as dummy atoms

  > Arguments:

  >   - mol: molecule to be modified

  >   - addAsQueries: if true, the dummy atoms will be added as null queries

  >       (i.e. they will match any atom in a substructure search)

  >   - addCoords: if true and the molecule has one or more conformers,

  >       positions for the attachment points will be added to the conformer(s)

  C++ signature :

    void ExpandAttachmentPoints(RDKit::ROMol {lvalue} [,bool=True [,bool=True]])

rdkit.Chem.rdmolops.FastFindRings((rdkit.Chem.rdchem.Mol)mol) → None :

  Does a non-SSSR ring finding for a molecule.

  > ARGUMENTS:

  > > - mol: the molecule to use.

  > RETURNS: Nothing

  C++ signature :

    void FastFindRings(RDKit::ROMol)

rdkit.Chem.rdmolops.FindAllPathsOfLengthN((rdkit.Chem.rdchem.Mol)mol, (int)length[, (bool)useBonds=True[, (bool)useHs=False[, (int)rootedAtAtom=-1[, (bool)onlyShortestPaths=False]]]]) → rdkit.rdBase._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.

  > > - onlyShortestPaths: (optional) if set then only paths which are <= the shortest path between the begin and end atoms will be included in the results

  > 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::__cxx11::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 [,bool=False]]]])

rdkit.Chem.rdmolops.FindAllSubgraphsOfLengthMToN((rdkit.Chem.rdchem.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]])

rdkit.Chem.rdmolops.FindAllSubgraphsOfLengthN((rdkit.Chem.rdchem.Mol)mol, (int)length[, (bool)useHs=False[, (int)rootedAtAtom=-1]]) → rdkit.rdBase._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::__cxx11::list<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > FindAllSubgraphsOfLengthN(RDKit::ROMol,unsigned int [,bool=False [,int=-1]])

rdkit.Chem.rdmolops.FindAtomEnvironmentOfRadiusN((rdkit.Chem.rdchem.Mol)mol, (int)radius, (int)rootedAtAtom[, (bool)useHs=False[, (bool)enforceSize=True[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomMap=None]]]) → rdkit.rdBase._vecti :
  Find bonds of a particular radius around an atom.

    > Return empty result if there is no bond at the requested radius.

    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.

    > - enforceSize (optional) If set to False, all bonds within the requested radius is collected. Defaults to 1.

    > - atomMap: (optional) If provided, it will measure the minimum distance of the atom from the rooted atom (start with 0 from the rooted atom). The result is a pair of the atom ID and the distance.

    RETURNS: a vector of bond IDs

  C++ signature :

    std::vector<int, std::allocator<int> > FindAtomEnvironmentOfRadiusN(RDKit::ROMol,unsigned int,unsigned int [,bool=False [,bool=True [,boost::python::api::object=None]]])

rdkit.Chem.rdmolops.FindMesoCenters((rdkit.Chem.rdchem.Mol)mol[, (bool)includeIsotopes=True[, (bool)includeAtomMaps=False]]) → object :

  returns the meso centers in a molecule (if any).

  > ARGUMENTS:

  > > - mol: the molecule to use

  > > - includeIsotopes: (optional) toggles whether or not isotopes should be included in the calculation.

  > > - includeAtomMaps: (optional) toggles whether or not atom maps should be included in the calculation.

  C++ signature :

    boost::python::api::object FindMesoCenters(RDKit::ROMol [,bool=True [,bool=False]])

rdkit.Chem.rdmolops.FindPotentialStereo((rdkit.Chem.rdchem.Mol)mol[, (bool)cleanIt=False[, (bool)flagPossible=True]]) → _vectN5RDKit9Chirality10StereoInfoE :

  find potential stereo elements in a molecule and returns them as StereoInfo objects Note that this function is still somewhat experimental and the API and results may change in a future release.

  C++ signature :

    std::vector<RDKit::Chirality::StereoInfo, std::allocator<RDKit::Chirality::StereoInfo> > FindPotentialStereo(RDKit::ROMol {lvalue} [,bool=False [,bool=True]])

rdkit.Chem.rdmolops.FindPotentialStereoBonds((rdkit.Chem.rdchem.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])

rdkit.Chem.rdmolops.FindRingFamilies((rdkit.Chem.rdchem.Mol)mol[, (bool)includeDativeBonds=False[, (bool)includeHydrogenBonds=False]]) → None :

  Generate Unique Ring Families.

  > ARGUMENTS:

  > > - mol: the molecule to use.

  > > - includeDativeBonds: whether or not dative bonds should be included in the ring families finding.

  > > - includeHydrogenBonds: whether or not hydrogen bonds should be included in the ring families .

  > RETURNS: Nothing

  C++ signature :

    void FindRingFamilies(RDKit::ROMol [,bool=False [,bool=False]])

rdkit.Chem.rdmolops.FindUniqueSubgraphsOfLengthN((rdkit.Chem.rdchem.Mol)mol, (int)length[, (bool)useHs=False[, (bool)useBO=True[, (int)rootedAtAtom=-1]]]) → rdkit.rdBase._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::__cxx11::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]]])

rdkit.Chem.rdmolops.FragmentOnBRICSBonds((rdkit.Chem.rdchem.Mol)mol) → rdkit.Chem.rdchem.Mol :

  Return a new molecule with all BRICS bonds broken

  C++ signature :

    RDKit::ROMol* FragmentOnBRICSBonds(RDKit::ROMol)

rdkit.Chem.rdmolops.FragmentOnBonds((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondIndices[, (bool)addDummies=True[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)dummyLabels=None[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondTypes=None[, (list)cutsPerAtom=[]]]]]) → rdkit.Chem.rdchem.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=[]]]]])

rdkit.Chem.rdmolops.FragmentOnSomeBonds((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondIndices[, (int)numToBreak=1[, (bool)addDummies=True[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)dummyLabels=None[, (rdkit.Chem.rdMolDescriptors.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]]]]])

rdkit.Chem.rdmolops.Get3DDistanceMatrix((rdkit.Chem.rdchem.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*=’’]]]])

rdkit.Chem.rdmolops.GetAdjacencyMatrix((rdkit.Chem.rdchem.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*=’’]]]])

rdkit.Chem.rdmolops.GetAllowNontetrahedralChirality() → bool :

  returns whether or not recognition of non-tetrahedral chirality from 3D structures is enabled

  C++ signature :

    bool GetAllowNontetrahedralChirality()

rdkit.Chem.rdmolops.GetDistanceMatrix((rdkit.Chem.rdchem.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*=’’]]]])

rdkit.Chem.rdmolops.GetFormalCharge((rdkit.Chem.rdchem.Mol)mol) → int :

  Returns the formal charge for the molecule.

  > ARGUMENTS:

  > > - mol: the molecule to use

  C++ signature :

    int GetFormalCharge(RDKit::ROMol)

rdkit.Chem.rdmolops.GetMolFrags((rdkit.Chem.rdchem.Mol)mol[, (bool)asMols=False[, (bool)sanitizeFrags=True[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)frags=None[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)fragsMolAtomMapping=None]]]]) → 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.

  > > - frags: (optional, defaults to None) if asMols is true and this is provided

  > >     as an empty list, the result will be mol.GetNumAtoms() long on return and will contain the fragment assignment for each Atom

  > > - fragsMolAtomMapping: (optional, defaults to None) if asMols is true and this is provided as an empty list, the result will be numFrags long on return, and each entry will contain the indices of the Atoms in that fragment: [(0, 1, 2, 3), (4, 5)]

  > 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 [,boost::python::api::object=None [,boost::python::api::object=None]]]])

rdkit.Chem.rdmolops.GetMostSubstitutedCoreMatch((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)core, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)matches) → object :

  Postprocesses the results of a mol.GetSubstructMatches(core) call where mol has explicit Hs and core bears terminal dummy atoms (i.e., R groups). It returns the match with the largest number of non-hydrogen matches to the terminal dummy atoms.

  > ARGUMENTS:

  > > - mol: the molecule GetSubstructMatches was run on

  > > - core: the molecule used as a substructure query

  > > - matches: the result returned by GetSubstructMatches

  > RETURNS: the tuple where terminal dummy atoms in the core match the largest

  >   number of non-hydrogen atoms in mol

  C++ signature :

    _object* GetMostSubstitutedCoreMatch(RDKit::ROMol,RDKit::ROMol,boost::python::api::object)

rdkit.Chem.rdmolops.GetSSSR((rdkit.Chem.rdchem.Mol)mol[, (bool)includeDativeBonds=False[, (bool)includeHydrogenBonds=False]]) → rdkit.rdBase._vectSt6vectorIiSaIiEE :

  Get the smallest set of simple rings for a molecule.

  > ARGUMENTS:

  > > - mol: the molecule to use.

  > > - includeDativeBonds: whether or not dative bonds should be included in the ring finding.

  > > - includeHydrogenBonds: whether or not hydrogen bonds should be included in the ring finding.

  > 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 :

    std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > GetSSSR(RDKit::ROMol {lvalue} [,bool=False [,bool=False]])

rdkit.Chem.rdmolops.GetShortestPath((rdkit.Chem.rdchem.Mol)mol, (int)aid1, (int)aid2) → 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)

rdkit.Chem.rdmolops.GetSymmSSSR((rdkit.Chem.rdchem.Mol)mol[, (bool)includeDativeBonds=False[, (bool)includeHydrogenBonds=False]]) → rdkit.rdBase._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.

  > > - includeDativeBonds: whether or not dative bonds should be included in the ring finding.

  > > - includeHydrogenBonds: whether or not hydrogen bonds should be included in the ring finding.

  > 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} [,bool=False [,bool=False]])

rdkit.Chem.rdmolops.GetUseLegacyStereoPerception() → bool :

  returns whether or not the legacy stereo perception code is being used

  C++ signature :

    bool GetUseLegacyStereoPerception()

rdkit.Chem.rdmolops.HapticBondsToDative((rdkit.Chem.rdchem.Mol)mol) → rdkit.Chem.rdchem.Mol :

  One way of showing haptic bonds (such as cyclopentadiene to iron in ferrocene) is to use a dummy atom with a dative bond to the iron atom with the bond labelled with the atoms involved in the organic end of the bond. Another way is to have explicit dative bonds from the atoms of the haptic group to the metal atom. This function converts the former representation to the latter.

  Parameters:

    mol (-) – the molecule to use

  Returns:

    a modified copy of the molecule

  C++ signature :

    RDKit::ROMol* HapticBondsToDative(RDKit::ROMol)

rdkit.Chem.rdmolops.HasQueryHs((rdkit.Chem.rdchem.Mol)mol) → tuple :

  Check to see if the molecule has query Hs, this is normally used on query molecules such as those returned from MolFromSmarts .. rubric:: Example

  (hasQueryHs, hasUnmergeableQueryHs) = HasQueryHs(mol)

  if hasUnmergeableQueryHs, these query hs cannot be removed by calling MergeQueryHs

  C++ signature :

    boost::python::tuple HasQueryHs(RDKit::ROMol)

rdkit.Chem.rdmolops.Kekulize((rdkit.Chem.rdchem.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 False.

  > NOTES:

  > > - The molecule is modified in place.

  > > - this does not modify query bonds which have bond type queries (like those which come from SMARTS) or rings containing them.

  > > - even if clearAromaticFlags is False the BondType for all modified aromatic bonds will be changed from AROMATIC to SINGLE or DOUBLE Kekulization.

  C++ signature :

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

rdkit.Chem.rdmolops.KekulizeIfPossible((rdkit.Chem.rdchem.Mol)mol[, (bool)clearAromaticFlags=False]) → None :

  Kekulizes the molecule if possible. Otherwise the molecule is not modified

  > 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 if the kekulization succeds. Default value is False.

  > NOTES:

  > > - The molecule is modified in place.

  C++ signature :

    void KekulizeIfPossible(RDKit::ROMol {lvalue} [,bool=False])

rdkit.Chem.rdmolops.LayeredFingerprint((rdkit.Chem.rdchem.Mol)mol[, (int)layerFlags=4294967295[, (int)minPath=1[, (int)maxPath=7[, (int)fpSize=2048[, (list)atomCounts=[][, (rdkit.DataStructs.cDataStructs.ExplicitBitVect)setOnlyBits=None[, (bool)branchedPaths=True[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)fromAtoms=0]]]]]]]]) → rdkit.DataStructs.cDataStructs.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]]]]]]]])

rdkit.Chem.rdmolops.MergeQueryHs((rdkit.Chem.rdchem.Mol)mol[, (bool)mergeUnmappedOnly=False[, (bool)mergeIsotopes=False]]) → rdkit.Chem.rdchem.Mol :

  merges hydrogens into their neighboring atoms as queries

  C++ signature :

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

rdkit.Chem.rdmolops.MolAddRecursiveQueries((rdkit.Chem.rdchem.Mol)mol, (dict)queries, (str)propName) → None :

  Adds named recursive queries to atoms

  C++ signature :

    void MolAddRecursiveQueries(RDKit::ROMol {lvalue},boost::python::dict,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdmolops.MolzipLabel

  Bases: `enum`

  AtomMapNumber = rdkit.Chem.rdmolops.MolzipLabel.AtomMapNumber
  AtomType = rdkit.Chem.rdmolops.MolzipLabel.AtomType
  FragmentOnBonds = rdkit.Chem.rdmolops.MolzipLabel.FragmentOnBonds
  Isotope = rdkit.Chem.rdmolops.MolzipLabel.Isotope
  names = {'AtomMapNumber': rdkit.Chem.rdmolops.MolzipLabel.AtomMapNumber, 'AtomType': rdkit.Chem.rdmolops.MolzipLabel.AtomType, 'FragmentOnBonds': rdkit.Chem.rdmolops.MolzipLabel.FragmentOnBonds, 'Isotope': rdkit.Chem.rdmolops.MolzipLabel.Isotope}
  values = {0: rdkit.Chem.rdmolops.MolzipLabel.AtomMapNumber, 1: rdkit.Chem.rdmolops.MolzipLabel.Isotope, 2: rdkit.Chem.rdmolops.MolzipLabel.FragmentOnBonds, 3: rdkit.Chem.rdmolops.MolzipLabel.AtomType}

class rdkit.Chem.rdmolops.MolzipParams((object)self) → None :

  Bases: `instance`

  Parameters controlling how to zip molecules together

  OPTIONS:

    label : set the MolzipLabel option [default MolzipLabel.AtomMapNumber]

  MolzipLabel.AtomMapNumber: atom maps are on dummy atoms, zip together the corresponding

    attached atoms, i.e. zip ‘C[:1]’ ‘N[:1]’ results in ‘CN’

  MolzipLabel.Isotope: isotope labels are on dummy atoms, zip together the corresponding

    attached atoms, i.e. zip ‘C[1*]’ ‘N[1*]’ results in ‘CN’

  MolzipLabel.FragmentOnBonds: zip together molecules generated by fragment on bonds.

    Note the atom indices cannot change or be reordered from the output of fragmentOnBonds

  MolzipLabel.AtomTypes: choose the atom types to act as matching dummy atoms.

    i.e. ‘C[V]’ and ‘N[Xe]’ with atoms pairs [(‘V’, ‘Xe’)] results in ‘CN’

  C++ signature :

    void __init__(_object*)

  property alignCoordinates

    if true and the input fragments have coordinates, the fragments will be aligned along connection vectors in the output molecule

  property enforceValenceRules

    If true (default) enforce valences after zipping Setting this to false allows assembling chemically incorrect fragments.

  property generateCoordinates

    If true will add depiction coordinates to input molecules and zipped molecule (for molzipFragments only)

  property label

    Set the atom labeling system to zip together

  setAtomSymbols((MolzipParams)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)symbols) → None :

    Set the atom symbols used to zip mols together when using AtomType labeling

    C++ signature :

      void setAtomSymbols(RDKit::MolzipParams {lvalue},boost::python::api::object)

rdkit.Chem.rdmolops.MurckoDecompose((rdkit.Chem.rdchem.Mol)mol) → rdkit.Chem.rdchem.Mol :

  Do a Murcko decomposition and return the scaffold

  C++ signature :

    RDKit::ROMol* MurckoDecompose(RDKit::ROMol)

rdkit.Chem.rdmolops.NeedsHs((rdkit.Chem.rdchem.Mol)mol) → bool :

  returns whether or not the molecule needs to have Hs added

  C++ signature :

    bool NeedsHs(RDKit::ROMol)

rdkit.Chem.rdmolops.ParseMolQueryDefFile((rdkit.Chem.rdMolDescriptors.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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’t’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’//’ [,unsigned int=0 [,unsigned int=1]]]]])

rdkit.Chem.rdmolops.PathToSubmol((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)path[, (bool)useQuery=False[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomMap=None]]) → rdkit.Chem.rdchem.Mol :
  C++ signature :

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

rdkit.Chem.rdmolops.PatternFingerprint((rdkit.Chem.rdchem.Mol)mol[, (int)fpSize=2048[, (list)atomCounts=[][, (rdkit.DataStructs.cDataStructs.ExplicitBitVect)setOnlyBits=None[, (bool)tautomerFingerprints=False]]]]) → rdkit.DataStructs.cDataStructs.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 [,bool=False]]]])

  PatternFingerprint( (rdkit.Chem.rdchem.MolBundle)mol [, (int)fpSize=2048 [, (rdkit.DataStructs.cDataStructs.ExplicitBitVect)setOnlyBits=None [, (bool)tautomerFingerprints=False]]]) -> rdkit.DataStructs.cDataStructs.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::MolBundle [,unsigned int=2048 [,ExplicitBitVect*=None [,bool=False]]])

rdkit.Chem.rdmolops.RDKFingerprint((rdkit.Chem.rdchem.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[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomInvariants=0[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)fromAtoms=0[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomBits=None[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bitInfo=None]]]]]]]]]]]]]) → rdkit.DataStructs.cDataStructs.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]]]]]]]]]]]]])

rdkit.Chem.rdmolops.ReapplyMolBlockWedging((rdkit.Chem.rdchem.Mol)mol[, (bool)allBondTypes=True[, (bool)verify=False]]) → None :
  Set the wedging to that which was read from the original

    MolBlock, over-riding anything that was originally there.

    > ARGUMENTS:

    > > - molecule: the molecule to update

    > > - allBondTypes: reapply the wedging also on bonds other than single and aromatic ones

    > > - verify: if true, the function will check that the wedges are only applied in sensible places (i.e.single bonds connected to chiral centers or atropisomeric bonds)

  C++ signature :

    void ReapplyMolBlockWedging(RDKit::ROMol {lvalue} [,bool=True [,bool=False]])

rdkit.Chem.rdmolops.RemoveAllHs((rdkit.Chem.rdchem.Mol)mol[, (bool)sanitize=True]) → rdkit.Chem.rdchem.Mol :

  Returns a copy of the molecule with all Hs removed.

  C++ signature :

    RDKit::ROMol* RemoveAllHs(RDKit::ROMol [,bool=True])

rdkit.Chem.rdmolops.RemoveHs((rdkit.Chem.rdchem.Mol)mol[, (bool)implicitOnly=False[, (bool)updateExplicitCount=False[, (bool)sanitize=True]]]) → rdkit.Chem.rdchem.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.

  > > > - Hydrogens which aren’t connected to a heavy atom will not be removed. This prevents molecules like [H][H] from having all atoms removed.

  > > > - Labelled hydrogen (e.g. atoms with atomic number=1, but isotope > 1), will not be removed.

  > > > - two coordinate Hs, like the central H in C[H-]C, will not be removed

  > > > - Hs connected to dummy atoms will not be removed

  > > > - Hs that are part of the definition of double bond Stereochemistry will not be removed

  > > > - Hs that are not connected to anything else will not be removed

  > C++ signature :

  >   RDKit::ROMol* RemoveHs(RDKit::ROMol [,bool=False [,bool=False [,bool=True]]])

  RemoveHs( (rdkit.Chem.rdchem.Mol)mol, (RemoveHsParameters)params [, (bool)sanitize=True]) -> rdkit.Chem.rdchem.Mol :

    Returns a copy of the molecule with Hs removed. Which Hs are removed is controlled by the params argument

    C++ signature :

      RDKit::ROMol* RemoveHs(RDKit::ROMol,RDKit::MolOps::RemoveHsParameters [,bool=True])

class rdkit.Chem.rdmolops.RemoveHsParameters((object)arg1) → None :

  Bases: `instance`

  Parameters controlling which Hs are removed.

  C++ signature :

    void __init__(_object*)

  property removeAndTrackIsotopes

    hydrogens with non-default isotopes and store them in the _isotopicHs atom property such that AddHs() can add the same isotope at a later stage

  property removeDefiningBondStereo

    hydrogens defining bond stereochemistry

  property removeDegreeZero

    hydrogens that have no bonds

  property removeDummyNeighbors

    hydrogens with at least one dummy-atom neighbor

  property removeHigherDegrees

    hydrogens with two (or more) bonds

  property removeHydrides

    hydrogens with formal charge -1

  property removeInSGroups

    hydrogens involved in SubstanceGroups

  property removeIsotopes

    hydrogens with non-default isotopes

  property removeMapped

    mapped hydrogens

  property removeNonimplicit

    DEPRECATED

  property removeNontetrahedralNeighbors

    hydrogens with neighbors that have non-tetrahedral stereochemistry

  property removeOnlyHNeighbors

    hydrogens with bonds only to other hydrogens

  property removeWithQuery

    hydrogens with queries defined

  property removeWithWedgedBond

    hydrogens with wedged bonds to them

  property showWarnings

    display warning messages for some classes of removed Hs

  property updateExplicitCount

    DEPRECATED

rdkit.Chem.rdmolops.RemoveNonExplicit3DChirality((rdkit.Chem.rdchem.Mol)mol) → None :
  Remove chiral markings that were derived from a 3D mol but were not

    explicity marked in the mol block. (wedge bond or CFG indication

    > ARGUMENTS:

    > > - molecule: the molecule to update

  C++ signature :

    void RemoveNonExplicit3DChirality(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.RemoveStereochemistry((rdkit.Chem.rdchem.Mol)mol) → None :

  Removes all stereochemistry info from the molecule.

  C++ signature :

    void RemoveStereochemistry(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.RenumberAtoms((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)newOrder) → rdkit.Chem.rdchem.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})

rdkit.Chem.rdmolops.ReplaceCore((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)core, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)matches[, (bool)replaceDummies=True[, (bool)labelByIndex=False[, (bool)requireDummyMatch=False]]]) → rdkit.Chem.rdchem.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')

    >     >>> MolToSmiles(ReplaceCore(mol, core, mol.GetSubstructMatch(core)))
    >     '[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))
    >     ...     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( (rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)coreQuery [, (bool)replaceDummies=True [, (bool)labelByIndex=False [, (bool)requireDummyMatch=False [, (bool)useChirality=False]]]]) -> rdkit.Chem.rdchem.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]]]])

rdkit.Chem.rdmolops.ReplaceSidechains((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)coreQuery[, (bool)useChirality=False]) → rdkit.Chem.rdchem.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])

rdkit.Chem.rdmolops.ReplaceSubstructs((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)query, (rdkit.Chem.rdchem.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.

  > > - A bond is only formed to the remaining atoms, if any, that were bonded to the first atom in the substructure query. (For finer control over substructure replacement, consider using ChemicalReaction.)

  > EXAMPLES:

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

  > > > - ReplaceSubstructs(‘CCOC’,’O[CH3]’,’NC’) -> (‘CCNC’,)

  > > > - ReplaceSubstructs(‘COCCOC’,’O[CH3]’,’NC’) -> (‘COCCNC’,’CNCCOC’)

  > > > - ReplaceSubstructs(‘COCCOC’,’O[CH3]’,’NC’,True) -> (‘CNCCNC’,)

  > > > - ReplaceSubstructs(‘COCCOC’,’O[CH3]’,’CN’,True,1) -> (‘CNCCNC’,)

  > > > - ReplaceSubstructs(‘CCOC’,’[CH3]O’,’NC’) -> (‘CC.CN’,)

  C++ signature :

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

class rdkit.Chem.rdmolops.SanitizeFlags

  Bases: `enum`

  SANITIZE_ADJUSTHS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS
  SANITIZE_ALL = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL
  SANITIZE_CLEANUP = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP
  SANITIZE_CLEANUPATROPISOMERS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPATROPISOMERS
  SANITIZE_CLEANUPCHIRALITY = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPCHIRALITY
  SANITIZE_CLEANUP_ORGANOMETALLICS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP_ORGANOMETALLICS
  SANITIZE_FINDRADICALS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_FINDRADICALS
  SANITIZE_KEKULIZE = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE
  SANITIZE_NONE = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
  SANITIZE_PROPERTIES = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES
  SANITIZE_SETAROMATICITY = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETAROMATICITY
  SANITIZE_SETCONJUGATION = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETCONJUGATION
  SANITIZE_SETHYBRIDIZATION = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETHYBRIDIZATION
  SANITIZE_SYMMRINGS = rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SYMMRINGS
  names = {'SANITIZE_ADJUSTHS': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS, 'SANITIZE_ALL': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL, 'SANITIZE_CLEANUP': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP, 'SANITIZE_CLEANUPATROPISOMERS': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPATROPISOMERS, 'SANITIZE_CLEANUPCHIRALITY': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPCHIRALITY, 'SANITIZE_CLEANUP_ORGANOMETALLICS': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP_ORGANOMETALLICS, 'SANITIZE_FINDRADICALS': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_FINDRADICALS, 'SANITIZE_KEKULIZE': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE, 'SANITIZE_NONE': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE, 'SANITIZE_PROPERTIES': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES, 'SANITIZE_SETAROMATICITY': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETAROMATICITY, 'SANITIZE_SETCONJUGATION': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETCONJUGATION, 'SANITIZE_SETHYBRIDIZATION': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETHYBRIDIZATION, 'SANITIZE_SYMMRINGS': rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SYMMRINGS}
  values = {0: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE, 1: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP, 2: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES, 4: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SYMMRINGS, 8: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE, 16: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_FINDRADICALS, 32: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETAROMATICITY, 64: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETCONJUGATION, 128: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_SETHYBRIDIZATION, 256: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPCHIRALITY, 512: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS, 1024: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUP_ORGANOMETALLICS, 2048: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_CLEANUPATROPISOMERS, 268435455: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL}

rdkit.Chem.rdmolops.SanitizeMol((rdkit.Chem.rdchem.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]])

rdkit.Chem.rdmolops.SetAllowNontetrahedralChirality((bool)val) → None :

  toggles recognition of non-tetrahedral chirality from 3D structures

  C++ signature :

    void SetAllowNontetrahedralChirality(bool)

rdkit.Chem.rdmolops.SetAromaticity((rdkit.Chem.rdchem.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])

rdkit.Chem.rdmolops.SetBondStereoFromDirections((rdkit.Chem.rdchem.Mol)mol) → None :

  Uses the directions of neighboring bonds to set cis/trans stereo on double bonds.

  > ARGUMENTS:

  > > - mol: the molecule to be modified

  C++ signature :

    void SetBondStereoFromDirections(RDKit::ROMol {lvalue})

rdkit.Chem.rdmolops.SetConjugation((rdkit.Chem.rdchem.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})

rdkit.Chem.rdmolops.SetDoubleBondNeighborDirections((rdkit.Chem.rdchem.Mol)mol[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)conf=None]) → None :

  Uses the stereo info on double bonds to set the directions of neighboring single bonds

  > ARGUMENTS:

  > > - mol: the molecule to be modified

  C++ signature :

    void SetDoubleBondNeighborDirections(RDKit::ROMol {lvalue} [,boost::python::api::object=None])

rdkit.Chem.rdmolops.SetGenericQueriesFromProperties((rdkit.Chem.rdchem.Mol)mol[, (bool)useAtomLabels=True[, (bool)useSGroups=True]]) → None :

  documentation

  C++ signature :

    void SetGenericQueriesFromProperties(RDKit::ROMol {lvalue} [,bool=True [,bool=True]])

rdkit.Chem.rdmolops.SetHybridization((rdkit.Chem.rdchem.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})

rdkit.Chem.rdmolops.SetTerminalAtomCoords((rdkit.Chem.rdchem.Mol)mol, (int)idx, (int)otherIdx) → None :

  Sets Cartesian coordinates for a terminal atom.

  > Useful for growing an atom off a molecule with sensible coordinates based on the geometry of the neighbor.

  > NOTE: this sets the appropriate coordinates in all of the molecule’s conformers ARGUMENTS:

  > > - mol: the molecule the atoms belong to.

  > > - idx: index of the terminal atom whose coordinates are set.

  > > - mol: index of the bonded neighbor atom.

  > RETURNS: Nothing

  C++ signature :

    void SetTerminalAtomCoords(RDKit::ROMol {lvalue},unsigned int,unsigned int)

rdkit.Chem.rdmolops.SetUseLegacyStereoPerception((bool)val) → None :

  sets usage of the legacy stereo perception code

  C++ signature :

    void SetUseLegacyStereoPerception(bool)

rdkit.Chem.rdmolops.SimplifyEnhancedStereo((rdkit.Chem.rdchem.Mol)mol[, (bool)removeAffectedStereoGroups=True]) → None :

  Simplifies the stereochemical representation of a molecule where all specified stereocenters are in the same StereoGroup

  > Arguments:

  >   - mol: molecule to modify

  >   - removeAffectedStereoGroups: if set then the affected StereoGroups will be removed

  If all specified stereocenters are in the same AND or OR stereogroup, a moleculeNote property will be set on the molecule with the value “AND enantiomer” or “OR enantiomer”. CIP labels, if present, are removed.

  C++ signature :

    void SimplifyEnhancedStereo(RDKit::ROMol {lvalue} [,bool=True])

rdkit.Chem.rdmolops.SortMatchesByDegreeOfCoreSubstitution((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Mol)core, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)matches) → object :

  Postprocesses the results of a mol.GetSubstructMatches(core) call where mol has explicit Hs and core bears terminal dummy atoms (i.e., R groups). It returns a copy of matches sorted by decreasing number of non-hydrogen matches to the terminal dummy atoms.

  > ARGUMENTS:

  > > - mol: the molecule GetSubstructMatches was run on

  > > - core: the molecule used as a substructure query

  > > - matches: the result returned by GetSubstructMatches

  > RETURNS: a copy of matches sorted by decreasing number of non-hydrogen matches

  >   to the terminal dummy atoms

  C++ signature :

    _object* SortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol,RDKit::ROMol,boost::python::api::object)

rdkit.Chem.rdmolops.SplitMolByPDBChainId((rdkit.Chem.rdchem.Mol)mol[, (rdkit.Chem.rdMolDescriptors.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]])

rdkit.Chem.rdmolops.SplitMolByPDBResidues((rdkit.Chem.rdchem.Mol)mol[, (rdkit.Chem.rdMolDescriptors.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]])

class rdkit.Chem.rdmolops.StereoBondThresholds

  Bases: `instance`

  Constants used to set the thresholds for which single bonds can be made wavy.

  Raises an exception This class cannot be instantiated from Python

  CHIRAL_ATOM = 100000
  DBL_BOND_NO_STEREO = 1000
  DBL_BOND_SPECIFIED_STEREO = 10000
  DIRECTION_SET = 1000000

class rdkit.Chem.rdmolops.StereoGroupAbsOptions

  Bases: `enum`

  AlwaysInclude = rdkit.Chem.rdmolops.StereoGroupAbsOptions.AlwaysInclude
  NeverInclude = rdkit.Chem.rdmolops.StereoGroupAbsOptions.NeverInclude
  OnlyIncludeWhenOtherGroupsExist = rdkit.Chem.rdmolops.StereoGroupAbsOptions.OnlyIncludeWhenOtherGroupsExist
  names = {'AlwaysInclude': rdkit.Chem.rdmolops.StereoGroupAbsOptions.AlwaysInclude, 'NeverInclude': rdkit.Chem.rdmolops.StereoGroupAbsOptions.NeverInclude, 'OnlyIncludeWhenOtherGroupsExist': rdkit.Chem.rdmolops.StereoGroupAbsOptions.OnlyIncludeWhenOtherGroupsExist}
  values = {0: rdkit.Chem.rdmolops.StereoGroupAbsOptions.OnlyIncludeWhenOtherGroupsExist, 1: rdkit.Chem.rdmolops.StereoGroupAbsOptions.NeverInclude, 2: rdkit.Chem.rdmolops.StereoGroupAbsOptions.AlwaysInclude}

class rdkit.Chem.rdmolops.SubsetInfo((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  property atomMapping

    mapping from the original atom index to the subset atom index

  property bondMapping

    mapping from the original bond index to the subset bond index

class rdkit.Chem.rdmolops.SubsetMethod

  Bases: `enum`

  BONDS = rdkit.Chem.rdmolops.SubsetMethod.BONDS
  BONDS_BETWEEN_ATOMS = rdkit.Chem.rdmolops.SubsetMethod.BONDS_BETWEEN_ATOMS
  names = {'BONDS': rdkit.Chem.rdmolops.SubsetMethod.BONDS, 'BONDS_BETWEEN_ATOMS': rdkit.Chem.rdmolops.SubsetMethod.BONDS_BETWEEN_ATOMS}
  values = {0: rdkit.Chem.rdmolops.SubsetMethod.BONDS_BETWEEN_ATOMS, 1: rdkit.Chem.rdmolops.SubsetMethod.BONDS}

class rdkit.Chem.rdmolops.SubsetOptions((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  property clearComputedProps

    clear all computed props on the subsetted molecule

  property conformerIdx

    What conformer idx to use for the coordinates default is -1

  property copyAsQuery

    Return the subset as a query

  property copyCoordinates

    Copy the active coordinates from the molecule

  property method

    Subsetting method to use

  property sanitize

    Sanitize the resulting subset

rdkit.Chem.rdmolops.TranslateChiralFlagToStereoGroups((rdkit.Chem.rdchem.Mol)mol[, (rdkit.Chem.rdchem.StereoGroupType)zeroFlagGroupType=rdkit.Chem.rdchem.StereoGroupType.STEREO_AND]) → None :

  Generate enhanced stereo groups based on the status of the chiral flag property.

  > Arguments:

  >   - mol: molecule to be modified

  >   - zeroFlagGroupType: how to handle non-grouped stereo centers when the

  >       chiral flag is set to zero

  > If the chiral flag is set to a value of 1 then all specified tetrahedral chiral centers which are not already in StereoGroups will be added to an ABS StereoGroup.

  > If the chiral flag is set to a value of 0 then all specified tetrahedral chiral centers will be added to a StereoGroup of the type zeroFlagGroupType

  > If there is no chiral flag set (i.e. the property is not present), the molecule will not be modified.

  C++ signature :

    void TranslateChiralFlagToStereoGroups(RDKit::ROMol {lvalue} [,RDKit::StereoGroupType=rdkit.Chem.rdchem.StereoGroupType.STEREO_AND])

class rdkit.Chem.rdmolops.UIntUIntMap((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

rdkit.Chem.rdmolops.UnfoldedRDKFingerprintCountBased((rdkit.Chem.rdchem.Mol)mol[, (int)minPath=1[, (int)maxPath=7[, (bool)useHs=True[, (bool)branchedPaths=True[, (bool)useBondOrder=True[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomInvariants=0[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)fromAtoms=0[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomBits=None[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bitInfo=None]]]]]]]]]) → rdkit.DataStructs.cDataStructs.ULongSparseIntVect :

  Returns an unfolded count-based version of the RDKit fingerprint for a molecule

  Parameters:

    - 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]]]]]]]]])

rdkit.Chem.rdmolops.WedgeBond((rdkit.Chem.rdchem.Bond)bond, (int)fromAtomIdx, (rdkit.Chem.rdchem.Conformer)conf) → None :
  Set the wedging on an individual bond from a molecule.

    > The wedging scheme used is that from Mol files.

    ARGUMENTS:

      - bond: the bond to update

      - atom ID: the atom from which to do the wedging

      - conformer: the conformer to use to determine wedge direction

  C++ signature :

    void WedgeBond(RDKit::Bond*,unsigned int,RDKit::Conformer const*)

rdkit.Chem.rdmolops.WedgeMolBonds((rdkit.Chem.rdchem.Mol)mol, (rdkit.Chem.rdchem.Conformer)conformer[, (BondWedgingParameters)params=None]) → 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

    > - conformer: the conformer to use to determine wedge direction

  C++ signature :

    void WedgeMolBonds(RDKit::ROMol {lvalue},RDKit::Conformer const* [,RDKit::Chirality::BondWedgingParameters const*=None])

class rdkit.Chem.rdmolops.map_indexing_suite_UIntUIntMap_entry((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  data((map_indexing_suite_UIntUIntMap_entry)arg1) → int :
    C++ signature :

      unsigned int data(std::pair<unsigned int const, unsigned int> {lvalue})

  key((map_indexing_suite_UIntUIntMap_entry)arg1) → int :
    C++ signature :

      unsigned int key(std::pair<unsigned int const, unsigned int> {lvalue})

rdkit.Chem.rdmolops.molzip((rdkit.Chem.rdchem.Mol)a, (rdkit.Chem.rdchem.Mol)b[, (MolzipParams)params=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c2610>]) → rdkit.Chem.rdchem.Mol :

  zip together two molecules using the given matching parameters

  > C++ signature :

  >   RDKit::ROMol* molzip(RDKit::ROMol,RDKit::ROMol [,RDKit::MolzipParams=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c2610>])

  molzip( (rdkit.Chem.rdchem.Mol)a [, (MolzipParams)params=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c26c0>]) -> rdkit.Chem.rdchem.Mol :

    zip together multiple molecules within a combined molecule using the given matching parameters

    C++ signature :

      RDKit::ROMol* molzip(RDKit::ROMol [,RDKit::MolzipParams=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c26c0>])

  molzip( (dict)row [, (MolzipParams)params=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c28d0>]) -> rdkit.Chem.rdchem.Mol :

    zip an RGroupRow together to recreate the original molecule. This correctly handles broken cycles that can occur in decompositions.

    > example:

    >     >>> from rdkit import Chem
    >     >>> from rdkit.Chem import rdRGroupDecomposition as rgd
    >     >>> core = Chem.MolFromSmiles('CO')
    >     >>> mols = [Chem.MolFromSmiles('C1NNO1')]
    >     >>> rgroups, unmatched = rgd.RGroupDecompose(core, mols)
    >     >>> for rgroup in rgroups:
    >     ...     mol = rgd.molzip(rgroup)

    C++ signature :

      RDKit::ROMol* molzip(boost::python::dict [,RDKit::MolzipParams=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c28d0>])

rdkit.Chem.rdmolops.molzipFragments((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)mols[, (MolzipParams)params=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c2820>]) → rdkit.Chem.rdchem.Mol :

  zip together multiple molecules from an R group decomposition using the given matching parameters. The first molecule in the list must be the core

  C++ signature :

    RDKit::ROMol* molzipFragments(boost::python::api::object {lvalue} [,RDKit::MolzipParams=<rdkit.Chem.rdmolops.MolzipParams object at 0x7b87fc4c2820>])