rdkit.Chem.rdchem

Package rdkit :: Package Chem :: Module rdchem |
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# Module rdchem

    Module containing the core chemistry functionality of the RDKit

Classes | [hide private]
| Atom The class to store Atoms.
| AtomMonomerInfo The class to store monomer information attached to Atoms
| AtomMonomerType
| AtomPDBResidueInfo The class to store PDB residue information attached to Atoms
| Bond The class to store Bonds.
| BondDir
| BondStereo
| BondType
| ChiralType
| CompositeQueryType
| Conformer The class to store 2D or 3D conformation of a molecule
| EditableMol an editable molecule class
| HybridizationType
| Mol The Molecule class.
| MolBundle A class for storing gropus of related molecules.
| PeriodicTable A class which stores information from the Periodic Table.
| PropertyPickleOptions
| QueryAtom The class to store QueryAtoms.
| QueryBond The class to store QueryBonds.
| RWMol The RW molecule class (read/write)
| ResonanceFlags
| ResonanceMolSupplier A class which supplies resonance structures (as mols) from a mol.
| RingInfo contains information about a molecule's rings
| _ROAtomSeq Read-only sequence of atoms, not constructable from Python.
| _ROBondSeq Read-only sequence of bonds, not constructable from Python.
| _ROQAtomSeq Read-only sequence of atoms matching a query, not constructable from Python.
| _listPN5RDKit4AtomE
| _listPN5RDKit4BondE

Functions | [hide private]
GetAtomAlias(...) GetAtomAlias( (Atom)atom) -> str : Returns the atom's MDL alias text |
GetAtomRLabel(...) GetAtomRLabel( (Atom)atom) -> int : Returns the atom's MDL AtomRLabel (this is an integer from 0 to 99) |
GetAtomValue(...) GetAtomValue( (Atom)atom) -> str : Returns the atom's MDL alias text |
    int :
GetDefaultPickleProperties() Get the current global mol pickler options. |
    PeriodicTable :
GetPeriodicTable() Returns the application's PeriodicTable instance. |
GetSupplementalSmilesLabel(...) GetSupplementalSmilesLabel( (Atom)atom) -> str : Gets the supplemental smiles label on an atom, returns an empty string if not present. |
LogErrorMsg(...) LogErrorMsg( (str)arg1) -> None : Log a warning message to the RDKit error logs |
LogWarningMsg(...) LogWarningMsg( (str)arg1) -> None : Log a warning message to the RDKit warning logs |
SetAtomAlias(...) SetAtomAlias( (Atom)atom, (str)rlabel) -> None : Sets the atom's MDL alias text. |
SetAtomRLabel(...) SetAtomRLabel( (Atom)atom, (int)rlabel) -> None : Sets the atom's MDL RLabel (this is an integer from 0 to 99). |
SetAtomValue(...) SetAtomValue( (Atom)atom, (str)rlabel) -> None : Sets the atom's MDL alias text. |
SetDefaultPickleProperties(...) SetDefaultPickleProperties( (int)arg1) -> None : Set the current global mol pickler options. |
SetSupplementalSmilesLabel(...) SetSupplementalSmilesLabel( (Atom)atom, (str)label) -> None : Sets a supplemental label on an atom that is written to the smiles string. |
    None :
WrapLogs() Wrap the internal RDKit streams so they go to python's SysStdErr |
_HasSubstructMatchStr(...) _HasSubstructMatchStr( (str)pkl, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool : This function is included to speed substructure queries from databases, it's probably not of general interest. |
    None :
tossit() C++ signature :... |

Variables | [hide private]
| ALLOW_CHARGE_SEPARATION = `rdkit.Chem.rdchem.ResonanceFlags.ALL`...``
| ALLOW_INCOMPLETE_OCTETS = `rdkit.Chem.rdchem.ResonanceFlags.ALL`...``
| AllProps = `rdkit.Chem.rdchem.PropertyPickleOptions.AllProps`
| AtomProps = `rdkit.Chem.rdchem.PropertyPickleOptions.AtomProps`
| BondProps = `rdkit.Chem.rdchem.PropertyPickleOptions.BondProps`
| CHI_OTHER = `rdkit.Chem.rdchem.ChiralType.CHI_OTHER`
| CHI_TETRAHEDRAL_CCW = `rdkit.Chem.rdchem.ChiralType.CHI_TETRAHE`...``
| CHI_TETRAHEDRAL_CW = `rdkit.Chem.rdchem.ChiralType.CHI_TETRAHED`...``
| CHI_UNSPECIFIED = `rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED`
| COMPOSITE_AND = `rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE`...``
| COMPOSITE_OR = `rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_OR`
| COMPOSITE_XOR = `rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE`...``
| ComputedProps = `rdkit.Chem.rdchem.PropertyPickleOptions.Comput`...``
| KEKULE_ALL = `rdkit.Chem.rdchem.ResonanceFlags.KEKULE_ALL`
| MolProps = `rdkit.Chem.rdchem.PropertyPickleOptions.MolProps`
| NoProps = `rdkit.Chem.rdchem.PropertyPickleOptions.NoProps`
| PrivateProps = `rdkit.Chem.rdchem.PropertyPickleOptions.Private`...``
| QueryAtomData = `rdkit.Chem.rdchem.PropertyPickleOptions.QueryA`...``
| UNCONSTRAINED_ANIONS = `rdkit.Chem.rdchem.ResonanceFlags.UNCONS`...``
| UNCONSTRAINED_CATIONS = `rdkit.Chem.rdchem.ResonanceFlags.UNCON`...``
| __package__ = `None` hash(x)

Function Details | [hide private]

### GetAtomAlias(...) |
    GetAtomAlias( (Atom)atom) -> str :
        Returns the atom's MDL alias text

        C++ signature :
            std::string GetAtomAlias(RDKit::Atom const*)

### GetAtomRLabel(...) |
    GetAtomRLabel( (Atom)atom) -> int :
        Returns the atom's MDL AtomRLabel (this is an integer from 0 to 99)

        C++ signature :
            int GetAtomRLabel(RDKit::Atom const*)

### GetAtomValue(...) |
    GetAtomValue( (Atom)atom) -> str :
        Returns the atom's MDL alias text

        C++ signature :
            std::string GetAtomValue(RDKit::Atom const*)

### GetDefaultPickleProperties() |
        Get the current global mol pickler options.

        C++ signature :
            unsigned int GetDefaultPickleProperties()
Returns:
    int :

### GetPeriodicTable() |
        Returns the application's PeriodicTable instance.

        C++ signature :
            RDKit::PeriodicTable* GetPeriodicTable()
Returns:
    PeriodicTable :

### GetSupplementalSmilesLabel(...) |
    GetSupplementalSmilesLabel( (Atom)atom) -> str :
        Gets the supplemental smiles label on an atom, returns an empty string if not present.

        C++ signature :
            std::string GetSupplementalSmilesLabel(RDKit::Atom const*)

### LogErrorMsg(...) |
    LogErrorMsg( (str)arg1) -> None :
        Log a warning message to the RDKit error logs

        C++ signature :
            void LogErrorMsg(std::string)

### LogWarningMsg(...) |
    LogWarningMsg( (str)arg1) -> None :
        Log a warning message to the RDKit warning logs

        C++ signature :
            void LogWarningMsg(std::string)

### SetAtomAlias(...) |
    SetAtomAlias( (Atom)atom, (str)rlabel) -> None :
        Sets the atom's MDL alias text.
        Setting to an empty string clears the alias.

        C++ signature :
            void SetAtomAlias(RDKit::Atom*,std::string)

### SetAtomRLabel(...) |
    SetAtomRLabel( (Atom)atom, (int)rlabel) -> None :
        Sets the atom's MDL RLabel (this is an integer from 0 to 99).
        Setting to 0 clears the rlabel.

        C++ signature :
            void SetAtomRLabel(RDKit::Atom*,int)

### SetAtomValue(...) |
    SetAtomValue( (Atom)atom, (str)rlabel) -> None :
        Sets the atom's MDL alias text.
        Setting to an empty string clears the alias.

        C++ signature :
            void SetAtomValue(RDKit::Atom*,std::string)

### SetDefaultPickleProperties(...) |
    SetDefaultPickleProperties( (int)arg1) -> None :
        Set the current global mol pickler options.

        C++ signature :
            void SetDefaultPickleProperties(unsigned int)

### SetSupplementalSmilesLabel(...) |
    SetSupplementalSmilesLabel( (Atom)atom, (str)label) -> None :
        Sets a supplemental label on an atom that is written to the smiles string.
        >>> m = Chem.MolFromSmiles("C")
        >>> Chem.SetSupplementalSmilesLabel(m.GetAtomWithIdx(0), '<xxx>')
        >>> Chem.MolToSmiles(m)
        'C<xxx>'

        C++ signature :
            void SetSupplementalSmilesLabel(RDKit::Atom*,std::string)

### WrapLogs() |
        Wrap the internal RDKit streams so they go to python's SysStdErr

        C++ signature :
            void WrapLogs()
Returns:
    None :

### _HasSubstructMatchStr(...) |
    _HasSubstructMatchStr( (str)pkl, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :
        This function is included to speed substructure queries from databases,
        it's probably not of
        general interest.

          ARGUMENTS:
            - pkl: a Molecule pickle

            - query: a Molecule

            - recursionPossible: (optional)

            - useChirality: (optional)

            - useQueryQueryMatches: use query-query matching logic

          RETURNS: True or False

        C++ signature :
            bool _HasSubstructMatchStr(std::string,RDKit::ROMol [,bool=True [,bool=False [,bool=False]]])

### tossit() |
        C++ signature :
            void tossit()
Returns:
    None :

Variables Details | [hide private]

  ### ALLOW_CHARGE_SEPARATION Value:
      rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION

  ### ALLOW_INCOMPLETE_OCTETS Value:
      rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS

  ### CHI_TETRAHEDRAL_CCW Value:
      rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW

  ### CHI_TETRAHEDRAL_CW Value:
      rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW

  ### COMPOSITE_AND Value:
      rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND

  ### COMPOSITE_XOR Value:
      rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR

  ### ComputedProps Value:
      rdkit.Chem.rdchem.PropertyPickleOptions.ComputedProps

  ### PrivateProps Value:
      rdkit.Chem.rdchem.PropertyPickleOptions.PrivateProps

  ### QueryAtomData Value:
      rdkit.Chem.rdchem.PropertyPickleOptions.QueryAtomData

  ### UNCONSTRAINED_ANIONS Value:
      rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS

  ### UNCONSTRAINED_CATIONS Value:
      rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS