Chem.rdchem.Atom

Package Chem :: Module rdchem :: Class Atom |
[hide private]
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# Class Atom

     object --+
              |
    ??.instance --+
                  |
                 Atom

    The class to store Atoms.
    Note that, though it is possible to create one, having an Atom on its own
    (i.e not associated with a molecule) is not particularly useful.

Instance Methods | [hide private]
GetAtomicNum(...) Returns the atomic number. |
GetBonds(...) Returns a read-only sequence of the atom's bonds... |
GetChiralTag(...) C++ signature:... |
GetDegree(...) Returns the degree of the atom in the molecule. |
GetExplicitValence(...) C++ signature: GetExplicitValence(RDKit::Atom {lvalue}, bool forceCalc) -> int Returns the number of explicit Hs on the atom. |
GetFormalCharge(...) C++ signature:... |
GetHybridization(...) Returns the atom's hybridization. |
GetIdx(...) Returns the atom's index (ordering in the molecule)... |
GetImplicitValence(...) C++ signature: GetImplicitValence(RDKit::Atom {lvalue}, bool forceCalc) -> int Returns the number of implicit Hs on the atom. |
GetIsAromatic(...) C++ signature:... |
GetMass(...) C++ signature:... |
GetNeighbors(...) Returns a read-only sequence of the atom's neighbors... |
GetNoImplicit(...) Returns whether or not the atom is *allowed* to have implicit Hs. |
GetNumExplicitHs(...) C++ signature:... |
GetNumImplicitHs(...) Returns the total number of implicit Hs on the atom. |
GetOwningMol(...) Returns the Mol that owns this atom. |
GetProp(...) Returns the value of the property. |
GetSmarts(...) returns the SMARTS (or SMILES) string for an Atom... |
GetSymbol(...) Returns the atomic number (a string)... |
GetTotalNumHs(...) C++ signature: GetTotalNumHs(RDKit::Atom {lvalue}, bool includeNeighbors) -> unsigned int Returns the total number of Hs (explicit and implicit) on the atom. |
HasProp(...) Queries a Atom to see if a particular property has been assigned. |
HasQuery(...) Returns whether or not the atom has an associated query... |
InvertChirality(...) C++ signature:... |
IsInRing(...) Returns whether or not the atom is in a ring... |
IsInRingSize(...) Returns whether or not the atom is in a ring of a particular size. |
Match(...) Returns whether or not this atom matches another Atom. |
SetAtomicNum(...) Sets the atomic number, takes an integer value as an argument... |
SetChiralTag(...) C++ signature:... |
SetFormalCharge(...) C++ signature:... |
SetHybridization(...) Sets the hybridization of the atom. |
SetIsAromatic(...) C++ signature:... |
SetMass(...) C++ signature:... |
SetNoImplicit(...) Sets a marker on the atom that *disallows* implicit Hs. |
SetNumExplicitHs(...) C++ signature:... |
SetProp(...) Sets an atomic property ARGUMENTS: - key: the name of the property to be set (a string). |
__init__(...) C++ signature: __init__(_object*, std::string) -> void* Constructor, takes either an int (atomic number) or a string (atomic symbol). |
Inherited from `unreachable.instance`: `__new__` Inherited from `object`: `__delattr__`, `__getattribute__`, `__hash__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__str__`

Class Variables | [hide private]
| __instance_size__ = `68`

Properties | [hide private]
Inherited from `object`: `__class__`

Method Details | [hide private]

### GetAtomicNum(...) |
    Returns the atomic number.
    C++ signature:
        GetAtomicNum(RDKit::Atom {lvalue}) -> int

### GetBonds(...) |
    Returns a read-only sequence of the atom's bonds

    C++ signature:
        GetBonds(RDKit::Atom*) -> boost::python::tuple

### GetChiralTag(...) |
    C++ signature:
    GetChiralTag(RDKit::Atom {lvalue}) -> RDKit::Atom::ChiralType

### GetDegree(...) |
    Returns the degree of the atom in the molecule.

      The degree of an atom is defined to be its number of
      directly-bonded neighbors.
      The degree is independent of bond orders.

    C++ signature:
        GetDegree(RDKit::Atom {lvalue}) -> unsigned int

### GetExplicitValence(...) |
    C++ signature:
        GetExplicitValence(RDKit::Atom {lvalue}, bool forceCalc) -> int

    Returns the number of explicit Hs on the atom.

      ARGUMENTS:

        - forceCalc: (optional) forces the value to be calculated, even if already cached.
          Defaults to 0.

    C++ signature:
        GetExplicitValence(RDKit::Atom {lvalue}) -> int

### GetFormalCharge(...) |
    C++ signature:
    GetFormalCharge(RDKit::Atom {lvalue}) -> int

### GetHybridization(...) |
    Returns the atom's hybridization.

    C++ signature:
        GetHybridization(RDKit::Atom {lvalue}) -> RDKit::Atom::HybridizationType

### GetIdx(...) |
    Returns the atom's index (ordering in the molecule)

    C++ signature:
        GetIdx(RDKit::Atom {lvalue}) -> unsigned int

### GetImplicitValence(...) |
    C++ signature:
        GetImplicitValence(RDKit::Atom {lvalue}, bool forceCalc) -> int

    Returns the number of implicit Hs on the atom.

      ARGUMENTS:

        - forceCalc: (optional) forces the value to be calculated, even if already cached.
          Defaults to 0.

    C++ signature:
        GetImplicitValence(RDKit::Atom {lvalue}) -> int

### GetIsAromatic(...) |
    C++ signature:
    GetIsAromatic(RDKit::Atom {lvalue}) -> bool

### GetMass(...) |
    C++ signature:
    GetMass(RDKit::Atom {lvalue}) -> double

### GetNeighbors(...) |
    Returns a read-only sequence of the atom's neighbors

    C++ signature:
        GetNeighbors(RDKit::Atom*) -> boost::python::tuple

### GetNoImplicit(...) |
    Returns whether or not the atom is *allowed* to have implicit Hs.

    C++ signature:
        GetNoImplicit(RDKit::Atom {lvalue}) -> bool

### GetNumExplicitHs(...) |
    C++ signature:
    GetNumExplicitHs(RDKit::Atom {lvalue}) -> unsigned int

### GetNumImplicitHs(...) |
    Returns the total number of implicit Hs on the atom.

    C++ signature:
        GetNumImplicitHs(RDKit::Atom {lvalue}) -> unsigned int

### GetOwningMol(...) |
    Returns the Mol that owns this atom.

    C++ signature:
        GetOwningMol(RDKit::Atom {lvalue}) -> RDKit::ROMol

### GetProp(...) |
    Returns the value of the property.

      ARGUMENTS:
        - key: the name of the property to return (a string).

      RETURNS: a string

      NOTE:
        - If the property has not been set, a KeyError exception will be raised.

    C++ signature:
        GetProp(RDKit::Atom const*, char const*) -> std::string

### GetSmarts(...) |
    returns the SMARTS (or SMILES) string for an Atom

    C++ signature:
        GetSmarts(RDKit::Atom const*) -> std::string

### GetSymbol(...) |
    Returns the atomic number (a string)

    C++ signature:
        GetSymbol(RDKit::Atom {lvalue}) -> std::string

### GetTotalNumHs(...) |
    C++ signature:
        GetTotalNumHs(RDKit::Atom {lvalue}, bool includeNeighbors) -> unsigned int

    Returns the total number of Hs (explicit and implicit) on the atom.

      ARGUMENTS:

        - includeNeighbors: (optional) toggles inclusion of neighboring H atoms in the sum.
          Defaults to 0.

    C++ signature:
        GetTotalNumHs(RDKit::Atom {lvalue}) -> unsigned int

### HasProp(...) |
    Queries a Atom to see if a particular property has been assigned.

      ARGUMENTS:
        - key: the name of the property to check for (a string).

    C++ signature:
        HasProp(RDKit::Atom const*, char const*) -> int

### HasQuery(...) |
    Returns whether or not the atom has an associated query

    C++ signature:
        HasQuery(RDKit::Atom {lvalue}) -> bool

### InvertChirality(...) |
    C++ signature:
    InvertChirality(RDKit::Atom {lvalue}) -> void*

### IsInRing(...) |
    Returns whether or not the atom is in a ring

    C++ signature:
        IsInRing(RDKit::Atom const*) -> bool

### IsInRingSize(...) |
    Returns whether or not the atom is in a ring of a particular size.

      ARGUMENTS:
        - size: the ring size to look for

    C++ signature:
        IsInRingSize(RDKit::Atom const*, int) -> bool

### Match(...) |
    Returns whether or not this atom matches another Atom.

      Each Atom (or query Atom) has a query function which is
      used for this type of matching.

      ARGUMENTS:
        - other: the other Atom to which to compare

    C++ signature:
        Match(RDKit::Atom {lvalue}, RDKit::Atom const*) -> bool

### SetAtomicNum(...) |
    Sets the atomic number, takes an integer value as an argument
    C++ signature:
        SetAtomicNum(RDKit::Atom {lvalue}, int) -> void*

### SetChiralTag(...) |
    C++ signature:
    SetChiralTag(RDKit::Atom {lvalue}, RDKit::Atom::ChiralType) -> void*

### SetFormalCharge(...) |
    C++ signature:
    SetFormalCharge(RDKit::Atom {lvalue}, int) -> void*

### SetHybridization(...) |
    Sets the hybridization of the atom.
      The argument should be a HybridizationType

    C++ signature:
        SetHybridization(RDKit::Atom {lvalue}, RDKit::Atom::HybridizationType) -> void*

### SetIsAromatic(...) |
    C++ signature:
    SetIsAromatic(RDKit::Atom {lvalue}, bool) -> void*

### SetMass(...) |
    C++ signature:
    SetMass(RDKit::Atom {lvalue}, double) -> void*

### SetNoImplicit(...) |
    Sets a marker on the atom that *disallows* implicit Hs.
      This holds even if the atom would otherwise have implicit Hs added.

    C++ signature:
        SetNoImplicit(RDKit::Atom {lvalue}, bool) -> void*

### SetNumExplicitHs(...) |
    C++ signature:
    SetNumExplicitHs(RDKit::Atom {lvalue}, unsigned int) -> void*

### SetProp(...) |
    Sets an atomic property

      ARGUMENTS:
        - key: the name of the property to be set (a string).
        - value: the property value (a string).

    C++ signature:
        SetProp(RDKit::Atom const* self, char const* key, std::string val) -> void*

### __init__(...) (Constructor) |
    C++ signature:
        __init__(_object*, std::string) -> void*

    Constructor, takes either an int (atomic number) or a string (atomic symbol).

    C++ signature:
        __init__(_object*, unsigned int) -> void*
Overrides: object.__init__