Package rdkit :: Package Chem :: Module rdmolfiles :: Class SDWriter

class SDWriter

 object --+    
          |    
??.instance --+
              |
             SDWriter

A class for writing molecules to SD files.

Usage examples:

  1) writing to a named file:
     >>> writer = SDWriter('out.sdf')
     >>> for mol in list_of_mols:
     ...    writer.write(mol)

  2) writing to a file-like object: 
     >>> import gzip
     >>> outf=gzip.open('out.sdf.gz','w+')
     >>> writer = SDWriter(outf)
     >>> for mol in list_of_mols:
      ...   writer.write(mol)
     >>> writer.close()
     >>> outf.close()

By default all non-private molecular properties are written to the SD file.
This can be changed using the SetProps method:
     >>> writer = SDWriter('out.sdf')
     >>> writer.SetProps(['prop1','prop2'])

Instance Methods

[hide private]

GetForceV3000(...)
GetForceV3000( (SDWriter)arg1) -> bool : Returns whether or not V3000 mol file writing is being forced.

GetKekulize(...)
GetKekulize( (SDWriter)arg1) -> bool : Returns whether or not molecules are kekulized on writing.

NumMols(...)
NumMols( (SDWriter)arg1) -> int : Returns the number of molecules written so far.

SetForceV3000(...)
SetForceV3000( (SDWriter)arg1, (bool)arg2) -> None : Sets whether or not V3000 mol file writing is being forced.

SetKekulize(...)
SetKekulize( (SDWriter)arg1, (bool)arg2) -> None : Sets whether or not molecules are kekulized on writing.

SetProps(...)
SetProps( (SDWriter)arg1, (AtomPairsParameters)arg2) -> None : Sets the properties to be written to the output file

__init__(...)
__init__( (AtomPairsParameters)arg1, (AtomPairsParameters)arg2) -> object :

__reduce__(...)

close(...)
close( (SDWriter)arg1) -> None : Flushes the output file and closes it.

flush(...)
flush( (SDWriter)arg1) -> None : Flushes the output file (forces the disk file to be updated).

write(...)
write( (SDWriter)self, (Mol)mol [, (int)confId=-1]) -> None : Writes a molecule to the output file.

Inherited from unreachable.instance: __new__

Static Methods

[hide private]

GetText(...)
GetText( (Mol)mol [, (int)confId=-1 [, (bool)kekulize=True [, (bool)force_v3000=False [, (int)molid=-1]]]]) -> str : returns the SD text for a molecule

Method Details

[hide private]

GetForceV3000(...)


GetForceV3000( (SDWriter)arg1) -> bool :
    Returns whether or not V3000 mol file writing is being forced.
    
    

    C++ signature :
        bool GetForceV3000(RDKit::SDWriter {lvalue})

GetKekulize(...)


GetKekulize( (SDWriter)arg1) -> bool :
    Returns whether or not molecules are kekulized on writing.
    
    

    C++ signature :
        bool GetKekulize(RDKit::SDWriter {lvalue})

GetText(...)
Static Method


GetText( (Mol)mol [, (int)confId=-1 [, (bool)kekulize=True [, (bool)force_v3000=False [, (int)molid=-1]]]]) -> str :
    returns the SD text for a molecule

    C++ signature :
        std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetText(RDKit::ROMol [,int=-1 [,bool=True [,bool=False [,int=-1]]]])

NumMols(...)


NumMols( (SDWriter)arg1) -> int :
    Returns the number of molecules written so far.
    
    

    C++ signature :
        unsigned int NumMols(RDKit::SDWriter {lvalue})

SetForceV3000(...)


SetForceV3000( (SDWriter)arg1, (bool)arg2) -> None :
    Sets whether or not V3000 mol file writing is being forced.
    
    

    C++ signature :
        void SetForceV3000(RDKit::SDWriter {lvalue},bool)

SetKekulize(...)


SetKekulize( (SDWriter)arg1, (bool)arg2) -> None :
    Sets whether or not molecules are kekulized on writing.
    
    

    C++ signature :
        void SetKekulize(RDKit::SDWriter {lvalue},bool)

SetProps(...)


SetProps( (SDWriter)arg1, (AtomPairsParameters)arg2) -> None :
    Sets the properties to be written to the output file
    
      ARGUMENTS:
    
        - props: a list or tuple of property names
    
    

    C++ signature :
        void SetProps(RDKit::SDWriter {lvalue},boost::python::api::object)

init(...)
(Constructor)


__init__( (AtomPairsParameters)arg1, (AtomPairsParameters)arg2) -> object :

    C++ signature :
        void* __init__(boost::python::api::object,boost::python::api::object {lvalue})

__init__( (object)arg1, (str)fileName) -> None :
    Constructor.
    
       If a string argument is provided, it will be treated as the name of the output file.
       If a file-like object is provided, output will be sent there.
    
    

    C++ signature :
        void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

Overrides: object.__init__

reduce(...)

Overrides: object.__reduce__: (inherited documentation)

close(...)


close( (SDWriter)arg1) -> None :
    Flushes the output file and closes it. The Writer cannot be used after this.
    
    

    C++ signature :
        void close(RDKit::SDWriter {lvalue})

flush(...)


flush( (SDWriter)arg1) -> None :
    Flushes the output file (forces the disk file to be updated).
    
    

    C++ signature :
        void flush(RDKit::SDWriter {lvalue})

write(...)


write( (SDWriter)self, (Mol)mol [, (int)confId=-1]) -> None :
    Writes a molecule to the output file.
    
      ARGUMENTS:
    
        - mol: the Mol to be written
        - confId: (optional) ID of the conformation to write
    
    

    C++ signature :
        void write(RDKit::SDWriter {lvalue},RDKit::ROMol {lvalue} [,int=-1])

class SDWriter

GetForceV3000(...)

GetKekulize(...)

GetText(...) Static Method

NumMols(...)

SetForceV3000(...)

SetKekulize(...)

SetProps(...)

__init__(...) (Constructor)

__reduce__(...)

close(...)

flush(...)

write(...)

GetText(...)
Static Method

init(...)
(Constructor)

reduce(...)