Package rdkit :: Package Chem :: Module rdmolfiles
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Module rdmolfiles

Module containing RDKit functionality for working with molecular file formats.

Classes [hide private]
  ForwardSDMolSupplier
A class which supplies molecules from file-like object containing SD data.
  PDBWriter
A class for writing molecules to PDB files.
  SDMolSupplier
A class which supplies molecules from an SD file.
  SDWriter
A class for writing molecules to SD files.
  SmilesMolSupplier
A class which supplies molecules from a text file.
  SmilesWriter
A class for writing molecules to text files.
  TDTMolSupplier
A class which supplies molecules from a TDT file.
  TDTWriter
A class for writing molecules to TDT files.
Functions [hide private]
 
MolFragmentToSmiles(...)
MolFragmentToSmiles( (Mol)mol, (AtomPairsParameters)atomsToUse [, (AtomPairsParameters)bondsToUse=0 [, (AtomPairsParameters)atomSymbols=0 [, (AtomPairsParameters)bondSymbols=0 [, (bool)isomericSmiles=False [, (bool)kekuleSmiles=False [, (int)rootedAtAtom=-1 [, (bool)canonical=True [, (bool)allBondsExplicit=False]]]]]]]]) -> str : Returns the canonical SMILES string for a fragment of a molecule ARGUMENTS:
 
MolFromMol2Block(...)
MolFromMol2Block( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True]]) -> Mol : Construct a molecule from a Tripos Mol2 block.
 
MolFromMol2File(...)
MolFromMol2File( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True]]) -> Mol : Construct a molecule from a Tripos Mol2 file.
 
MolFromMolBlock(...)
MolFromMolBlock( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol : Construct a molecule from a Mol block.
 
MolFromMolFile(...)
MolFromMolFile( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol : Construct a molecule from a Mol file.
 
MolFromPDBBlock(...)
MolFromPDBBlock( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True [, (int)flavor=0]]]) -> Mol : Construct a molecule from a PDB block.
 
MolFromPDBFile(...)
MolFromPDBFile( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True [, (int)flavor=0]]]) -> Mol : Construct a molecule from a PDB file.
 
MolFromSmarts(...)
MolFromSmarts( (str)SMARTS [, (bool)mergeHs=False [, (dict)replacements={}]]) -> Mol : Construct a molecule from a SMARTS string.
 
MolFromSmiles(...)
MolFromSmiles( (str)SMILES [, (bool)sanitize=True [, (dict)replacements={}]]) -> Mol : Construct a molecule from a SMILES string.
 
MolFromTPLBlock(...)
MolFromTPLBlock( (str)tplBlock [, (bool)sanitize=True [, (bool)skipFirstConf=False]]) -> Mol : Construct a molecule from a TPL block.
 
MolFromTPLFile(...)
MolFromTPLFile( (str)fileName [, (bool)sanitize=True [, (bool)skipFirstConf=False]]) -> Mol : Construct a molecule from a TPL file.
 
MolToMolBlock(...)
MolToMolBlock( (Mol)mol [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True]]]) -> str : Returns a Mol block for a molecule ARGUMENTS:
 
MolToMolFile(...)
MolToMolFile( (Mol)mol, (str)filename [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True]]]) -> None : Writes a Mol file for a molecule ARGUMENTS:
 
MolToPDBBlock(...)
MolToPDBBlock( (Mol)mol [, (int)confId=-1 [, (int)flavor=0]]) -> str : Returns a PDB block for a molecule ARGUMENTS:
 
MolToPDBFile(...)
MolToPDBFile( (Mol)mol, (str)filename [, (int)confId=-1 [, (int)flavor=0]]) -> None : Writes a PDB file for a molecule ARGUMENTS:
 
MolToSmarts(...)
MolToSmarts( (Mol)mol [, (bool)isomericSmiles=False]) -> str : Returns a SMARTS string for a molecule ARGUMENTS:
 
MolToSmiles(...)
MolToSmiles( (Mol)mol [, (bool)isomericSmiles=False [, (bool)kekuleSmiles=False [, (int)rootedAtAtom=-1 [, (bool)canonical=True [, (bool)allBondsExplicit=False]]]]]) -> str : Returns the canonical SMILES string for a molecule ARGUMENTS:
 
MolToTPLBlock(...)
MolToTPLBlock( (Mol)mol [, (str)partialChargeProp='_GasteigerCharge' [, (bool)writeFirstConfTwice=False]]) -> str : Returns the Tpl block for a molecule.
 
MolToTPLFile(...)
MolToTPLFile( (Mol)mol, (str)fileName [, (str)partialChargeProp='_GasteigerCharge' [, (bool)writeFirstConfTwice=False]]) -> None : Writes a molecule to a TPL file.
 
SmilesMolSupplierFromText(...)
SmilesMolSupplierFromText( (str)text [, (str)delimiter=' ' [, (int)smilesColumn=0 [, (int)nameColumn=1 [, (bool)titleLine=True [, (bool)sanitize=True]]]]]) -> SmilesMolSupplier :
Variables [hide private]
  __package__ = None
hash(x)
Function Details [hide private]

MolFragmentToSmiles(...)

 

MolFragmentToSmiles( (Mol)mol, (AtomPairsParameters)atomsToUse [, (AtomPairsParameters)bondsToUse=0 [, (AtomPairsParameters)atomSymbols=0 [, (AtomPairsParameters)bondSymbols=0 [, (bool)isomericSmiles=False [, (bool)kekuleSmiles=False [, (int)rootedAtAtom=-1 [, (bool)canonical=True [, (bool)allBondsExplicit=False]]]]]]]]) -> str :
    Returns the canonical SMILES string for a fragment of a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - atomsToUse : a list of atoms to include in the fragment
        - bondsToUse : (optional) a list of bonds to include in the fragment
                       if not provided, all bonds between the atoms provided
                       will be included.
        - atomSymbols : (optional) a list with the symbols to use for the atoms
                        in the SMILES. This should have be mol.GetNumAtoms() long.
        - bondSymbols : (optional) a list with the symbols to use for the bonds
                        in the SMILES. This should have be mol.GetNumBonds() long.
        - isomericSmiles: (optional) include information about stereochemistry in
          the SMILES.  Defaults to false.
        - kekuleSmiles: (optional) use the Kekule form (no aromatic bonds) in
          the SMILES.  Defaults to false.
        - rootedAtAtom: (optional) if non-negative, this forces the SMILES 
          to start at a particular atom. Defaults to -1.
        - canonical: (optional) if false no attempt will be made to canonicalize
          the molecule. Defaults to true.
        - allBondsExplicit: (optional) if true, all bond orders will be explicitly indicated
          in the output SMILES. Defaults to false.
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        std::string MolFragmentToSmiles(RDKit::ROMol,boost::python::api::object [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=False [,bool=False [,int=-1 [,bool=True [,bool=False]]]]]]]])

MolFromMol2Block(...)

 

MolFromMol2Block( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True]]) -> Mol :
    Construct a molecule from a Tripos Mol2 block.
    
      NOTE:
         The parser expects the atom-typing scheme used by Corina.
        Atom types from Tripos' dbtranslate are less supported.
        Other atom typing schemes are unlikely to work.
    
      ARGUMENTS:
    
        - mol2Block: string containing the Mol2 block
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to 1.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromMol2Block(std::string [,bool=True [,bool=True]])

MolFromMol2File(...)

 

MolFromMol2File( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True]]) -> Mol :
    Construct a molecule from a Tripos Mol2 file.
    
      NOTE:
         The parser expects the atom-typing scheme used by Corina.
        Atom types from Tripos' dbtranslate are less supported.
        Other atom typing schemes are unlikely to work.
    
      ARGUMENTS:
                                      
        - fileName: name of the file to read
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to true.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromMol2File(char const* [,bool=True [,bool=True]])

MolFromMolBlock(...)

 

MolFromMolBlock( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol :
    Construct a molecule from a Mol block.
    
      ARGUMENTS:
    
        - molBlock: string containing the Mol block
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to 1.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
        - strictParsing: (optional) if this is false, the parser is more lax about.
          correctness of the content.
          Defaults to true.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

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

MolFromMolBlock( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol :
    Construct a molecule from a Mol block.
    
      ARGUMENTS:
    
        - molBlock: string containing the Mol block
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to 1.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
        - strictParsing: (optional) if this is false, the parser is more lax about.
          correctness of the content.
          Defaults to true.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

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

MolFromMolFile(...)

 

MolFromMolFile( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol :
    Construct a molecule from a Mol file.
    
      ARGUMENTS:
    
        - fileName: name of the file to read
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to true.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
        - strictParsing: (optional) if this is false, the parser is more lax about.
          correctness of the content.
          Defaults to true.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromMolFile(char const* [,bool=True [,bool=True [,bool=True]]])

MolFromMolFile( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True [, (bool)strictParsing=True]]]) -> Mol :
    Construct a molecule from a Mol file.
    
      ARGUMENTS:
    
        - fileName: name of the file to read
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to true.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
        - strictParsing: (optional) if this is false, the parser is more lax about.
          correctness of the content.
          Defaults to true.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromMolFile(char const* [,bool=True [,bool=True [,bool=True]]])

MolFromPDBBlock(...)

 

MolFromPDBBlock( (str)molBlock [, (bool)sanitize=True [, (bool)removeHs=True [, (int)flavor=0]]]) -> Mol :
    Construct a molecule from a PDB block.
    
      ARGUMENTS:
    
        - molBlock: string containing the PDB block
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to 1.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
        - flavor: (optional) 
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromPDBBlock(std::string [,bool=True [,bool=True [,unsigned int=0]]])

MolFromPDBFile(...)

 

MolFromPDBFile( (str)molFileName [, (bool)sanitize=True [, (bool)removeHs=True [, (int)flavor=0]]]) -> Mol :
    Construct a molecule from a PDB file.
    
      ARGUMENTS:
    
        - fileName: name of the file to read
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to true.
    
        - removeHs: (optional) toggles removing hydrogens from the molecule.
          This only make sense when sanitization is done.
          Defaults to true.
    
        - flavor: (optional) 
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromPDBFile(char const* [,bool=True [,bool=True [,unsigned int=0]]])

MolFromSmarts(...)

 

MolFromSmarts( (str)SMARTS [, (bool)mergeHs=False [, (dict)replacements={}]]) -> Mol :
    Construct a molecule from a SMARTS string.
    
      ARGUMENTS:
    
        - SMARTS: the smarts string
    
        - mergeHs: (optional) toggles the merging of explicit Hs in the query into the attached
          atoms.  So, for example, 'C[H]' becomes '[C;!H0]'.
          Defaults to 0.
    
        - replacements: (optional) a dictionary of replacement strings (see below)
          Defaults to {}. See the documentation for MolFromSmiles for an explanation.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromSmarts(char const* [,bool=False [,boost::python::dict={}]])

MolFromSmiles(...)

 

MolFromSmiles( (str)SMILES [, (bool)sanitize=True [, (dict)replacements={}]]) -> Mol :
    Construct a molecule from a SMILES string.
    
      ARGUMENTS:
    
        - SMILES: the smiles string
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to 1.
    
        - replacements: (optional) a dictionary of replacement strings (see below)
          Defaults to {}.
    
      RETURNS:
    
        a Mol object, None on failure.
    
       The optional replacements dict can be used to do string substitution of abbreviations 
       in the input SMILES. The set of substitutions is repeatedly looped through until 
       the string no longer changes. It is the responsiblity of the caller to make sure 
       that substitutions results in legal and sensible SMILES. 
     
       Examples of replacements: 
     
         CC{Q}C with {'{Q}':'OCCO'} -> CCOCCOC  
         C{A}C{Q}C with {'{Q}':'OCCO', '{A}':'C1(CC1)'} -> CC1(CC1)COCCOC  
         C{A}C{Q}C with {'{Q}':'{X}CC{X}', '{A}':'C1CC1', '{X}':'N'} -> CC1CC1CCNCCNC  
    
    

    C++ signature :
        RDKit::ROMol* MolFromSmiles(std::string [,bool=True [,boost::python::dict={}]])

MolFromTPLBlock(...)

 

MolFromTPLBlock( (str)tplBlock [, (bool)sanitize=True [, (bool)skipFirstConf=False]]) -> Mol :
    Construct a molecule from a TPL block.
    
      ARGUMENTS:
    
        - fileName: name of the file to read
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to True.
    
        - skipFirstConf: (optional) skips reading the first conformer.
          Defaults to False.
          This should be set to True when reading TPLs written by 
          the CombiCode.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

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

MolFromTPLFile(...)

 

MolFromTPLFile( (str)fileName [, (bool)sanitize=True [, (bool)skipFirstConf=False]]) -> Mol :
    Construct a molecule from a TPL file.
    
      ARGUMENTS:
    
        - fileName: name of the file to read
    
        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to True.
    
        - skipFirstConf: (optional) skips reading the first conformer.
          Defaults to False.
          This should be set to True when reading TPLs written by 
          the CombiCode.
    
      RETURNS:
    
        a Mol object, None on failure.
    
    

    C++ signature :
        RDKit::ROMol* MolFromTPLFile(char const* [,bool=True [,bool=False]])

MolToMolBlock(...)

 

MolToMolBlock( (Mol)mol [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True]]]) -> str :
    Returns a Mol block for a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - includeStereo: (optional) toggles inclusion of stereochemical
                         information in the output
        - confId: (optional) selects which conformation to output (-1 = default)
        - kekulize: (optional) triggers kekulization of the molecule before it's written,
                    as suggested by the MDL spec.
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        std::string MolToMolBlock(RDKit::ROMol [,bool=False [,int=-1 [,bool=True]]])

MolToMolFile(...)

 

MolToMolFile( (Mol)mol, (str)filename [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True]]]) -> None :
    Writes a Mol file for a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - filename: the file to write to
        - includeStereo: (optional) toggles inclusion of stereochemical
                         information in the output
        - confId: (optional) selects which conformation to output (-1 = default)
        - kekulize: (optional) triggers kekulization of the molecule before it's written,
                    as suggested by the MDL spec.
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        void MolToMolFile(RDKit::ROMol,std::string [,bool=False [,int=-1 [,bool=True]]])

MolToPDBBlock(...)

 

MolToPDBBlock( (Mol)mol [, (int)confId=-1 [, (int)flavor=0]]) -> str :
    Returns a PDB block for a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - confId: (optional) selects which conformation to output (-1 = default)
        - flavor: (optional) 
                flavor & 1 : Write MODEL/ENDMDL lines around each record 
                flavor & 2 : Don't write any CONECT records 
                flavor & 4 : Write CONECT records in both directions 
                flavor & 8 : Don't use multiple CONECTs to encode bond order 
                flavor & 16 : Write MASTER record 
                flavor & 32 : Write TER record 
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        std::string MolToPDBBlock(RDKit::ROMol [,int=-1 [,unsigned int=0]])

MolToPDBFile(...)

 

MolToPDBFile( (Mol)mol, (str)filename [, (int)confId=-1 [, (int)flavor=0]]) -> None :
    Writes a PDB file for a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - filename: name of the file to write
        - confId: (optional) selects which conformation to output (-1 = default)
        - flavor: (optional) 
                flavor & 1 : Write MODEL/ENDMDL lines around each record 
                flavor & 2 : Don't write any CONECT records 
                flavor & 4 : Write CONECT records in both directions 
                flavor & 8 : Don't use multiple CONECTs to encode bond order 
                flavor & 16 : Write MASTER record 
                flavor & 32 : Write TER record 
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        void MolToPDBFile(RDKit::ROMol,std::string [,int=-1 [,unsigned int=0]])

MolToSmarts(...)

 

MolToSmarts( (Mol)mol [, (bool)isomericSmiles=False]) -> str :
    Returns a SMARTS string for a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - isomericSmarts: (optional) include information about stereochemistry in
          the SMARTS.  Defaults to false.
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        std::string MolToSmarts(RDKit::ROMol {lvalue} [,bool=False])

MolToSmiles(...)

 

MolToSmiles( (Mol)mol [, (bool)isomericSmiles=False [, (bool)kekuleSmiles=False [, (int)rootedAtAtom=-1 [, (bool)canonical=True [, (bool)allBondsExplicit=False]]]]]) -> str :
    Returns the canonical SMILES string for a molecule
      ARGUMENTS:
    
        - mol: the molecule
        - isomericSmiles: (optional) include information about stereochemistry in
          the SMILES.  Defaults to false.
        - kekuleSmiles: (optional) use the Kekule form (no aromatic bonds) in
          the SMILES.  Defaults to false.
        - rootedAtAtom: (optional) if non-negative, this forces the SMILES 
          to start at a particular atom. Defaults to -1.
        - canonical: (optional) if false no attempt will be made to canonicalize
          the molecule. Defaults to true.
        - allBondsExplicit: (optional) if true, all bond orders will be explicitly indicated
          in the output SMILES. Defaults to false.
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        std::string MolToSmiles(RDKit::ROMol [,bool=False [,bool=False [,int=-1 [,bool=True [,bool=False]]]]])

MolToTPLBlock(...)

 

MolToTPLBlock( (Mol)mol [, (str)partialChargeProp='_GasteigerCharge' [, (bool)writeFirstConfTwice=False]]) -> str :
    Returns the Tpl block for a molecule.
    
      ARGUMENTS:
    
        - mol: the molecule
        - partialChargeProp: name of the property to use for partial charges
          Defaults to '_GasteigerCharge'.
        - writeFirstConfTwice: Defaults to False.
          This should be set to True when writing TPLs to be read by 
          the CombiCode.
    
      RETURNS:
    
        a string
    
    

    C++ signature :
        std::string MolToTPLBlock(RDKit::ROMol [,std::string='_GasteigerCharge' [,bool=False]])

MolToTPLFile(...)

 

MolToTPLFile( (Mol)mol, (str)fileName [, (str)partialChargeProp='_GasteigerCharge' [, (bool)writeFirstConfTwice=False]]) -> None :
    Writes a molecule to a TPL file.
    
      ARGUMENTS:
    
        - mol: the molecule
        - fileName: name of the file to write
        - partialChargeProp: name of the property to use for partial charges
          Defaults to '_GasteigerCharge'.
        - writeFirstConfTwice: Defaults to False.
          This should be set to True when writing TPLs to be read by 
          the CombiCode.
    
    

    C++ signature :
        void MolToTPLFile(RDKit::ROMol,std::string [,std::string='_GasteigerCharge' [,bool=False]])

SmilesMolSupplierFromText(...)

 

SmilesMolSupplierFromText( (str)text [, (str)delimiter=' ' [, (int)smilesColumn=0 [, (int)nameColumn=1 [, (bool)titleLine=True [, (bool)sanitize=True]]]]]) -> SmilesMolSupplier :

    C++ signature :
        RDKit::SmilesMolSupplier* SmilesMolSupplierFromText(std::string [,std::string=' ' [,int=0 [,int=1 [,bool=True [,bool=True]]]]])