rdkit.Chem.rdmolfiles

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.
| SmilesParserParams Parameters controlling SMILES Parsing
| 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]
CanonicalRankAtoms(...) CanonicalRankAtoms( (Mol)mol [, (bool)breakTies=True [, (bool)includeChirality=True [, (bool)includeIsotopes=True]]]) -> _vectj : Returns the canonical atom ranking for each atom of a molecule fragment. |
CanonicalRankAtomsInFragment(...) CanonicalRankAtomsInFragment( (Mol)mol, (AtomPairsParameters)atomsToUse [, (AtomPairsParameters)bondsToUse=0 [, (AtomPairsParameters)atomSymbols=0 [, (AtomPairsParameters)bondSymbols=0 [, (bool)breakTies=True]]]]) -> _vecti : Returns the canonical atom ranking for each atom of a molecule fragment See help(CanonicalRankAtoms) for more information. |
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 [, (bool)allHsExplicit=False]]]]]]]]]) -> str : Returns the canonical SMILES string for a fragment of a molecule ARGUMENTS: |
MolFromFASTA(...) MolFromFASTA( (AtomPairsParameters)text [, (bool)sanitize=True [, (int)flavor=0]]) -> Mol : Construct a molecule from a FASTA string (currently only supports peptides). |
MolFromHELM(...) MolFromHELM( (AtomPairsParameters)text [, (bool)sanitize=True]) -> Mol : Construct a molecule from a HELM string (currently only supports peptides). |
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( (AtomPairsParameters)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( (AtomPairsParameters)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. |
MolFromSequence(...) MolFromSequence( (AtomPairsParameters)text [, (bool)sanitize=True [, (int)flavor=0]]) -> Mol : Construct a molecule from a sequence string (currently only supports peptides). |
MolFromSmarts(...) MolFromSmarts( (AtomPairsParameters)SMARTS [, (bool)mergeHs=False [, (dict)replacements={}]]) -> Mol : Construct a molecule from a SMARTS string. |
MolFromSmiles(...) MolFromSmiles( (AtomPairsParameters)SMILES, (SmilesParserParams)params) -> Mol : Construct a molecule from a SMILES string. |
MolFromTPLBlock(...) MolFromTPLBlock( (AtomPairsParameters)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. |
MolToFASTA(...) MolToFASTA( (Mol)mol) -> str : Returns the FASTA string for a molecule ARGUMENTS: |
MolToHELM(...) MolToHELM( (Mol)mol) -> str : Returns the HELM string for a molecule ARGUMENTS: |
MolToMolBlock(...) MolToMolBlock( (Mol)mol [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True [, (bool)forceV3000=False]]]]) -> str : Returns a Mol block for a molecule ARGUMENTS: |
MolToMolFile(...) MolToMolFile( (Mol)mol, (str)filename [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True [, (bool)forceV3000=False]]]]) -> 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: |
MolToSequence(...) MolToSequence( (Mol)mol) -> str : Returns the sequence string 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 [, (bool)allHsExplicit=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]

### CanonicalRankAtoms(...) |
    CanonicalRankAtoms( (Mol)mol [, (bool)breakTies=True [, (bool)includeChirality=True [, (bool)includeIsotopes=True]]]) -> _vectj :
        Returns the canonical atom ranking for each atom of a molecule fragment.
          If breakTies is False, this returns the symmetry class for each atom.  The symmetry
          class is used by the canonicalization routines to type each atom based on the whole
          chemistry of the molecular graph.  Any atom with the same rank (symmetry class) is
          indistinguishable.  For example:

            > mol = MolFromSmiles('C1NCN1')
            > list(CanonicalRankAtoms(mol, breakTies=False))
            [0,1,0,1]

          In this case the carbons have the same symmetry class and the nitrogens have the same
          symmetry class.  From the perspective of the Molecular Graph, they are indentical.

          ARGUMENTS:

            - mol: the molecule
            - breakTies: (optional) force breaking of ranked ties [default=True]
            - includeChirality: (optional) use chiral information when computing rank [default=True]
            - includeIsotopes: (optional) use isotope information when computing rank [default=True]

          RETURNS:

            a string

        C++ signature :
            std::vector<unsigned int, std::allocator<unsigned int> > CanonicalRankAtoms(RDKit::ROMol [,bool=True [,bool=True [,bool=True]]])

### CanonicalRankAtomsInFragment(...) |
    CanonicalRankAtomsInFragment( (Mol)mol, (AtomPairsParameters)atomsToUse [, (AtomPairsParameters)bondsToUse=0 [, (AtomPairsParameters)atomSymbols=0 [, (AtomPairsParameters)bondSymbols=0 [, (bool)breakTies=True]]]]) -> _vecti :
        Returns the canonical atom ranking for each atom of a molecule fragment
          See help(CanonicalRankAtoms) for more information.

           > mol = MolFromSmiles('C1NCN1.C1NCN1')
           > list(CanonicalRankAtomsInFragment(mol, atomsToUse=range(0,4), breakTies=False))
           [0,1,0,1,-1,-1,-1,-1]
           > list(CanonicalRankAtomsInFragment(mol, atomsToUse=range(4,8), breakTies=False))
           [-1,-1,-1,-1,0,1,0,1]

          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.
            - breakTies: (optional) force breaking of ranked ties

          RETURNS:

            a string

        C++ signature :
            std::vector<int, std::allocator<int> > CanonicalRankAtomsInFragment(RDKit::ROMol,boost::python::api::object [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=True]]]])

### 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 [, (bool)allHsExplicit=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.
            - allHsExplicit: (optional) if true, all H counts 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 [,bool=False]]]]]]]]])

### MolFromFASTA(...) |
    MolFromFASTA( (AtomPairsParameters)text [, (bool)sanitize=True [, (int)flavor=0]]) -> Mol :
        Construct a molecule from a FASTA string (currently only supports peptides).

          ARGUMENTS:

            - text: string containing the FASTA

            - sanitize: (optional) toggles sanitization of the molecule.
              Defaults to True.

        - flavor: (optional)
          0 Protein, L amino acids (default)
          1 Protein, D amino acids
          2 RNA, no cap
          3 RNA, 5' cap
          4 RNA, 3' cap
          5 RNA, both caps
          6 DNA, no cap
          7 DNA, 5' cap
          8 DNA, 3' cap
          9 DNA, both caps
          RETURNS:

            a Mol object, None on failure.

        C++ signature :
            RDKit::ROMol* MolFromFASTA(boost::python::api::object [,bool=True [,int=0]])

### MolFromHELM(...) |
    MolFromHELM( (AtomPairsParameters)text [, (bool)sanitize=True]) -> Mol :
        Construct a molecule from a HELM string (currently only supports peptides).

          ARGUMENTS:

            - text: string containing the HELM

            - sanitize: (optional) toggles sanitization of the molecule.
              Defaults to true.

          RETURNS:

            a Mol object, None on failure.

        C++ signature :
            RDKit::ROMol* MolFromHELM(boost::python::api::object [,bool=True])

### 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 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* 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( (AtomPairsParameters)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 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* MolFromMolBlock(boost::python::api::object [,bool=True [,bool=True [,bool=True]]])

    MolFromMolBlock( (AtomPairsParameters)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 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* MolFromMolBlock(boost::python::api::object [,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( (AtomPairsParameters)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 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* MolFromPDBBlock(boost::python::api::object [,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]]])

### MolFromSequence(...) |
    MolFromSequence( (AtomPairsParameters)text [, (bool)sanitize=True [, (int)flavor=0]]) -> Mol :
        Construct a molecule from a sequence string (currently only supports peptides).

          ARGUMENTS:

            - text: string containing the sequence

            - sanitize: (optional) toggles sanitization of the molecule.
              Defaults to True.

            - flavor: (optional)
              0 Protein, L amino acids (default)
              1 Protein, D amino acids
              2 RNA, no cap
              3 RNA, 5' cap
              4 RNA, 3' cap
              5 RNA, both caps
              6 DNA, no cap
              7 DNA, 5' cap
              8 DNA, 3' cap
              9 DNA, both caps

          RETURNS:

            a Mol object, None on failure.

        C++ signature :
            RDKit::ROMol* MolFromSequence(boost::python::api::object [,bool=True [,int=0]])

### MolFromSmarts(...) |
    MolFromSmarts( (AtomPairsParameters)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(boost::python::api::object [,bool=False [,boost::python::dict={}]])

### MolFromSmiles(...) |
    MolFromSmiles( (AtomPairsParameters)SMILES, (SmilesParserParams)params) -> Mol :
        Construct a molecule from a SMILES string.

             ARGUMENTS:

               - SMILES: the smiles string

               - params: used to provide optional parameters for the SMILES parsing

             RETURNS:

               a Mol object, None on failure.

        C++ signature :
            RDKit::ROMol* MolFromSmiles(boost::python::api::object,RDKit::SmilesParserParams)

    MolFromSmiles( (AtomPairsParameters)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 True.

            - 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(boost::python::api::object [,bool=True [,boost::python::dict={}]])

### MolFromTPLBlock(...) |
    MolFromTPLBlock( (AtomPairsParameters)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(boost::python::api::object [,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]])

### MolToFASTA(...) |
    MolToFASTA( (Mol)mol) -> str :
        Returns the FASTA string for a molecule
          ARGUMENTS:

            - mol: the molecule

          NOTE: the molecule should contain monomer information in AtomMonomerInfo structures

          RETURNS:

            a string

        C++ signature :
            std::string MolToFASTA(RDKit::ROMol)

### MolToHELM(...) |
    MolToHELM( (Mol)mol) -> str :
        Returns the HELM string for a molecule
          ARGUMENTS:

            - mol: the molecule

          NOTE: the molecule should contain monomer information in AtomMonomerInfo structures

          RETURNS:

            a string

        C++ signature :
            std::string MolToHELM(RDKit::ROMol)

### MolToMolBlock(...) |
    MolToMolBlock( (Mol)mol [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True [, (bool)forceV3000=False]]]]) -> 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.
            - forceV3000 (optional) force generation a V3000 mol block (happens automatically with
                         more than 999 atoms or bonds)

          RETURNS:

            a string

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

### MolToMolFile(...) |
    MolToMolFile( (Mol)mol, (str)filename [, (bool)includeStereo=False [, (int)confId=-1 [, (bool)kekulize=True [, (bool)forceV3000=False]]]]) -> 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.
            - forceV3000 (optional) force generation a V3000 mol block (happens automatically with
                         more than 999 atoms or bonds)

          RETURNS:

            a string

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

### 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]])

### MolToSequence(...) |
    MolToSequence( (Mol)mol) -> str :
        Returns the sequence string for a molecule
          ARGUMENTS:

            - mol: the molecule

          NOTE: the molecule should contain monomer information in AtomMonomerInfo structures

          RETURNS:

            a string

        C++ signature :
            std::string MolToSequence(RDKit::ROMol)

### MolToSmarts(...) |
    MolToSmarts( (Mol)mol [, (bool)isomericSmiles=False]) -> str :
        Returns a SMARTS string for a molecule
          ARGUMENTS:

            - mol: the molecule
            - isomericSmiles: (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 [, (bool)allHsExplicit=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.
            - allHsExplicit: (optional) if true, all H counts 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 [,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]]]]])