Chem.rdmolfiles

Package Chem :: Module rdmolfiles |
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# Module rdmolfiles

    Module containing RDKit functionality for working with molecular file formats.

Classes | [hide private]
| 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]
MolFromMolBlock(...) Construct a molecule from a Mol block. | source code
MolFromMolFile(...) Construct a molecule from a Mol file. | source code
MolFromSmarts(...) Construct a molecule from a SMARTS string. | source code
MolFromSmiles(...) Construct a molecule from a SMILES string. | source code
MolFromTPLBlock(...) Construct a molecule from a TPL block. | source code
MolFromTPLFile(...) Construct a molecule from a TPL file. | source code
MolToMolBlock(...) Returns the a Mol block for a molecule... | source code
MolToSmarts(...) Returns a SMARTS string for a molecule ARGUMENTS: - mol: the molecule - isomericSmarts: (optional) include information about stereochemistry in the SMARTS. | source code
MolToSmiles(...) Returns the canonical SMILES string for a molecule ARGUMENTS: - mol: the molecule - isomericSmiles: (optional) include information about stereochemistry in the SMILES. | source code
MolToTPLBlock(...) Returns the Tpl block for a molecule. | source code
MolToTPLFile(...) Writes a molecule to a TPL file. | source code
SmilesMolSupplierFromText(...) C++ signature:... | source code

Function Details | [hide private]

### MolFromMolBlock(...) | source code
    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.

      RETURNS:

        a Mol object, None on failure.

    C++ signature:
        MolFromMolBlock(std::string molBlock, bool sanitize=True, bool removeHs=True) -> RDKit::ROMol*

### MolFromMolFile(...) | source code
    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.

      RETURNS:

        a Mol object, None on failure.

    C++ signature:
        MolFromMolFile(char const* molFileName, bool sanitize=True, bool removeHs=True) -> RDKit::ROMol*

### MolFromSmarts(...) | source code
    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.

      RETURNS:

        a Mol object, None on failure.

    C++ signature:
        MolFromSmarts(char const* SMARTS, bool mergeHs=False) -> RDKit::ROMol*

### MolFromSmiles(...) | source code
    Construct a molecule from a SMILES string.

      ARGUMENTS:

        - SMILES: the smiles string

        - sanitize: (optional) toggles sanitization of the molecule.
          Defaults to 1.

      RETURNS:

        a Mol object, None on failure.

    C++ signature:
        MolFromSmiles(std::string SMILES, bool sanitize=True) -> RDKit::ROMol*

### MolFromTPLBlock(...) | source code
    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:
        MolFromTPLBlock(std::string tplBlock, bool sanitize=True, bool skipFirstConf=False) -> RDKit::ROMol*

### MolFromTPLFile(...) | source code
    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:
        MolFromTPLFile(char const* fileName, bool sanitize=True, bool skipFirstConf=False) -> RDKit::ROMol*

### MolToMolBlock(...) | source code
    Returns the 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)

      RETURNS:

        a string

    C++ signature:
        MolToMolBlock(RDKit::ROMol mol, bool includeStereo=False, int confId=-1) -> std::string

### MolToSmarts(...) | source code
    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:
        MolToSmarts(RDKit::ROMol {lvalue} mol, bool isomericSmiles=False) -> std::string

### MolToSmiles(...) | source code
    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.

      RETURNS:

        a string

    C++ signature:
        MolToSmiles(RDKit::ROMol {lvalue} mol, bool isomericSmiles=False, bool kekuleSmiles=False, int rootedAtAtom=-1) -> std::string

### MolToTPLBlock(...) | source code
    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:
        MolToTPLBlock(RDKit::ROMol mol, std::string partialChargeProp='_GasteigerCharge', bool writeFirstConfTwice=False) -> std::string

### MolToTPLFile(...) | source code
    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:
        MolToTPLFile(RDKit::ROMol mol, std::string fileName, std::string partialChargeProp='_GasteigerCharge', bool writeFirstConfTwice=False) -> void*

### SmilesMolSupplierFromText(...) | source code
    C++ signature:
    SmilesMolSupplierFromText(std::string text, std::string delimiter=' ', int smilesColumn=0, int nameColumn=1, bool titleLine=True, bool sanitize=True) -> RDKit::SmilesMolSupplier*