Module rdmolfiles

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*

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*

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*

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*

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*

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*

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

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

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

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

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*

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