Generate 2D coordinates for a molecule.

Some file formats such as SMILES do not support 2D (or 3D) coordinates for the atoms. Other formats such as SD or MOL have support for coordinates but may not include them. This method will generate reasonable 2D coordinates based purely on connectivity information, overwriting any existing coordinates if present.

Usage

generate.2d.coordinates(mol)

Arguments

mol

The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`

Value

The input molecule, with 2D coordinates added

Details

Note that when depicting a molecule (view.molecule.2d), 2D coordinates are generated, but since it does not modify the input molecule, we do not have access to the generated coordinates.

See also

get.point2d, view.molecule.2d

Author

Rajarshi Guha (rajarshi.guha@gmail.com)