BioSimSpace.Convert.smiles(smiles_string, add_hydrogens=True, generate_coordinates=True, property_map={})[source]#

Generate a BioSimSpace Molecule froma SMILES string.

  • smiles_string (str) – The molecule in SMILES string format.

  • add_hydrogens (bool) – Whether or not to automatically add hydrogens.

  • generate_coordinates (bool) – Whether or not to automatically generate coordinates. Note that generating the coordinates will automatically switch on addition of hydrogens.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }


molecule – A BioSimSpace molecule.

Return type: