Implicit/Explicit Hydrogens

Implicit hydrogens are the hydrogens that are associated with the parent atom, they are not stored as an atom. Explicit hydrogens are the hydrogens that are specified by the user, they are stored as atoms. The default search for SMARTS is conducted using implicit hydrogens. The two options can be toggled at the bottom of PICTO by checking the Retain Explicit Hydrogens checkbox. Using explicit hydrogens allows the user to refine their search for a specific substructure, while implicit hydrogens gives more of a broad search.

An example of a benzene and a SMARTS query with implicit hydrogens can be seen in Figure: Implicit Hydrogens

There are two way to input explicit hydrogens in SMILES notation ([H] and ([H])), each one is dependent on where the hydrogen is added into the input. An example of a chloroethane and a SMARTS query with explicit hydrogens presented in the SMILES input can be seen in Figure: SMILES inputted Explicit Hydrogens

Changes to the sketcher will take in account any existing explicit hydrogens depicted, and hydrogens can be added using the Element tool which will be reflected in the Input text box and the Isomeric SMILES output when the Retain Explicit Hydrogens checkbox is checked.

When opening a file with explicit hydrogens, PICTO will automatically check the Retain Explicit Hydrogens checkbox. Figure: File opened Explicit Hydrogens displays what occurs after opening a file with explicit hydrogens. The explicit hydrogens will be visible in the sketcher, the SMILES input, and Isomeric SMILES output.

When selecting the atoms of a molecule in the Isomeric SMILES output, the SMILES input will reset to the implicit hydrogen based isomeric SMILES of the molecules depicted. The depiction in the sketcher will also reset to display the molecule without explicit hydrogens, and the Retain Explicit Hydrogens checkbox will be unchecked.

Molecule with Explicit Hydrogens in SMILES Input	Molecule Reset due to Selection
Molecule with Explicit Hydrogens in a File	Molecule Reset due to Selection