Implicit/Explicit HydrogensΒΆ

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 in their SMILES input, 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. There are two use case for the different depictions of hydrogens, through SMILES Input and opening a file.

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

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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

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When opening a file with explicit hydrogens PICTO will automatically check the Retain Explicit Hydrogens checkbox, but it will not display the hydrogens in the SMILES input. Figure: File opened Explicit Hydrogens displays what occurs after opening a file with explicit hydrogens. The explicit hydrogens will be visible in the sketcher but not in the SMILES input.

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

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Molecule with Explicit Hydrogens in SMILES Input

Molecule Reset due to Selection

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Molecule with Explicit Hydrogens in a File

Molecule Reset due to Selection