Named Reactions
ADMET Predictor maintains an internal list of special names that are used to request fixed reactions. The list of recognized names is shown below.
Remove_Smallest_Fragments removes the smallest fragments (connected components) from a compound, such that only the fragment (molecule) having the largest number of atoms is retained. This reaction is generally used to strip counter ions, salts and other "spectator" fragments from a molecule.
Remove_Common_Fragments removes fragments contained in "CommonFragments.smi", a user-modifiable file contained in the ADMET Predictor installation folder. This reaction is generally used to strip counter ions from salts and water from hydrates.
Standardize_Functional_Groups converts certain functional groups to a standardized representation. For example, nitro groups with pentavalent nitrogen (SMILES N(=O)(=O)) are converted to tetravalent nitrogen ([N+](=O)[O-]).
Standardize_Masses converts all atoms to their most common isotopes.
Standardize_Tautomers converts the molecule to a standardized tautomeric form. The algorithms used for tautomer enumeration and tautomer standardization are based on the advanced tautomer settings described here. Two additional fixed reactions are available to force the use of a particular standardization algorithm: Standardize_Tautomers_Rules invokes the rule-based method, while Standardize_Tautomers_Model invokes the model-based method.
Neutralize converts certain ionized acidic and basic groups to their neutral form. For example, [O-] is converted to [OH] and [NH+] is converted to [N].
Remove_Stereocenters removes all atom and bond stereocenters.
Remove_Atom_Stereocenters removes all atom stereocenters.
Remove_Bond_Stereocenters removes all bond stereocenters.
Remove_Invalid_Stereo removes all up and down wedges not connected to a valid stereocenter.
Split_Connected_Components generates a separate product molecule for each connected component.
Generally, these names are used in conjunction with the “NRX” tag to form an encoded reaction (discussed in the Encoded Reactions section). For instance, the reaction
NRX Remove_Small_Fragments + NRX Neutralize
can be used to strip salts and ions from a molecule and then neutralize the remaining portion. Note that when performing reactions, the “NRX” tag is optional; thus the reaction “Remove_Small_Fragments + Neutralize” will be recognized as valid. See the Encoded Reactions section for more information about this syntax.