DeprecatedDeprecated Nodes version 220.127.116.11102141445 by Schrödinger
Reagent preparation ensures that the input structures are all-atom, 3D structures, and that they have the appropriate information stored with them to construct the molecules that are used in screening or are added to the library. Apart from 2D-to-3D conversion and structure variation and cleanup, which is performed by LigPrep, the main task in this node is to select a reagent type (a functional group) and to identify the bond in the functional group that is replaced when the reagent is added to the core. The reagent preparation job attempts to identify the selected functional group in each structure. Structures that match are then prepared using LigPrep. The structure source does not therefore need to contain only structures that have the desired functional group: structures that don't are filtered out. Duplicates are not filtered out, however, so you should ensure that the input file does not contain duplicates. The output file contains the prepared reagents. There might be several output structures per input structure if the molecule can exist in several low-energy forms. You must run this node for each reagent type that will be used in combinatorial screening or combinatorial library enumeration.
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