Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger
The combinatorial library enumeration is carried out by substitution of attachments on the core structure with fragments from the reagent structures. For both the core and the reagents, the bonds to be broken must be designated before-hand. The fragments from the reagents are then attached to the core at the site of the broken bond. This process can be regarded as "growing" the new attachment onto the core in place of the old attachment, and the bond that is replaced (with its attached atoms) is called the grow bond. These bonds are not necessarily the bonds that are broken and formed in the real chemical reaction, but represent a means of varying the attachments to a core structure that might include part of the real reagent. To generate a combinatorial library, you must have a core structure whose attachments you want to replace are defined by setting the s_m_grow_name property of the first atom that defines the attachment bond to '1f' and the second atom to to '1t'. This can be done by either manually editing the core structure file or within Maestro. The second attachment point would be labeled with '2f' and '2t' and so on. For each attachment point, a set of reagent files that define the replacements must be prepared individually using the CombiGen Reagent Preparation node.
To use this node in KNIME, install Schrödinger Nodes for Suite2018-1 from the following update site: