This script joins molecules together based on how well C-H bonds are aligned. The input can be structures in which the molecules are in the same frame of reference, for example from a fragment docking calculation. Also, input can come from the script fragment_molecule.py that breaks molecules into fragments. In that case, the input to fragment_molecule.py should either be docked ligands or ligands from crystal structures in which the proteins have been superimposed. The joined molecules are ranked by the join_score, which combines the bond deviation, angle deviation, and the GlideScore of the fragments, if present.

Backend implementation

combine_fragments.py
The script combine_fragments.py is used to implement this node.

Options

Number of molecules to output

Number of molecules to output based on join_score

Maximum angle deviation for new bond

Maximum angle deviation (in degrees) between two comparison X-H bonds to make a new bond

Maximum distance deviation from optimal bond length

Distance threshold to skip fragments

Fragments are skipped if their centers are closer to each other than this value

Number of rounds

For each round, new molecules can be made with the resulting molecules from the previous round.

Input Ports

Input data table containing molecules in Maestro format

Output Ports

Joined (adjusted) structures in Maestro format

Views

Std output/error of fragment_join.py

Std output/error of fragment_join.py

Best Friends (Incoming)

• Molecule Reader (to MAE) (25 %) 
• Molecule-to-MAE (25 %) 
• MMP Fragmentation Type Loop Start (25 %) 
• Concatenate (Optional in) (25 %) Streamable

Best Friends (Outgoing)

• Molecule Writer (from MAE) (100 %) 

Installation

To use this node in KNIME, install Schrödinger extension for KNIME Workbench from the following update site: