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.
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