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.
The script combine_fragments.py is used to implement this node.
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 data table containing molecules in Maestro format
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