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fix readme example
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clami66 committed May 16, 2024
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Expand Up @@ -142,7 +142,17 @@ Then DockQ will find the interface in the model that best matches the WX interfa
Small molecules in PDB or mmCIF files can be scored and the mapping optimized in the same way as for proteins. Just add the flag `--small_molecules`:

```
$ DockQ examples/example_hetatm.pdb examples/7bbv.cif --small_molecule --mapping :ACDEFGH
# Compare docking of hemoglobin chains (chain A and B in native) as well as HEM and PO4 groups (chains E, F, G)
$ DockQ examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG --short
Total DockQ-small_molecules over 7 native interfaces: 0.614 with ABDCF:ABEFG model:native mapping
DockQ 0.950 irms 0.455 Lrms 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
Lrms 0.592 mapping AD:AE (HEM) examples/1HHO_hem.cif A D -> examples/2HHB_hem.cif A E
Lrms 28.986 mapping AC:AF (PO4) examples/1HHO_hem.cif A C -> examples/2HHB_hem.cif A F
Lrms 2.264 mapping AF:AG (HEM) examples/1HHO_hem.cif A F -> examples/2HHB_hem.cif A G
Lrms 1.267 mapping BD:BE (HEM) examples/1HHO_hem.cif B D -> examples/2HHB_hem.cif B E
Lrms 27.937 mapping BC:BF (PO4) examples/1HHO_hem.cif B C -> examples/2HHB_hem.cif B F
Lrms 1.351 mapping BF:BG (HEM) examples/1HHO_hem.cif B F -> examples/2HHB_hem.cif B G
```

Only LRMSD is reported for small molecules.
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