Remove duplicated calculation of coordinates.

In function quasi_newton::operator(), the model coordinates are always updated with the conformer searched from BFGS optimization. https://github.com/ccsb-scripps/AutoDock-Vina/blob/350bb7f28d65265f1c86fa2362d0e469cad8b8fc/src/lib/quasi_newton.cpp#L43-L51

Thus, there is no need to calculate model coordinates in function monte_carlo::operator(). https://github.com/ccsb-scripps/AutoDock-Vina/blob/350bb7f28d65265f1c86fa2362d0e469cad8b8fc/src/lib/monte_carlo.cpp#L59-L74

To ensure consistency, a test is executed between the base commit and the updated one. Bash commands are pasted below:

cd example/basic_docking/
time vina \
  --receptor solution/1iep_receptor.pdbqt \
  --ligand solution/1iep_ligand.pdbqt \
  --config solution/1iep_receptor_vina_box.txt \
  --exhaustiveness 16 \
  --seed 137 \
  --cpu 6 \
  --no_refine  # Observe the output of Monte-Carlo search

It can be verified that generated files solution/1iep_ligand_out.pdbqt are exactly alike.

With this pull request merged, we are convinced that CPU cost will be reduced slightly. My CPU type is `Intel(R) Xeon(R) Platinum 8336C CPU @ 2.30GHz` and average time of 10 runs are: version	real	user	sys
baseline	33.83s	180.47s	0.37s
updated	33.76s	180.20s	0.35s

ccsb-scripps / AutoDock-Vina

Remove duplicated calculation of coordinates. #278