Correct ligand-receptor energy when no_refine is enabled.

[shishaochen]

According to vina.cpp#L719-L722, function igrid.eval() should return energy between receptor and ligand when vina/vinardo score function is selected.

// Inter
if (m_no_refine || !m_receptor_initialized)
    all_grids = m_grid.eval(m_model, authentic_v[1]); // [1] ligand & flex -- grid
else
    all_grids = m_non_cache.eval(m_model, authentic_v[1]); // [1] ligand & flex -- grid
lig_grids = all_grids - flex_grids;

In default, m_no_refine is false and the behavior of function non_cache.eval() is correct. However, this is not true in function cache.eval().

Since ligand-receptor energy is calculated from all_grids minus flex_grids, this fix is necessary for a correct energy report when no_refine option is enabled in Vina.

Since both non_cache.eval() and cache.eval() are called only when scoring a model, search & optimization procedures won't be affected.

We can quickly verify the behavior change in Vina's score_only mode:

cd example/flexible_docking/solution
vina \
  --receptor 1fpu_receptor_rigid.pdbqt \
  --flex 1fpu_receptor_flex.pdbqt \
  --ligand ../data/1iep_ligand.pdbqt \
  --config 1fpu_receptor_rigid_vina_box.txt \
  --score_only \
  --seed 137 \
  --no_refine \
  --verbosity 2

Inserting extra log lines in vina.cpp, value delta of all_grids between unfixed and fixed equals exactly the value of flex_grids.

• Vina without this fix

[no_refine] all_grids=-4.38079
[no_refine] flex_grids=1.32849

• Vina with this fix

[no_refine] all_grids=-3.0523
[no_refine] flex_grids=1.32849

[diogomart]

Good catch, thank you!