Merge pull request #482 from carlocamilloni/main

small fix to general repulsion rule and updated regtest

Author: carlocamilloni

src/multiego/ensemble.py

@@ -911,13 +911,14 @@ def set_sig_epsilon(meGO_LJ, needed_fields):
     )
 
     # General repulsive term
-    # this is used only when MD_p < RC_p eventually corrected by the ZF
+    # this is used only when MD_th < MD_p < RC_p eventually corrected by the ZF
     # negative epsilon are used to identify non-attractive interactions
     meGO_LJ.loc[
         (
             np.maximum(meGO_LJ["probability"], meGO_LJ["rc_threshold"])
             < meGO_LJ["zf"] * np.maximum(meGO_LJ["rc_probability"], meGO_LJ["rc_threshold"])
-        ),
+        )
+        & (meGO_LJ["probability"] > meGO_LJ["md_threshold"]),
         "epsilon",
     ] = -(meGO_LJ["epsilon_0"] / (np.log(meGO_LJ["zf"] * meGO_LJ["rc_threshold"]))) * meGO_LJ["distance"] ** 12 * (
         np.log(

test/test_outputs/abetaref/case_1/ffnonbonded.itp

@@ -3765,4 +3765,4 @@ OE2_GB_1_Protein_56 OE2_GB_1_Protein_56     1 0.000000e+00 1.965819e-06 ; 0.4321
    O_GB_1_Protein_9   O_GB_1_Protein_53     1 0.000000e+00 3.000001e-06 ; 0.447668 -0.000003          1.0             1.0           1.0           1.0 0.000003 0.502491        True  basic       NaN       NaN
    O_GB_1_Protein_9   O_GB_1_Protein_54     1 0.000000e+00 3.000001e-06 ; 0.447668 -0.000003          1.0             1.0           1.0           1.0 0.000003 0.502491        True  basic       NaN       NaN
    O_GB_1_Protein_9   O_GB_1_Protein_55     1 0.000000e+00 3.000001e-06 ; 0.447668 -0.000003          1.0             1.0           1.0           1.0 0.000003 0.502491        True  basic       NaN       NaN
-   O_GB_1_Protein_9    O_GB_1_Protein_9     1 0.000000e+00 3.000001e-06 ; 0.447668 -0.000003          1.0             1.0           1.0           1.0 0.000003 0.502491        True  basic       NaN       NaN
+   O_GB_1_Protein_9    O_GB_1_Protein_9     1 0.000000e+00 3.000001e-06 ; 0.447668 -0.000003          1.0             1.0           1.0           1.0 0.000003 0.502491        True  basic       NaN       NaN

test/test_outputs/gpref/case_1/ffnonbonded.itp

@@ -29,7 +29,7 @@ while read case; do
     case=${case/"TEST_ROOT"/$TEST_DIR}
     IFS='#' read -r -a array <<< "$case"
     case=$(echo "${array[0]}")
-    out_dir=$(python ${MEGO_ROOT}/multiego.py $case | grep "Output files written to" | awk '{print $5}')
+    out_dir=$(python ${MEGO_ROOT}/multiego.py $case | grep "Output files written to" | awk '{print $6}')
     out_dir=$(realpath $out_dir)
     system=$(dirname $out_dir)
     system=$(basename $system)