diff --git a/scoring/src/all_atom_clash_score.cc b/scoring/src/all_atom_clash_score.cc
index 1334ad429d8480f7c1a33b279572d143f5cf4ae0..6fb75959d3d45652f2cfaada239ad1d8e6defdfa 100644
--- a/scoring/src/all_atom_clash_score.cc
+++ b/scoring/src/all_atom_clash_score.cc
@@ -38,13 +38,18 @@ AllAtomClashScorer::AllAtomClashScorer(): attached_environment_(false),
}
}
}
+ // special treatment for disulfid bridges
+ clash_type_[loop::CYS_CB] = ALL_ATOM_CLASH_CYS_CB;
+ clash_type_[loop::CYS_SG] = ALL_ATOM_CLASH_CYS_SG;
// setup radii
- Real radius[ALL_ATOM_CLASH_NUM] = {1.6, 1.3, 1.3, 1.7};
+ Real radius[ALL_ATOM_CLASH_NUM] = {1.6, 1.3, 1.3, 1.7, 1.6, 1.7};
cutoff_[ALL_ATOM_CLASH_C] = 3.3;
cutoff_[ALL_ATOM_CLASH_N] = 3.0;
cutoff_[ALL_ATOM_CLASH_O] = 3.0;
cutoff_[ALL_ATOM_CLASH_S] = 3.4;
+ cutoff_[ALL_ATOM_CLASH_CYS_CB] = 3.3;
+ cutoff_[ALL_ATOM_CLASH_CYS_SG] = 3.4;
// energies for each AllAtomClashType pair
// -> see Eq. (11) in Canutescu et al., 2003 "A graph-theory algorithm ..."
@@ -54,7 +59,13 @@ AllAtomClashScorer::AllAtomClashScorer(): attached_environment_(false),
const AllAtomClashType a = AllAtomClashType(i);
for (uint j = 0; j < ALL_ATOM_CLASH_NUM; ++j) {
const AllAtomClashType b = AllAtomClashType(j);
- const Real Rij = radius[i] + radius[j];
+ Real Rij = radius[i] + radius[j];
+ // special treatment for disulfid bridges
+ if (a == ALL_ATOM_CLASH_CYS_SG && b == ALL_ATOM_CLASH_CYS_SG) Rij = 1.5;
+ else if ( (a == ALL_ATOM_CLASH_CYS_SG && b == ALL_ATOM_CLASH_CYS_CB)
+ || (a == ALL_ATOM_CLASH_CYS_CB && b == ALL_ATOM_CLASH_CYS_SG)) {
+ Rij = 2.5;
+ }
for (uint bin = 0; bin < bins_; ++bin) {
Real energy = 0;
const Real r = bin / bins_per_a_;
diff --git a/scoring/src/all_atom_clash_score.hh b/scoring/src/all_atom_clash_score.hh
index f2d11daceb4b1d7d6fc16652de83a2d134f1eb24..8421d59b2d69a21b9a888f244ce7e142438a0fd0 100644
--- a/scoring/src/all_atom_clash_score.hh
+++ b/scoring/src/all_atom_clash_score.hh
@@ -17,6 +17,8 @@ enum AllAtomClashType {
ALL_ATOM_CLASH_N,
ALL_ATOM_CLASH_O,
ALL_ATOM_CLASH_S,
+ ALL_ATOM_CLASH_CYS_CB,
+ ALL_ATOM_CLASH_CYS_SG,
ALL_ATOM_CLASH_NUM
};
diff --git a/scoring/tests/CMakeLists.txt b/scoring/tests/CMakeLists.txt
index 6cdfa7f6f4cd6e82353c9c5a6a678c94f313702f..14b83b104f7d815ebe941cc0b8ed18a39405a8fd 100644
--- a/scoring/tests/CMakeLists.txt
+++ b/scoring/tests/CMakeLists.txt
@@ -6,6 +6,7 @@ set(SCORING_UNIT_TESTS
)
set(SCORING_TEST_DATA
+ data/1CRNA.pdb
data/3DEFA.pdb
data/clash_test.pdb
)
diff --git a/scoring/tests/data/1CRNA.pdb b/scoring/tests/data/1CRNA.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..13ca618d438ae60a55a8ce1c532cd23bf545e200
--- /dev/null
+++ b/scoring/tests/data/1CRNA.pdb
@@ -0,0 +1,329 @@
+ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
+ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
+ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
+ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
+ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C
+ATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N
+ATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C
+ATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C
+ATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O
+ATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C
+ATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C
+ATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C
+ATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S
+ATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C
+ATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C
+ATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S
+ATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C
+ATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C
+ATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C
+ATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N
+ATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C
+ATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C
+ATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O
+ATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C
+ATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O
+ATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C
+ATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C
+ATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C
+ATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C
+ATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C
+ATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C
+ATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C
+ATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C
+ATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C
+ATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C
+ATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C
+ATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N
+ATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N
+ATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C
+ATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C
+ATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O
+ATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C
+ATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O
+ATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C
+ATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C
+ATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N
+ATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N
+ATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C
+ATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C
+ATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C
+ATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C
+ATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C
+ATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C
+ATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N
+ATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C
+ATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C
+ATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C
+ATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C
+ATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C
+ATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O
+ATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S
+ATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C
+ATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C
+ATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N
+ATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C
+ATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C
+ATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C
+ATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C
+ATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C
+ATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C
+ATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C
+ATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C
+ATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O
+ATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N
+ATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C
+ATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C
+ATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O
+ATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C
+ATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C
+ATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C
+ATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C
+ATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C
+ATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C
+ATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C
+ATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
+ATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C
+ATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C
+ATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C
+ATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N
+ATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C
+ATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C
+ATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O
+ATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C
+ATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C
+ATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C
+ATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C
+ATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N
+ATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C
+ATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C
+ATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O
+ATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C
+ATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S
+ATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N
+ATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C
+ATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C
+ATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O
+ATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C
+ATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N
+ATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C
+ATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C
+ATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O
+ATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C
+ATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O
+ATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C
+ATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N
+ATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C
+ATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C
+ATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O
+ATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C
+ATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C
+ATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C
+ATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C
+ATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C
+ATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C
+ATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C
+ATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O
+ATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N
+ATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C
+ATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C
+ATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O
+ATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C
+ATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O
+ATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C
+ATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N
+ATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C
+ATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C
+ATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O
+ATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C
+ATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C
+ATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S
+ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
+ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
+ATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C
+ATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C
+ATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C
+ATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O
+ATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C
+ATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C
+ATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C
+ATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C
+ATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C
+ATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C
+ATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C
+ATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N
+ATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C
+ATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C
+ATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O
+ATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C
+ATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C
+ATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C
+ATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N
+ATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C
+ATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C
+ATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O
+ATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C
+ATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C
+ATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C
+ATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S
+ATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C
+ATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C
+ATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C
+ATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C
+ATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C
+ATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O
+ATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C
+ATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C
+ATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O
+ATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C
+ATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C
+ATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O
+ATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C
+ATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C
+ATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C
+ATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C
+ATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C
+ATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O
+TER 328 ASN A 46
+END
diff --git a/scoring/tests/test_all_atom_scorer.cc b/scoring/tests/test_all_atom_scorer.cc
index b38ba91c82f60c771c050aea6a060a2b6f070560..f9104fbed8d5ddd0d57b9d8ae440abc665a6528a 100644
--- a/scoring/tests/test_all_atom_scorer.cc
+++ b/scoring/tests/test_all_atom_scorer.cc
@@ -155,6 +155,17 @@ BOOST_AUTO_TEST_CASE(test_aa_clash_score2) {
BOOST_CHECK_CLOSE(clash_score, 1.73935568333, Real(1e-3));
}
+BOOST_AUTO_TEST_CASE(test_aa_clash_score3) {
+ // check treatment of disulfid bridges
+ String pdb_name = "data/1CRNA.pdb";
+ promod3::loop::AllAtomEnv env = GenerateAllAtomEnv(pdb_name, "");
+ promod3::loop::AllAtomPositions new_pos = GenerateTestPos(pdb_name, 2, 46);
+ AllAtomClashScorerPtr scorer(new AllAtomClashScorer);
+ scorer->AttachEnvironment(env);
+ Real clash_score = scorer->CalculateScore(new_pos, 2, 0);
+ BOOST_CHECK_CLOSE(clash_score, 0.0, Real(1e-3));
+}
+
BOOST_AUTO_TEST_CASE(test_aa_overall_scorer) {
// setup env
promod3::loop::AllAtomEnv env = GenerateAllAtomEnv();