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add PUResNet rescoring, change name of rescoring output file (from <p…
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…rediction>_rescored.csv to <protein>_rescored.csv)
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@rdk
rdk committed May 31, 2024
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8 changes: 8 additions & 0 deletions distro/test_data/concavity.ds
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# Dataset for rescoring ConCavity predictions / evaluating rescoring.

# Note: 'prank rescore' expects 2 columns: prediction, protein
# Providing protein (with or without ligands) that was used to calculate the prediction is required.
# Proteins have to be liganated only if you want to calculate metrics by running 'prank eval-rescore'.


PARAM.PREDICTION_METHOD=concavity


# specifies that ligands are separated by TER record (relevant only for legacy CHEN11 and derived datasets)
# remove for other datasets
PARAM.LIGANDS_SEPARATED_BY_TER=true


HEADER: prediction protein

predictions/concavity/1a82a.pdb/1a82a_concavity_pocket.pdb liganated/1a82a.pdb
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10 changes: 8 additions & 2 deletions distro/test_data/fpocket.ds
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# Dataset for rescoring Fpocket 1 predictions / evaluating rescoring.
# (predictions generated with Fpocket 1.0)
#
# Note: this dataset (unlike fpocket3.ds) can be used for eval-rescore


# Note: 'prank rescore' expects 2 columns: prediction, protein
# Providing protein (with or without ligands) that was used to calculate the prediction is required.
# Proteins have to be liganated only if you want to calculate metrics by running 'prank eval-rescore'.

# Note: this dataset (unlike fpocket3.ds) CAN be used for eval-rescore
# because protein column points to proteins with known ligands.


PARAM.PREDICTION_METHOD=fpocket


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10 changes: 8 additions & 2 deletions distro/test_data/fpocket3.ds
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# Dataset for rescoring Fpocket 3 predictions.
# (predictions generated with Fpocket 3.1.2 on "./clean" structures)
#
# Note: this dataset (unlike fpocket.ds) cannot be used for eval-rescore


# Note: 'prank rescore' expects 2 columns: prediction, protein
# Providing protein (with or without ligands) that was used to calculate the prediction is required.
# Proteins have to be liganated only if you want to calculate metrics by running 'prank eval-rescore'.

# Note: this dataset (unlike fpocket.ds) CANNOT be used for eval-rescore
# because protein column points to proteins without known ligands.


PARAM.PREDICTION_METHOD=fpocket


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2,511 changes: 2,511 additions & 0 deletions distro/test_data/predictions/PUResNet/pdb/A.pdb
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13,050 changes: 13,050 additions & 0 deletions distro/test_data/predictions/PUResNet/pdb/B.pdb
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2,511 changes: 2,511 additions & 0 deletions distro/test_data/predictions/PUResNet/pdb/C.pdb
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1,018 changes: 1,018 additions & 0 deletions distro/test_data/predictions/PUResNet/pdb/D.pdb
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2,732 changes: 2,732 additions & 0 deletions distro/test_data/predictions/PUResNet/pdb/E.pdb
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3,840 changes: 3,840 additions & 0 deletions distro/test_data/predictions/PUResNet/pdb/F.pdb
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2,511 changes: 2,511 additions & 0 deletions distro/test_data/predictions/PUResNet/predictions/A_2024-05-21_11-58-03.995/pdb/protein.pdb
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108 changes: 108 additions & 0 deletions ...o/test_data/predictions/PUResNet/predictions/A_2024-05-21_11-58-03.995/pocket/0_A_pkt.pdb
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ATOM 967 N LYS A 135 -6.848 76.096 13.058 N
ATOM 968 CA LYS A 135 -7.735 77.215 13.295 C
ATOM 969 C LYS A 135 -7.498 78.385 12.344 C
ATOM 970 O LYS A 135 -6.366 78.785 12.100 O
ATOM 971 CB LYS A 135 -7.546 77.734 14.746 C
ATOM 972 CG LYS A 135 -8.530 78.846 15.153 C
ATOM 973 CD LYS A 135 -8.317 79.320 16.596 C
ATOM 974 CE LYS A 135 -9.257 80.465 16.977 C
ATOM 975 NZ LYS A 135 -8.991 80.873 18.373 N
ATOM 976 N ASN A 136 -8.581 78.997 11.819 N
ATOM 977 CA ASN A 136 -8.493 80.197 11.020 C
ATOM 978 C ASN A 136 -8.390 81.453 11.882 C
ATOM 979 O ASN A 136 -9.243 82.334 11.873 O
ATOM 980 CB ASN A 136 -9.671 80.277 10.031 C
ATOM 981 CG ASN A 136 -9.346 81.205 8.885 C
ATOM 982 OD1 ASN A 136 -8.208 81.068 8.312 O
ATOM 983 ND2 ASN A 136 -10.241 82.055 8.420 N
ATOM 984 N GLY A 137 -7.309 81.563 12.670 N
ATOM 985 CA GLY A 137 -7.051 82.753 13.445 C
ATOM 986 C GLY A 137 -5.608 82.753 13.792 C
ATOM 987 O GLY A 137 -4.906 81.782 13.545 O
ATOM 988 N MET A 138 -5.138 83.847 14.403 N
ATOM 989 CA MET A 138 -3.751 83.990 14.764 C
ATOM 990 C MET A 138 -3.613 84.033 16.264 C
ATOM 991 O MET A 138 -4.289 84.800 16.947 O
ATOM 992 CB MET A 138 -3.168 85.321 14.224 C
ATOM 993 CG MET A 138 -3.155 85.425 12.689 C
ATOM 994 SD MET A 138 -2.026 84.222 11.927 S
ATOM 995 CE MET A 138 -2.554 84.524 10.221 C
ATOM 996 N ASP A 139 -2.677 83.225 16.797 N
ATOM 997 CA ASP A 139 -2.054 83.453 18.080 C
ATOM 998 C ASP A 139 -1.273 84.741 18.040 C
ATOM 999 O ASP A 139 -0.824 85.188 16.988 O
ATOM 1000 CB ASP A 139 -1.036 82.361 18.477 C
ATOM 1001 CG ASP A 139 -1.700 81.023 18.717 C
ATOM 1002 OD1 ASP A 139 -2.944 80.913 18.589 O
ATOM 1003 OD2 ASP A 139 -0.925 80.102 19.074 O
ATOM 1004 N ARG A 140 -1.064 85.398 19.194 N
ATOM 1005 CA ARG A 140 -0.462 86.720 19.160 C
ATOM 1006 C ARG A 140 0.951 86.818 18.590 C
ATOM 1007 O ARG A 140 1.319 87.839 18.019 O
ATOM 1008 CB ARG A 140 -0.530 87.459 20.513 C
ATOM 1009 CG ARG A 140 -1.935 88.026 20.789 C
ATOM 1010 CD ARG A 140 -2.130 88.507 22.230 C
ATOM 1011 NE ARG A 140 -3.569 88.942 22.376 N
ATOM 1012 CZ ARG A 140 -4.066 90.151 22.079 C
ATOM 1013 NH1 ARG A 140 -3.313 91.147 21.631 N
ATOM 1014 NH2 ARG A 140 -5.359 90.421 22.248 N
ATOM 1031 N MET A 143 0.727 86.849 14.488 N
ATOM 1032 CA MET A 143 0.119 87.961 13.784 C
ATOM 1033 C MET A 143 1.084 88.715 12.867 C
ATOM 1034 O MET A 143 2.224 88.970 13.258 O
ATOM 1035 CB MET A 143 -0.567 88.971 14.734 C
ATOM 1036 CG MET A 143 -1.897 88.441 15.292 C
ATOM 1037 SD MET A 143 -2.829 89.637 16.305 S
ATOM 1038 CE MET A 143 -1.532 90.038 17.510 C
ATOM 1086 N THR A 151 -2.699 96.444 17.846 N
ATOM 1087 CA THR A 151 -3.288 95.289 18.496 C
ATOM 1088 C THR A 151 -4.536 95.626 19.279 C
ATOM 1089 O THR A 151 -4.669 96.700 19.855 O
ATOM 1090 CB THR A 151 -2.306 94.584 19.423 C
ATOM 1091 OG1 THR A 151 -1.702 95.485 20.338 O
ATOM 1092 CG2 THR A 151 -1.150 94.037 18.582 C
ATOM 1093 N LEU A 152 -5.490 94.679 19.317 N
ATOM 1094 CA LEU A 152 -6.683 94.793 20.122 C
ATOM 1095 C LEU A 152 -6.573 93.990 21.438 C
ATOM 1096 O LEU A 152 -5.863 92.983 21.501 O
ATOM 1097 CB LEU A 152 -7.860 94.280 19.257 C
ATOM 1098 CG LEU A 152 -9.232 94.518 19.904 C
ATOM 1099 CD1 LEU A 152 -9.479 95.961 20.366 C
ATOM 1100 CD2 LEU A 152 -10.440 94.134 19.070 C
ATOM 1109 N VAL A 154 -9.320 92.569 22.803 N
ATOM 1110 CA VAL A 154 -10.384 91.638 22.486 C
ATOM 1111 C VAL A 154 -9.925 90.574 21.481 C
ATOM 1112 O VAL A 154 -9.040 90.792 20.656 O
ATOM 1113 CB VAL A 154 -11.583 92.392 21.895 C
ATOM 1114 CG1 VAL A 154 -12.848 91.558 21.950 C
ATOM 1115 CG2 VAL A 154 -11.915 93.702 22.629 C
ATOM 1116 N GLY A 155 -10.527 89.364 21.528 N
ATOM 1117 CA GLY A 155 -10.432 88.353 20.474 C
ATOM 1118 C GLY A 155 -11.165 88.717 19.203 C
ATOM 1119 O GLY A 155 -11.955 89.647 19.177 O
ATOM 1120 N VAL A 156 -11.021 87.927 18.111 N
ATOM 1121 CA VAL A 156 -11.926 88.054 16.963 C
ATOM 1122 C VAL A 156 -13.356 87.736 17.337 C
ATOM 1123 O VAL A 156 -14.255 88.531 17.092 O
ATOM 1124 CB VAL A 156 -11.531 87.108 15.830 C
ATOM 1125 CG1 VAL A 156 -12.585 87.079 14.691 C
ATOM 1126 CG2 VAL A 156 -10.183 87.580 15.262 C
ATOM 1127 N ARG A 157 -13.582 86.592 18.016 N
ATOM 1128 CA ARG A 157 -14.881 86.161 18.499 C
ATOM 1129 C ARG A 157 -15.506 87.129 19.485 C
ATOM 1130 O ARG A 157 -16.699 87.399 19.392 O
ATOM 1131 CB ARG A 157 -14.745 84.781 19.194 C
ATOM 1132 CG ARG A 157 -16.068 84.205 19.761 C
ATOM 1133 CD ARG A 157 -15.890 83.184 20.890 C
ATOM 1134 NE ARG A 157 -15.274 83.887 22.071 N
ATOM 1135 CZ ARG A 157 -14.692 83.276 23.112 C
ATOM 1136 NH1 ARG A 157 -14.592 81.959 23.159 N
ATOM 1137 NH2 ARG A 157 -14.239 84.023 24.110 N
ATOM 1138 N ASP A 158 -14.727 87.679 20.431 N
ATOM 1139 CA ASP A 158 -15.232 88.575 21.443 C
ATOM 1140 C ASP A 158 -15.508 89.989 20.876 C
ATOM 1141 O ASP A 158 -16.298 90.749 21.432 O
ATOM 1142 CB ASP A 158 -14.170 88.611 22.583 C
ATOM 1143 CG ASP A 158 -13.954 87.299 23.305 C
ATOM 1144 OD1 ASP A 158 -14.750 86.355 23.101 O
ATOM 1145 OD2 ASP A 158 -12.932 87.193 24.027 O
95 changes: 95 additions & 0 deletions ...o/test_data/predictions/PUResNet/predictions/A_2024-05-21_11-58-03.995/pocket/0_B_pkt.pdb
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ATOM 1239 N LEU B 17 -1.057 95.843 0.300 N
ATOM 1240 CA LEU B 17 0.243 96.054 0.874 C
ATOM 1241 C LEU B 17 1.205 95.337 -0.052 C
ATOM 1242 O LEU B 17 1.219 94.115 -0.146 O
ATOM 1243 CB LEU B 17 0.280 95.475 2.310 C
ATOM 1244 CG LEU B 17 1.593 95.676 3.095 C
ATOM 1245 CD1 LEU B 17 1.913 97.156 3.360 C
ATOM 1246 CD2 LEU B 17 1.493 94.923 4.428 C
ATOM 1379 N TYR B 36 -0.279 101.479 2.217 N
ATOM 1380 CA TYR B 36 -1.311 100.724 1.515 C
ATOM 1381 C TYR B 36 -1.788 101.463 0.299 C
ATOM 1382 O TYR B 36 -1.846 102.693 0.292 O
ATOM 1383 CB TYR B 36 -2.624 100.528 2.322 C
ATOM 1384 CG TYR B 36 -2.351 99.731 3.541 C
ATOM 1385 CD1 TYR B 36 -2.236 98.331 3.517 C
ATOM 1386 CD2 TYR B 36 -2.160 100.415 4.740 C
ATOM 1387 CE1 TYR B 36 -1.917 97.636 4.694 C
ATOM 1388 CE2 TYR B 36 -1.728 99.737 5.877 C
ATOM 1389 CZ TYR B 36 -1.636 98.345 5.866 C
ATOM 1390 OH TYR B 36 -1.333 97.667 7.056 O
ATOM 1497 N PRO B 51 -2.711 105.443 4.984 N
ATOM 1498 CA PRO B 51 -1.782 104.961 5.998 C
ATOM 1499 C PRO B 51 -2.307 103.733 6.726 C
ATOM 1500 O PRO B 51 -1.514 103.079 7.400 O
ATOM 1501 CB PRO B 51 -1.604 106.157 6.947 C
ATOM 1502 CG PRO B 51 -2.865 107.022 6.779 C
ATOM 1503 CD PRO B 51 -3.462 106.622 5.423 C
ATOM 1504 N THR B 52 -3.611 103.394 6.670 N
ATOM 1505 CA THR B 52 -4.137 102.265 7.434 C
ATOM 1506 C THR B 52 -5.362 101.715 6.726 C
ATOM 1507 O THR B 52 -6.042 102.495 6.053 O
ATOM 1508 CB THR B 52 -4.438 102.635 8.900 C
ATOM 1509 OG1 THR B 52 -4.843 101.535 9.699 O
ATOM 1510 CG2 THR B 52 -5.524 103.705 9.058 C
ATOM 1511 N PRO B 53 -5.697 100.420 6.762 N
ATOM 1512 CA PRO B 53 -7.006 99.932 6.355 C
ATOM 1513 C PRO B 53 -8.149 100.396 7.226 C
ATOM 1514 O PRO B 53 -7.955 100.868 8.337 O
ATOM 1515 CB PRO B 53 -6.870 98.411 6.424 C
ATOM 1516 CG PRO B 53 -5.856 98.202 7.532 C
ATOM 1517 CD PRO B 53 -4.874 99.344 7.316 C
ATOM 1560 N VAL B 59 -6.988 93.324 3.889 N
ATOM 1561 CA VAL B 59 -5.593 93.663 3.661 C
ATOM 1562 C VAL B 59 -5.044 92.590 2.775 C
ATOM 1563 O VAL B 59 -4.966 91.435 3.172 O
ATOM 1564 CB VAL B 59 -4.749 93.747 4.928 C
ATOM 1565 CG1 VAL B 59 -3.237 93.881 4.597 C
ATOM 1566 CG2 VAL B 59 -5.233 94.986 5.698 C
ATOM 1937 N MET B 106 -9.008 89.317 11.754 N
ATOM 1938 CA MET B 106 -8.190 89.786 12.834 C
ATOM 1939 C MET B 106 -8.949 90.830 13.564 C
ATOM 1940 O MET B 106 -9.630 91.665 12.977 O
ATOM 1941 CB MET B 106 -6.936 90.523 12.342 C
ATOM 1942 CG MET B 106 -5.879 89.592 11.747 C
ATOM 1943 SD MET B 106 -4.420 90.501 11.137 S
ATOM 1944 CE MET B 106 -5.273 91.709 10.070 C
ATOM 1950 N VAL B 108 -8.336 94.174 15.527 N
ATOM 1951 CA VAL B 108 -7.330 95.212 15.465 C
ATOM 1952 C VAL B 108 -7.887 96.457 16.122 C
ATOM 1953 O VAL B 108 -9.086 96.559 16.376 O
ATOM 1954 CB VAL B 108 -6.927 95.562 14.032 C
ATOM 1955 CG1 VAL B 108 -6.591 94.303 13.204 C
ATOM 1956 CG2 VAL B 108 -8.037 96.328 13.310 C
ATOM 1957 N ALA B 109 -7.021 97.459 16.354 N
ATOM 1958 CA ALA B 109 -7.475 98.817 16.535 C
ATOM 1959 C ALA B 109 -6.957 99.608 15.322 C
ATOM 1960 O ALA B 109 -5.915 99.323 14.745 O
ATOM 1961 CB ALA B 109 -7.188 99.359 17.959 C
ATOM 1962 N VAL B 110 -7.779 100.545 14.805 N
ATOM 1963 CA VAL B 110 -7.544 101.179 13.511 C
ATOM 1964 C VAL B 110 -8.019 102.623 13.607 C
ATOM 1965 O VAL B 110 -9.006 102.919 14.273 O
ATOM 1966 CB VAL B 110 -8.314 100.403 12.431 C
ATOM 1967 CG1 VAL B 110 -8.874 101.241 11.278 C
ATOM 1968 CG2 VAL B 110 -7.427 99.325 11.793 C
ATOM 2044 N ILE B 121 -10.542 93.253 10.629 N
ATOM 2045 CA ILE B 121 -9.853 93.373 9.350 C
ATOM 2046 C ILE B 121 -9.700 91.966 8.821 C
ATOM 2047 O ILE B 121 -9.550 91.023 9.588 O
ATOM 2048 CB ILE B 121 -8.461 93.990 9.507 C
ATOM 2049 CG1 ILE B 121 -8.557 95.413 10.103 C
ATOM 2050 CG2 ILE B 121 -7.641 93.988 8.186 C
ATOM 2051 CD1 ILE B 121 -8.809 96.520 9.085 C
ATOM 2061 N TYR B 123 -7.228 89.628 6.929 N
ATOM 2062 CA TYR B 123 -5.880 89.510 6.428 C
ATOM 2063 C TYR B 123 -5.842 88.484 5.326 C
ATOM 2064 O TYR B 123 -6.262 87.345 5.504 O
ATOM 2065 CB TYR B 123 -4.900 89.087 7.545 C
ATOM 2066 CG TYR B 123 -3.493 89.090 7.043 C
ATOM 2067 CD1 TYR B 123 -2.905 90.282 6.601 C
ATOM 2068 CD2 TYR B 123 -2.777 87.890 6.957 C
ATOM 2069 CE1 TYR B 123 -1.596 90.278 6.114 C
ATOM 2070 CE2 TYR B 123 -1.459 87.889 6.481 C
ATOM 2071 CZ TYR B 123 -0.862 89.093 6.086 C
ATOM 2072 OH TYR B 123 0.499 89.171 5.741 O
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