Layne-Huang
commented
2 months ago Hi,
Could you try the newest model file models/epsnet/MDM_pocket_coor_shared.py and sample_frag.py? We have modified these two scripts.
Closed BLEACH366 closed 1 month ago
Layne-Huang
commented
2 months ago Hi,
Could you try the newest model file models/epsnet/MDM_pocket_coor_shared.py and sample_frag.py? We have modified these two scripts.
BLEACH366
commented
2 months ago Hi，
These results are produced just by the newest model.
When I use the old model, I get a lot of '.' in smile, and I follow #12 to update the model, there are no '.' in smile in new results, but the problem I mentioned above happened.
Layne-Huang
commented
2 months ago You could provide you command, the molecule and pocket file. I will help you on it.
BLEACH366
commented
2 months ago Thank you. Here is the pocket .pdb file:
HEADER POCKET
COMPND POCKET
ATOM 195 N GLY B 108 134.553 106.556 -43.313 1.00 11.01 N
ATOM 196 CA GLY B 108 134.485 107.239 -42.019 1.00 11.49 C
ATOM 197 C GLY B 108 133.858 106.339 -40.939 1.00 11.71 C
ATOM 198 O GLY B 108 133.206 106.863 -40.038 1.00 11.06 O
ATOM 199 H GLY B 108 135.435 106.135 -43.571 1.00 0.00 H
ATOM 200 HA3 GLY B 108 133.906 108.160 -42.105 1.00 0.00 H
ATOM 201 HA2 GLY B 108 135.486 107.546 -41.725 1.00 0.00 H
ATOM 202 N PHE B 109 134.003 105.005 -41.052 1.00 10.68 N
ATOM 203 CA PHE B 109 133.350 104.000 -40.210 1.00 9.54 C
ATOM 204 C PHE B 109 133.770 104.033 -38.728 1.00 9.18 C
ATOM 205 O PHE B 109 134.960 103.971 -38.433 1.00 9.41 O
ATOM 206 CB PHE B 109 133.528 102.599 -40.837 1.00 8.22 C
ATOM 207 CG PHE B 109 132.886 101.459 -40.058 1.00 8.07 C
ATOM 208 CD1 PHE B 109 131.487 101.282 -40.105 1.00 9.46 C
ATOM 209 CD2 PHE B 109 133.645 100.690 -39.148 1.00 8.90 C
ATOM 210 CE1 PHE B 109 130.879 100.331 -39.298 1.00 11.92 C
ATOM 211 CE2 PHE B 109 133.018 99.741 -38.350 1.00 9.19 C
ATOM 212 CZ PHE B 109 131.641 99.564 -38.427 1.00 11.29 C
ATOM 213 H PHE B 109 134.584 104.640 -41.796 1.00 0.00 H
ATOM 214 HA PHE B 109 132.287 104.219 -40.255 1.00 0.00 H
ATOM 215 HB3 PHE B 109 134.587 102.385 -40.985 1.00 0.00 H
ATOM 216 HB2 PHE B 109 133.081 102.605 -41.831 1.00 0.00 H
ATOM 217 HD1 PHE B 109 130.883 101.891 -40.762 1.00 0.00 H
ATOM 218 HD2 PHE B 109 134.710 100.845 -39.059 1.00 0.00 H
ATOM 219 HE1 PHE B 109 129.808 100.194 -39.340 1.00 0.00 H
ATOM 220 HE2 PHE B 109 133.600 99.150 -37.657 1.00 0.00 H
ATOM 221 HZ PHE B 109 131.153 98.838 -37.796 1.00 0.00 H
ATOM 222 N ARG B 110 132.776 104.058 -37.829 1.00 8.52 N
ATOM 223 CA ARG B 110 132.956 103.963 -36.380 1.00 8.56 C
ATOM 224 C ARG B 110 131.637 103.554 -35.712 1.00 6.49 C
ATOM 225 O ARG B 110 130.565 103.713 -36.299 1.00 8.95 O
ATOM 226 CB ARG B 110 133.547 105.269 -35.783 1.00 9.96 C
ATOM 227 CG ARG B 110 132.606 106.488 -35.651 1.00 9.82 C
ATOM 228 CD ARG B 110 132.275 107.168 -36.985 1.00 8.92 C
ATOM 229 NE ARG B 110 131.344 108.292 -36.826 1.00 11.19 N
ATOM 230 CZ ARG B 110 131.063 109.182 -37.793 1.00 14.07 C
ATOM 231 NH1 ARG B 110 131.622 109.081 -39.005 1.00 17.53 N
ATOM 232 NH2 ARG B 110 130.217 110.190 -37.550 1.00 17.05 N1+
ATOM 233 H ARG B 110 131.816 104.099 -38.146 1.00 0.00 H
ATOM 234 HA ARG B 110 133.663 103.152 -36.192 1.00 0.00 H
ATOM 235 HB3 ARG B 110 134.444 105.559 -36.329 1.00 0.00 H
ATOM 236 HB2 ARG B 110 133.899 105.030 -34.778 1.00 0.00 H
ATOM 237 HG3 ARG B 110 133.168 107.217 -35.065 1.00 0.00 H
ATOM 238 HG2 ARG B 110 131.709 106.282 -35.066 1.00 0.00 H
ATOM 239 HD3 ARG B 110 131.932 106.475 -37.748 1.00 0.00 H
ATOM 240 HD2 ARG B 110 133.198 107.618 -37.353 1.00 0.00 H
ATOM 241 HE ARG B 110 130.881 108.372 -35.932 1.00 0.00 H
ATOM 242 HH12 ARG B 110 131.491 109.815 -39.703 1.00 0.00 H
ATOM 243 HH11 ARG B 110 132.246 108.313 -39.221 1.00 0.00 H
ATOM 244 HH22 ARG B 110 130.022 110.865 -38.276 1.00 0.00 H
ATOM 245 HH21 ARG B 110 129.783 110.294 -36.644 1.00 0.00 H
ATOM 742 N GLN B 144 125.273 100.938 -32.574 1.00 8.26 N
ATOM 743 CA GLN B 144 125.076 101.840 -33.707 1.00 7.82 C
ATOM 744 C GLN B 144 126.288 101.787 -34.647 1.00 7.37 C
ATOM 745 O GLN B 144 127.411 101.585 -34.191 1.00 8.72 O
ATOM 746 CB GLN B 144 124.898 103.288 -33.214 1.00 9.44 C
ATOM 747 CG GLN B 144 123.800 103.488 -32.152 1.00 10.93 C
ATOM 748 CD GLN B 144 123.695 104.948 -31.704 1.00 12.16 C
ATOM 749 OE1 GLN B 144 124.699 105.650 -31.592 1.00 11.91 O
ATOM 750 NE2 GLN B 144 122.476 105.409 -31.425 1.00 18.72 N
ATOM 751 H GLN B 144 125.605 101.370 -31.722 1.00 0.00 H
ATOM 752 HA GLN B 144 124.177 101.541 -34.248 1.00 0.00 H
ATOM 753 HB3 GLN B 144 124.671 103.921 -34.074 1.00 0.00 H
ATOM 754 HB2 GLN B 144 125.847 103.652 -32.830 1.00 0.00 H
ATOM 755 HG3 GLN B 144 124.007 102.887 -31.266 1.00 0.00 H
ATOM 756 HG2 GLN B 144 122.841 103.151 -32.547 1.00 0.00 H
ATOM 757 HE22 GLN B 144 122.354 106.363 -31.117 1.00 0.00 H
ATOM 758 HE21 GLN B 144 121.667 104.812 -31.523 1.00 0.00 H
ATOM 759 N LEU B 145 126.020 102.017 -35.935 1.00 8.64 N
ATOM 760 CA LEU B 145 126.998 102.079 -37.011 1.00 8.57 C
ATOM 761 C LEU B 145 126.867 103.465 -37.645 1.00 8.77 C
ATOM 762 O LEU B 145 125.756 103.860 -37.998 1.00 11.26 O
ATOM 763 CB LEU B 145 126.684 100.990 -38.062 1.00 10.39 C
ATOM 764 CG LEU B 145 126.538 99.547 -37.531 1.00 9.97 C
ATOM 765 CD1 LEU B 145 125.913 98.637 -38.603 1.00 12.54 C
ATOM 766 CD2 LEU B 145 127.866 98.989 -36.980 1.00 10.84 C
ATOM 767 H LEU B 145 125.059 102.146 -36.222 1.00 0.00 H
ATOM 768 HA LEU B 145 128.013 101.953 -36.630 1.00 0.00 H
ATOM 769 HB3 LEU B 145 127.455 101.007 -38.832 1.00 0.00 H
ATOM 770 HB2 LEU B 145 125.753 101.251 -38.568 1.00 0.00 H
ATOM 771 HG LEU B 145 125.832 99.554 -36.700 1.00 0.00 H
ATOM 772 HD11 LEU B 145 126.369 97.651 -38.612 1.00 0.00 H
ATOM 773 HD12 LEU B 145 124.849 98.494 -38.410 1.00 0.00 H
ATOM 774 HD13 LEU B 145 126.007 99.054 -39.606 1.00 0.00 H
ATOM 775 HD21 LEU B 145 127.702 98.434 -36.056 1.00 0.00 H
ATOM 776 HD22 LEU B 145 128.353 98.322 -37.689 1.00 0.00 H
ATOM 777 HD23 LEU B 145 128.585 99.776 -36.759 1.00 0.00 H
ATOM 778 N TRP B 146 127.999 104.168 -37.773 1.00 8.71 N
ATOM 779 CA TRP B 146 128.082 105.523 -38.310 1.00 7.83 C
ATOM 780 C TRP B 146 129.135 105.574 -39.419 1.00 10.73 C
ATOM 781 O TRP B 146 130.196 104.971 -39.272 1.00 9.85 O
ATOM 782 CB TRP B 146 128.463 106.498 -37.180 1.00 9.73 C
ATOM 783 CG TRP B 146 127.461 106.673 -36.078 1.00 9.99 C
ATOM 784 CD1 TRP B 146 127.375 105.915 -34.960 1.00 10.04 C
ATOM 785 CD2 TRP B 146 126.359 107.627 -36.000 1.00 9.51 C
ATOM 786 NE1 TRP B 146 126.326 106.359 -34.181 1.00 10.65 N
ATOM 787 CE2 TRP B 146 125.667 107.417 -34.768 1.00 9.99 C
ATOM 788 CE3 TRP B 146 125.873 108.655 -36.842 1.00 10.19 C
ATOM 789 CZ2 TRP B 146 124.561 108.197 -34.384 1.00 10.26 C
ATOM 790 CZ3 TRP B 146 124.762 109.439 -36.471 1.00 13.71 C
ATOM 791 CH2 TRP B 146 124.107 109.214 -35.244 1.00 10.83 C
ATOM 792 H TRP B 146 128.874 103.774 -37.451 1.00 0.00 H
ATOM 793 HA TRP B 146 127.125 105.838 -38.733 1.00 0.00 H
ATOM 794 HB3 TRP B 146 128.638 107.488 -37.604 1.00 0.00 H
ATOM 795 HB2 TRP B 146 129.408 106.194 -36.729 1.00 0.00 H
ATOM 796 HD1 TRP B 146 128.038 105.095 -34.729 1.00 0.00 H
ATOM 797 HE1 TRP B 146 126.083 105.944 -33.291 1.00 0.00 H
ATOM 798 HE3 TRP B 146 126.362 108.843 -37.787 1.00 0.00 H
ATOM 799 HZ2 TRP B 146 124.060 108.009 -33.445 1.00 0.00 H
ATOM 800 HZ3 TRP B 146 124.408 110.217 -37.132 1.00 0.00 H
ATOM 801 HH2 TRP B 146 123.255 109.817 -34.966 1.00 0.00 H
ATOM 802 N VAL B 147 128.828 106.333 -40.478 1.00 10.78 N
ATOM 803 CA VAL B 147 129.727 106.661 -41.585 1.00 11.03 C
ATOM 804 C VAL B 147 129.430 108.091 -42.069 1.00 11.77 C
ATOM 805 O VAL B 147 128.291 108.554 -41.980 1.00 13.86 O
ATOM 806 CB VAL B 147 129.576 105.696 -42.802 1.00 9.63 C
ATOM 807 CG1 VAL B 147 130.236 104.329 -42.568 1.00 13.35 C
ATOM 808 CG2 VAL B 147 128.134 105.531 -43.298 1.00 11.33 C
ATOM 809 H VAL B 147 127.931 106.796 -40.514 1.00 0.00 H
ATOM 810 HA VAL B 147 130.758 106.636 -41.229 1.00 0.00 H
ATOM 811 HB VAL B 147 130.114 106.131 -43.642 1.00 0.00 H
ATOM 812 HG11 VAL B 147 130.138 103.690 -43.446 1.00 0.00 H
ATOM 813 HG12 VAL B 147 131.301 104.442 -42.370 1.00 0.00 H
ATOM 814 HG13 VAL B 147 129.788 103.802 -41.727 1.00 0.00 H
ATOM 815 HG21 VAL B 147 128.077 104.868 -44.158 1.00 0.00 H
ATOM 816 HG22 VAL B 147 127.534 105.089 -42.512 1.00 0.00 H
ATOM 817 HG23 VAL B 147 127.679 106.477 -43.592 1.00 0.00 H
ATOM 818 N ASP B 148 130.475 108.746 -42.596 1.00 13.49 N
ATOM 819 CA ASP B 148 130.419 110.062 -43.243 1.00 14.24 C
ATOM 820 C ASP B 148 129.907 109.997 -44.692 1.00 17.12 C
ATOM 821 O ASP B 148 129.419 111.011 -45.190 1.00 18.93 O
ATOM 822 CB ASP B 148 131.782 110.796 -43.207 1.00 14.33 C
ATOM 823 CG ASP B 148 132.387 110.926 -41.807 1.00 14.29 C
ATOM 824 OD1 ASP B 148 131.600 111.132 -40.855 1.00 18.98 O
ATOM 825 OD2 ASP B 148 133.633 110.899 -41.721 1.00 19.29 O1-
ATOM 826 H ASP B 148 131.372 108.279 -42.643 1.00 0.00 H
ATOM 827 HA ASP B 148 129.702 110.674 -42.692 1.00 0.00 H
ATOM 828 HB3 ASP B 148 131.697 111.794 -43.638 1.00 0.00 H
ATOM 829 HB2 ASP B 148 132.488 110.239 -43.826 1.00 0.00 H
ATOM 830 N SER B 149 130.015 108.823 -45.337 1.00 15.70 N
ATOM 831 CA SER B 149 129.551 108.588 -46.702 1.00 17.77 C
ATOM 832 C SER B 149 129.054 107.144 -46.860 1.00 17.97 C
ATOM 833 O SER B 149 129.602 106.229 -46.246 1.00 16.17 O
ATOM 834 CB SER B 149 130.653 108.981 -47.711 1.00 21.40 C
ATOM 835 OG SER B 149 131.767 108.112 -47.673 1.00 24.29 O
ATOM 836 H SER B 149 130.424 108.028 -44.867 1.00 0.00 H
ATOM 837 HA SER B 149 128.691 109.237 -46.882 1.00 0.00 H
ATOM 838 HB3 SER B 149 130.994 110.002 -47.534 1.00 0.00 H
ATOM 839 HB2 SER B 149 130.250 108.962 -48.724 1.00 0.00 H
ATOM 840 HG SER B 149 132.250 108.273 -46.859 1.00 0.00 H
ATOM 841 N THR B 150 128.014 106.995 -47.694 1.00 18.68 N
ATOM 842 CA THR B 150 127.313 105.753 -48.026 1.00 17.77 C
ATOM 843 C THR B 150 128.257 104.707 -48.669 1.00 16.93 C
ATOM 844 O THR B 150 128.769 104.976 -49.759 1.00 16.49 O
ATOM 845 CB THR B 150 126.198 106.095 -49.062 1.00 22.93 C
ATOM 846 OG1 THR B 150 125.181 106.827 -48.407 1.00 28.47 O
ATOM 847 CG2 THR B 150 125.542 104.918 -49.814 1.00 23.35 C
ATOM 848 H THR B 150 127.634 107.817 -48.140 1.00 0.00 H
ATOM 849 HA THR B 150 126.844 105.390 -47.114 1.00 0.00 H
ATOM 850 HB THR B 150 126.610 106.767 -49.818 1.00 0.00 H
ATOM 851 HG1 THR B 150 124.454 106.957 -49.022 1.00 0.00 H
ATOM 852 HG21 THR B 150 124.635 105.231 -50.332 1.00 0.00 H
ATOM 853 HG22 THR B 150 126.207 104.504 -50.572 1.00 0.00 H
ATOM 854 HG23 THR B 150 125.281 104.110 -49.136 1.00 0.00 H
ATOM 855 N PRO B 151 128.463 103.532 -48.022 1.00 14.30 N
ATOM 856 CA PRO B 151 129.145 102.408 -48.684 1.00 13.52 C
ATOM 857 C PRO B 151 128.231 101.701 -49.720 1.00 11.67 C
ATOM 858 O PRO B 151 127.010 101.862 -49.640 1.00 13.65 O
ATOM 859 CB PRO B 151 129.519 101.496 -47.508 1.00 12.43 C
ATOM 860 CG PRO B 151 128.404 101.703 -46.497 1.00 14.77 C
ATOM 861 CD PRO B 151 128.090 103.188 -46.646 1.00 14.85 C
ATOM 862 HA PRO B 151 130.046 102.785 -49.157 1.00 0.00 H
ATOM 863 HB3 PRO B 151 130.468 101.827 -47.081 1.00 0.00 H
ATOM 864 HB2 PRO B 151 129.643 100.454 -47.794 1.00 0.00 H
ATOM 865 HG3 PRO B 151 128.677 101.417 -45.481 1.00 0.00 H
ATOM 866 HG2 PRO B 151 127.534 101.112 -46.789 1.00 0.00 H
ATOM 867 HD2 PRO B 151 127.047 103.383 -46.407 1.00 0.00 H
ATOM 868 HD3 PRO B 151 128.721 103.764 -45.972 1.00 0.00 H
ATOM 1953 N CYS B 220 125.007 95.428 -44.373 1.00 10.59 N
ATOM 1954 CA CYS B 220 125.166 96.804 -43.905 1.00 14.42 C
ATOM 1955 C CYS B 220 124.160 97.710 -44.638 1.00 15.84 C
ATOM 1956 O CYS B 220 124.530 98.407 -45.585 1.00 21.89 O
ATOM 1957 CB CYS B 220 126.620 97.287 -44.099 1.00 16.53 C
ATOM 1958 SG CYS B 220 126.913 98.889 -43.297 0.50 14.84 S
ATOM 1959 H CYS B 220 125.594 95.174 -45.159 1.00 0.00 H
ATOM 1960 HA CYS B 220 124.944 96.838 -42.837 1.00 0.00 H
ATOM 1961 HB3 CYS B 220 126.854 97.389 -45.157 1.00 0.00 H
ATOM 1962 HB2 CYS B 220 127.325 96.561 -43.701 1.00 0.00 H
ATOM 1963 HG CYS B 220 126.163 99.597 -44.147 0.50 0.00 H
ATOM 1964 N GLU B 221 122.894 97.661 -44.198 1.00 16.02 N
ATOM 1965 CA GLU B 221 121.804 98.456 -44.763 1.00 19.56 C
ATOM 1966 C GLU B 221 121.898 99.941 -44.353 1.00 17.88 C
ATOM 1967 O GLU B 221 122.509 100.232 -43.322 1.00 15.21 O
ATOM 1968 CB GLU B 221 120.454 97.858 -44.311 1.00 23.83 C
ATOM 1969 CG GLU B 221 120.176 96.427 -44.819 1.00 30.42 C
ATOM 1970 CD GLU B 221 120.105 96.287 -46.344 1.00 36.60 C
ATOM 1971 OE1 GLU B 221 120.282 95.138 -46.804 1.00 39.37 O
ATOM 1972 OE2 GLU B 221 119.848 97.304 -47.025 1.00 39.12 O1-
ATOM 1973 H GLU B 221 122.653 97.048 -43.432 1.00 0.00 H
ATOM 1974 HA GLU B 221 121.901 98.374 -45.843 1.00 0.00 H
ATOM 1975 HB3 GLU B 221 119.632 98.506 -44.618 1.00 0.00 H
ATOM 1976 HB2 GLU B 221 120.414 97.850 -43.221 1.00 0.00 H
ATOM 1977 HG3 GLU B 221 119.224 96.089 -44.409 1.00 0.00 H
ATOM 1978 HG2 GLU B 221 120.933 95.742 -44.436 1.00 0.00 H
ATOM 1979 N PRO B 222 121.250 100.852 -45.121 1.00 17.40 N
ATOM 1980 CA PRO B 222 121.064 102.252 -44.690 1.00 17.82 C
ATOM 1981 C PRO B 222 120.212 102.400 -43.406 1.00 17.53 C
ATOM 1982 O PRO B 222 119.435 101.494 -43.097 1.00 19.45 O
ATOM 1983 CB PRO B 222 120.356 102.917 -45.888 1.00 19.10 C
ATOM 1984 CG PRO B 222 120.627 102.012 -47.075 1.00 23.49 C
ATOM 1985 CD PRO B 222 120.680 100.628 -46.450 1.00 20.73 C
ATOM 1986 HA PRO B 222 122.062 102.665 -44.574 1.00 0.00 H
ATOM 1987 HB3 PRO B 222 120.703 103.935 -46.063 1.00 0.00 H
ATOM 1988 HB2 PRO B 222 119.278 102.967 -45.724 1.00 0.00 H
ATOM 1989 HG3 PRO B 222 121.601 102.253 -47.501 1.00 0.00 H
ATOM 1990 HG2 PRO B 222 119.884 102.101 -47.868 1.00 0.00 H
ATOM 1991 HD2 PRO B 222 119.677 100.212 -46.343 1.00 0.00 H
ATOM 1992 HD3 PRO B 222 121.265 99.964 -47.085 1.00 0.00 H
ATOM 1993 N PRO B 223 120.320 103.561 -42.718 1.00 17.55 N
ATOM 1994 CA PRO B 223 119.401 103.949 -41.634 1.00 19.64 C
ATOM 1995 C PRO B 223 117.935 104.003 -42.088 1.00 22.15 C
ATOM 1996 O PRO B 223 117.657 104.488 -43.187 1.00 22.72 O
ATOM 1997 CB PRO B 223 119.888 105.351 -41.218 1.00 17.75 C
ATOM 1998 CG PRO B 223 121.339 105.409 -41.649 1.00 18.23 C
ATOM 1999 CD PRO B 223 121.342 104.583 -42.924 1.00 16.21 C
ATOM 2000 HA PRO B 223 119.533 103.246 -40.809 1.00 0.00 H
ATOM 2001 HB3 PRO B 223 119.763 105.537 -40.152 1.00 0.00 H
ATOM 2002 HB2 PRO B 223 119.337 106.131 -41.746 1.00 0.00 H
ATOM 2003 HG3 PRO B 223 121.963 104.912 -40.906 1.00 0.00 H
ATOM 2004 HG2 PRO B 223 121.718 106.422 -41.782 1.00 0.00 H
ATOM 2005 HD2 PRO B 223 121.085 105.190 -43.794 1.00 0.00 H
ATOM 2006 HD3 PRO B 223 122.323 104.146 -43.066 1.00 0.00 H
ATOM 2045 N SER B 227 115.962 108.173 -38.710 1.00 31.84 N
ATOM 2046 CA SER B 227 117.175 107.829 -37.965 1.00 28.07 C
ATOM 2047 C SER B 227 118.421 108.199 -38.787 1.00 24.16 C
ATOM 2048 O SER B 227 118.406 108.092 -40.014 1.00 23.45 O
ATOM 2049 CB SER B 227 117.150 106.326 -37.610 1.00 28.93 C
ATOM 2050 OG SER B 227 118.250 105.974 -36.793 1.00 30.49 O
ATOM 2051 H SER B 227 115.940 107.850 -39.668 1.00 0.00 H
ATOM 2052 HA SER B 227 117.213 108.401 -37.035 1.00 0.00 H
ATOM 2053 HB3 SER B 227 117.174 105.708 -38.507 1.00 0.00 H
ATOM 2054 HB2 SER B 227 116.232 106.078 -37.076 1.00 0.00 H
ATOM 2055 HG SER B 227 118.295 105.016 -36.732 1.00 0.00 H
ATOM 2056 N ASP B 228 119.482 108.607 -38.073 1.00 18.59 N
ATOM 2057 CA ASP B 228 120.784 109.006 -38.623 1.00 17.42 C
ATOM 2058 C ASP B 228 121.827 107.871 -38.589 1.00 15.44 C
ATOM 2059 O ASP B 228 122.962 108.109 -39.001 1.00 16.12 O
ATOM 2060 CB ASP B 228 121.357 110.268 -37.926 1.00 19.62 C
ATOM 2061 CG ASP B 228 120.402 111.465 -37.853 1.00 23.26 C
ATOM 2062 OD1 ASP B 228 119.596 111.627 -38.796 1.00 27.49 O
ATOM 2063 OD2 ASP B 228 120.562 112.252 -36.895 1.00 19.84 O1-
ATOM 2064 H ASP B 228 119.401 108.656 -37.067 1.00 0.00 H
ATOM 2065 HA ASP B 228 120.655 109.255 -39.678 1.00 0.00 H
ATOM 2066 HB3 ASP B 228 122.267 110.603 -38.423 1.00 0.00 H
ATOM 2067 HB2 ASP B 228 121.627 109.999 -36.903 1.00 0.00 H
ATOM 2068 N CYS B 229 121.451 106.672 -38.111 1.00 15.26 N
ATOM 2069 CA CYS B 229 122.359 105.537 -37.945 1.00 14.08 C
ATOM 2070 C CYS B 229 121.608 104.204 -38.079 1.00 12.92 C
ATOM 2071 O CYS B 229 120.419 104.121 -37.768 1.00 14.76 O
ATOM 2072 CB CYS B 229 123.152 105.639 -36.622 1.00 14.23 C
ATOM 2073 SG CYS B 229 122.122 105.418 -35.140 1.00 14.02 S
ATOM 2074 H CYS B 229 120.500 106.527 -37.801 1.00 0.00 H
ATOM 2075 HA CYS B 229 123.081 105.563 -38.763 1.00 0.00 H
ATOM 2076 HB3 CYS B 229 123.661 106.598 -36.569 1.00 0.00 H
ATOM 2077 HB2 CYS B 229 123.928 104.876 -36.584 1.00 0.00 H
ATOM 2078 HG CYS B 229 123.098 105.646 -34.256 1.00 0.00 H
ATOM 2079 N THR B 230 122.349 103.177 -38.517 1.00 12.70 N
ATOM 2080 CA THR B 230 121.895 101.788 -38.556 1.00 12.03 C
ATOM 2081 C THR B 230 122.340 101.101 -37.258 1.00 11.22 C
ATOM 2082 O THR B 230 123.508 101.226 -36.901 1.00 14.47 O
ATOM 2083 CB THR B 230 122.550 101.024 -39.735 1.00 11.97 C
ATOM 2084 OG1 THR B 230 122.260 101.714 -40.930 1.00 14.71 O
ATOM 2085 CG2 THR B 230 122.105 99.559 -39.901 1.00 13.37 C
ATOM 2086 H THR B 230 123.319 103.326 -38.756 1.00 0.00 H
ATOM 2087 HA THR B 230 120.808 101.738 -38.653 1.00 0.00 H
ATOM 2088 HB THR B 230 123.635 101.035 -39.623 1.00 0.00 H
ATOM 2089 HG1 THR B 230 122.433 101.131 -41.678 1.00 0.00 H
ATOM 2090 HG21 THR B 230 122.569 99.106 -40.778 1.00 0.00 H
ATOM 2091 HG22 THR B 230 122.384 98.947 -39.044 1.00 0.00 H
ATOM 2092 HG23 THR B 230 121.023 99.488 -40.025 1.00 0.00 H
ATOM 2093 N THR B 231 121.425 100.397 -36.579 1.00 10.54 N
ATOM 2094 CA THR B 231 121.717 99.715 -35.317 1.00 10.40 C
ATOM 2095 C THR B 231 121.535 98.200 -35.489 1.00 12.15 C
ATOM 2096 O THR B 231 120.485 97.767 -35.965 1.00 13.73 O
ATOM 2097 CB THR B 231 120.773 100.205 -34.186 1.00 13.37 C
ATOM 2098 OG1 THR B 231 120.998 101.586 -33.978 1.00 16.81 O
ATOM 2099 CG2 THR B 231 120.951 99.503 -32.826 1.00 17.03 C
ATOM 2100 H THR B 231 120.482 100.307 -36.930 1.00 0.00 H
ATOM 2101 HA THR B 231 122.743 99.897 -34.999 1.00 0.00 H
ATOM 2102 HB THR B 231 119.734 100.092 -34.502 1.00 0.00 H
ATOM 2103 HG1 THR B 231 120.788 102.054 -34.790 1.00 0.00 H
ATOM 2104 HG21 THR B 231 120.309 99.961 -32.074 1.00 0.00 H
ATOM 2105 HG22 THR B 231 120.686 98.447 -32.869 1.00 0.00 H
ATOM 2106 HG23 THR B 231 121.980 99.576 -32.474 1.00 0.00 H
ATOM 174 N TYR B 107 135.072 105.411 -45.799 1.00 11.36 N
ATOM 175 CA TYR B 107 133.682 105.762 -45.495 1.00 10.31 C
ATOM 176 C TYR B 107 133.507 106.490 -44.155 1.00 10.18 C
ATOM 177 O TYR B 107 132.420 107.013 -43.925 1.00 13.37 O
ATOM 178 CB TYR B 107 132.806 104.493 -45.582 1.00 12.61 C
ATOM 179 CG TYR B 107 132.878 103.841 -46.951 1.00 13.38 C
ATOM 180 CD1 TYR B 107 132.283 104.475 -48.062 1.00 13.90 C
ATOM 181 CD2 TYR B 107 133.613 102.652 -47.134 1.00 12.93 C
ATOM 182 CE1 TYR B 107 132.461 103.948 -49.356 1.00 15.48 C
ATOM 183 CE2 TYR B 107 133.778 102.118 -48.427 1.00 13.62 C
ATOM 184 CZ TYR B 107 133.216 102.774 -49.539 1.00 16.05 C
ATOM 185 OH TYR B 107 133.412 102.273 -50.793 1.00 19.75 O
ATOM 186 H TYR B 107 135.405 104.533 -45.427 1.00 0.00 H
ATOM 187 HA TYR B 107 133.313 106.453 -46.252 1.00 0.00 H
ATOM 188 HB3 TYR B 107 131.763 104.735 -45.376 1.00 0.00 H
ATOM 189 HB2 TYR B 107 133.107 103.773 -44.819 1.00 0.00 H
ATOM 190 HD1 TYR B 107 131.717 105.385 -47.931 1.00 0.00 H
ATOM 191 HD2 TYR B 107 134.078 102.165 -46.290 1.00 0.00 H
ATOM 192 HE1 TYR B 107 132.018 104.452 -50.202 1.00 0.00 H
ATOM 193 HE2 TYR B 107 134.357 101.216 -48.565 1.00 0.00 H
ATOM 194 HH TYR B 107 133.005 102.805 -51.480 1.00 0.00 H
ATOM 869 N PRO B 152 128.817 100.927 -50.668 1.00 9.69 N
ATOM 870 CA PRO B 152 128.045 100.263 -51.742 1.00 13.69 C
ATOM 871 C PRO B 152 126.986 99.239 -51.267 1.00 13.46 C
ATOM 872 O PRO B 152 127.137 98.679 -50.180 1.00 12.11 O
ATOM 873 CB PRO B 152 129.126 99.542 -52.571 1.00 13.48 C
ATOM 874 CG PRO B 152 130.402 100.318 -52.316 1.00 14.74 C
ATOM 875 CD PRO B 152 130.257 100.745 -50.865 1.00 11.16 C
ATOM 876 HA PRO B 152 127.607 101.068 -52.330 1.00 0.00 H
ATOM 877 HB3 PRO B 152 128.879 99.496 -53.632 1.00 0.00 H
ATOM 878 HB2 PRO B 152 129.263 98.516 -52.224 1.00 0.00 H
ATOM 879 HG3 PRO B 152 130.419 101.203 -52.954 1.00 0.00 H
ATOM 880 HG2 PRO B 152 131.309 99.744 -52.510 1.00 0.00 H
ATOM 881 HD2 PRO B 152 130.618 99.969 -50.189 1.00 0.00 H
ATOM 882 HD3 PRO B 152 130.847 101.642 -50.703 1.00 0.00 H
ATOM 904 N THR B 155 127.821 95.662 -49.147 1.00 9.95 N
ATOM 905 CA THR B 155 128.641 95.873 -47.947 1.00 9.93 C
ATOM 906 C THR B 155 127.993 95.170 -46.737 1.00 8.59 C
ATOM 907 O THR B 155 126.765 95.138 -46.642 1.00 8.52 O
ATOM 908 CB THR B 155 128.788 97.388 -47.626 1.00 10.26 C
ATOM 909 OG1 THR B 155 129.490 97.991 -48.693 1.00 9.39 O
ATOM 910 CG2 THR B 155 129.539 97.774 -46.334 1.00 10.39 C
ATOM 911 H THR B 155 127.273 96.455 -49.452 1.00 0.00 H
ATOM 912 HA THR B 155 129.626 95.441 -48.128 1.00 0.00 H
ATOM 913 HB THR B 155 127.795 97.839 -47.587 1.00 0.00 H
ATOM 914 HG1 THR B 155 128.906 98.019 -49.457 1.00 0.00 H
ATOM 915 HG21 THR B 155 129.466 98.845 -46.148 1.00 0.00 H
ATOM 916 HG22 THR B 155 129.146 97.283 -45.448 1.00 0.00 H
ATOM 917 HG23 THR B 155 130.599 97.539 -46.399 1.00 0.00 H
ATOM 883 N PRO B 153 125.991 98.928 -52.132 1.00 12.57 N
ATOM 884 CA PRO B 153 125.166 97.709 -52.005 1.00 12.85 C
ATOM 885 C PRO B 153 126.014 96.421 -52.005 1.00 12.17 C
ATOM 886 O PRO B 153 126.858 96.252 -52.886 1.00 11.90 O
ATOM 887 CB PRO B 153 124.226 97.768 -53.225 1.00 15.31 C
ATOM 888 CG PRO B 153 124.193 99.232 -53.626 1.00 15.96 C
ATOM 889 CD PRO B 153 125.605 99.703 -53.311 1.00 14.96 C
ATOM 890 HA PRO B 153 124.584 97.792 -51.085 1.00 0.00 H
ATOM 891 HB3 PRO B 153 123.231 97.381 -53.004 1.00 0.00 H
ATOM 892 HB2 PRO B 153 124.623 97.184 -54.058 1.00 0.00 H
ATOM 893 HG3 PRO B 153 123.483 99.764 -52.991 1.00 0.00 H
ATOM 894 HG2 PRO B 153 123.902 99.393 -54.664 1.00 0.00 H
ATOM 895 HD2 PRO B 153 126.287 99.469 -54.130 1.00 0.00 H
ATOM 896 HD3 PRO B 153 125.611 100.780 -53.146 1.00 0.00 H
ATOM 897 N GLY B 154 125.788 95.564 -50.999 1.00 11.55 N
ATOM 898 CA GLY B 154 126.537 94.322 -50.807 1.00 11.16 C
ATOM 899 C GLY B 154 127.634 94.466 -49.740 1.00 9.96 C
ATOM 900 O GLY B 154 128.284 93.469 -49.431 1.00 11.29 O
ATOM 901 H GLY B 154 125.077 95.779 -50.315 1.00 0.00 H
ATOM 902 HA3 GLY B 154 126.983 93.965 -51.737 1.00 0.00 H
ATOM 903 HA2 GLY B 154 125.839 93.550 -50.482 1.00 0.00 H
ATOM 1939 N PRO B 219 124.170 91.992 -43.736 1.00 9.24 N
ATOM 1940 CA PRO B 219 124.104 93.171 -44.629 1.00 8.78 C
ATOM 1941 C PRO B 219 124.120 94.534 -43.908 1.00 11.00 C
ATOM 1942 O PRO B 219 123.344 94.741 -42.974 1.00 13.51 O
ATOM 1943 CB PRO B 219 122.791 92.967 -45.406 1.00 11.02 C
ATOM 1944 CG PRO B 219 122.589 91.465 -45.414 1.00 10.76 C
ATOM 1945 CD PRO B 219 123.091 91.048 -44.042 1.00 10.00 C
ATOM 1946 HA PRO B 219 124.944 93.105 -45.321 1.00 0.00 H
ATOM 1947 HB3 PRO B 219 122.829 93.384 -46.413 1.00 0.00 H
ATOM 1948 HB2 PRO B 219 121.951 93.435 -44.891 1.00 0.00 H
ATOM 1949 HG3 PRO B 219 123.220 91.018 -46.185 1.00 0.00 H
ATOM 1950 HG2 PRO B 219 121.561 91.162 -45.603 1.00 0.00 H
ATOM 1951 HD2 PRO B 219 122.301 91.145 -43.296 1.00 0.00 H
ATOM 1952 HD3 PRO B 219 123.417 90.009 -44.074 1.00 0.00 H
ATOM 942 N VAL B 157 128.629 93.981 -42.248 1.00 7.43 N
ATOM 943 CA VAL B 157 129.248 94.218 -40.946 1.00 7.06 C
ATOM 944 C VAL B 157 129.344 92.879 -40.204 1.00 6.57 C
ATOM 945 O VAL B 157 128.318 92.232 -39.991 1.00 6.94 O
ATOM 946 CB VAL B 157 128.430 95.205 -40.066 0.50 7.58 C
ATOM 947 CG1 VAL B 157 129.029 95.418 -38.662 0.50 10.18 C
ATOM 948 CG2 VAL B 157 128.279 96.562 -40.766 0.50 9.29 C
ATOM 949 H VAL B 157 127.761 93.459 -42.235 1.00 0.00 H
ATOM 950 HA VAL B 157 130.252 94.624 -41.072 1.00 0.00 H
ATOM 951 HB VAL B 157 127.425 94.805 -39.921 0.50 0.00 H
ATOM 952 HG11 VAL B 157 128.429 96.117 -38.082 0.50 0.00 H
ATOM 953 HG12 VAL B 157 129.075 94.501 -38.075 0.50 0.00 H
ATOM 954 HG13 VAL B 157 130.039 95.822 -38.736 0.50 0.00 H
ATOM 955 HG21 VAL B 157 127.994 97.357 -40.081 0.50 0.00 H
ATOM 956 HG22 VAL B 157 129.211 96.866 -41.240 0.50 0.00 H
ATOM 957 HG23 VAL B 157 127.507 96.505 -41.527 0.50 0.00 H
ATOM 2507 N LEU B 257 133.684 96.566 -40.876 1.00 7.35 N
ATOM 2508 CA LEU B 257 132.988 96.864 -42.122 1.00 9.28 C
ATOM 2509 C LEU B 257 133.737 96.146 -43.259 1.00 8.54 C
ATOM 2510 O LEU B 257 134.961 96.265 -43.342 1.00 8.97 O
ATOM 2511 CB LEU B 257 132.979 98.397 -42.325 1.00 9.53 C
ATOM 2512 CG LEU B 257 132.019 98.903 -43.427 1.00 8.94 C
ATOM 2513 CD1 LEU B 257 130.545 98.751 -43.007 1.00 10.83 C
ATOM 2514 CD2 LEU B 257 132.346 100.355 -43.838 1.00 10.35 C
ATOM 2515 H LEU B 257 134.448 97.191 -40.654 1.00 0.00 H
ATOM 2516 HA LEU B 257 131.962 96.498 -42.053 1.00 0.00 H
ATOM 2517 HB3 LEU B 257 133.995 98.723 -42.545 1.00 0.00 H
ATOM 2518 HB2 LEU B 257 132.719 98.887 -41.387 1.00 0.00 H
ATOM 2519 HG LEU B 257 132.169 98.293 -44.318 1.00 0.00 H
ATOM 2520 HD11 LEU B 257 129.922 99.561 -43.387 1.00 0.00 H
ATOM 2521 HD12 LEU B 257 130.129 97.820 -43.388 1.00 0.00 H
ATOM 2522 HD13 LEU B 257 130.433 98.739 -41.923 1.00 0.00 H
ATOM 2523 HD21 LEU B 257 132.400 100.448 -44.923 1.00 0.00 H
ATOM 2524 HD22 LEU B 257 131.596 101.066 -43.488 1.00 0.00 H
ATOM 2525 HD23 LEU B 257 133.305 100.690 -43.442 1.00 0.00 H
ATOM 2107 N ILE B 232 122.552 97.436 -35.058 1.00 10.64 N
ATOM 2108 CA ILE B 232 122.498 95.979 -34.950 1.00 8.62 C
ATOM 2109 C ILE B 232 122.361 95.621 -33.460 1.00 9.63 C
ATOM 2110 O ILE B 232 123.129 96.118 -32.635 1.00 11.02 O
ATOM 2111 CB ILE B 232 123.777 95.284 -35.515 0.50 8.69 C
ATOM 2112 CG1 ILE B 232 123.954 95.578 -37.024 0.50 10.83 C
ATOM 2113 CG2 ILE B 232 123.785 93.753 -35.280 0.50 7.24 C
ATOM 2114 CD1 ILE B 232 125.346 95.232 -37.575 0.50 8.68 C
ATOM 2115 H ILE B 232 123.379 97.875 -34.673 1.00 0.00 H
ATOM 2116 HA ILE B 232 121.633 95.587 -35.490 1.00 0.00 H
ATOM 2117 HB ILE B 232 124.644 95.702 -34.998 0.50 0.00 H
ATOM 2118 HG13 ILE B 232 123.779 96.635 -37.223 0.50 0.00 H
ATOM 2119 HG12 ILE B 232 123.194 95.044 -37.594 0.50 0.00 H
ATOM 2120 HG21 ILE B 232 124.648 93.274 -35.736 0.50 0.00 H
ATOM 2121 HG22 ILE B 232 123.824 93.490 -34.223 0.50 0.00 H
ATOM 2122 HG23 ILE B 232 122.896 93.289 -35.706 0.50 0.00 H
ATOM 2123 HD11 ILE B 232 125.427 95.537 -38.618 0.50 0.00 H
ATOM 2124 HD12 ILE B 232 126.130 95.741 -37.013 0.50 0.00 H
ATOM 2125 HD13 ILE B 232 125.552 94.164 -37.543 0.50 0.00 H
ATOM 246 N LEU B 111 131.755 103.047 -34.477 1.00 6.64 N
ATOM 247 CA LEU B 111 130.628 102.627 -33.649 1.00 7.13 C
ATOM 248 C LEU B 111 130.073 103.789 -32.812 1.00 9.35 C
ATOM 249 O LEU B 111 130.788 104.749 -32.518 1.00 9.95 O
ATOM 250 CB LEU B 111 131.080 101.479 -32.720 1.00 6.38 C
ATOM 251 CG LEU B 111 131.522 100.196 -33.456 1.00 7.38 C
ATOM 252 CD1 LEU B 111 132.160 99.191 -32.477 1.00 7.59 C
ATOM 253 CD2 LEU B 111 130.396 99.564 -34.296 1.00 7.84 C
ATOM 254 H LEU B 111 132.674 102.942 -34.059 1.00 0.00 H
ATOM 255 HA LEU B 111 129.832 102.273 -34.302 1.00 0.00 H
ATOM 256 HB3 LEU B 111 130.274 101.219 -32.031 1.00 0.00 H
ATOM 257 HB2 LEU B 111 131.900 101.839 -32.095 1.00 0.00 H
ATOM 258 HG LEU B 111 132.303 100.486 -34.154 1.00 0.00 H
ATOM 259 HD11 LEU B 111 133.042 98.723 -32.913 1.00 0.00 H
ATOM 260 HD12 LEU B 111 132.478 99.671 -31.551 1.00 0.00 H
ATOM 261 HD13 LEU B 111 131.468 98.398 -32.198 1.00 0.00 H
ATOM 262 HD21 LEU B 111 130.262 98.506 -34.089 1.00 0.00 H
ATOM 263 HD22 LEU B 111 129.434 100.035 -34.114 1.00 0.00 H
ATOM 264 HD23 LEU B 111 130.611 99.659 -35.361 1.00 0.00 H
ATOM 2038 N GLY B 226 113.881 108.614 -40.475 1.00 35.39 N
ATOM 2039 CA GLY B 226 113.770 109.266 -39.169 1.00 34.82 C
ATOM 2040 C GLY B 226 114.934 108.898 -38.230 1.00 34.39 C
ATOM 2041 O GLY B 226 114.888 109.291 -37.065 1.00 35.46 O
ATOM 2042 H GLY B 226 114.545 109.012 -41.123 1.00 0.00 H
ATOM 2043 HA3 GLY B 226 112.822 109.031 -38.682 1.00 0.00 H
ATOM 2044 HA2 GLY B 226 113.780 110.344 -39.324 1.00 0.00 H
ENDHere is the molecule .sdf file:
2VUK
3D
Schrodinger Suite 2023-1.
37 39 0 0 1 0 999 V2000
125.1950 105.2710 -41.1140 C 0 0 0 0 0 0
125.0460 106.6550 -41.1050 C 0 0 0 0 0 0
124.7060 107.3680 -42.2540 C 0 0 0 0 0 0
124.5170 106.7060 -43.4700 C 0 0 0 0 0 0
124.6770 105.3110 -43.5170 C 0 0 0 0 0 0
124.5570 104.3680 -44.5510 C 0 0 0 0 0 0
124.1920 104.4760 -45.9020 C 0 0 0 0 0 0
124.1480 103.3190 -46.6770 C 0 0 0 0 0 0
124.4970 102.0810 -46.1450 C 0 0 0 0 0 0
124.8780 101.9390 -44.8120 C 0 0 0 0 0 0
124.8780 103.0920 -44.0130 C 0 0 0 0 0 0
125.1420 103.2640 -42.6610 N 0 0 0 0 0 0
125.0160 104.6070 -42.3330 C 0 0 0 0 0 0
125.5650 102.2110 -41.7420 C 0 0 0 0 0 0
127.0990 102.1260 -41.6930 C 0 0 0 0 0 0
124.5640 108.8770 -42.1770 C 0 0 0 0 0 0
123.1730 109.3020 -41.6870 N 0 3 0 0 0 0
123.0130 110.8170 -41.4930 C 0 0 0 0 0 0
125.4640 104.7420 -40.2180 H 0 0 0 0 0 0
125.1980 107.1820 -40.1750 H 0 0 0 0 0 0
124.2570 107.2580 -44.3630 H 0 0 0 0 0 0
123.9270 105.4300 -46.3320 H 0 0 0 0 0 0
123.8290 103.3780 -47.7050 H 0 0 0 0 0 0
124.4570 101.2060 -46.7770 H 0 0 0 0 0 0
125.1210 100.9660 -44.4150 H 0 0 0 0 0 0
125.1290 101.2640 -42.0630 H 0 0 0 0 0 0
125.1600 102.4220 -40.7520 H 0 0 0 0 0 0
127.4220 101.2600 -41.1160 H 0 0 0 0 0 0
127.5280 102.0270 -42.6910 H 0 0 0 0 0 0
127.5290 103.0120 -41.2270 H 0 0 0 0 0 0
124.6970 109.3630 -43.1460 H 0 0 0 0 0 0
125.2680 109.3110 -41.4640 H 0 0 0 0 0 0
123.0010 108.8420 -40.8010 H 0 0 0 0 0 0
122.4780 108.9700 -42.3410 H 0 0 0 0 0 0
121.9910 110.9770 -41.1450 H 0 0 0 0 0 0
123.7420 111.1270 -40.7430 H 0 0 0 0 0 0
123.1880 111.2920 -42.4590 H 0 0 0 0 0 0
1 2 1 0 0 0
1 13 2 0 0 0
1 19 1 0 0 0
2 3 2 0 0 0
2 20 1 0 0 0
3 4 1 0 0 0
3 16 1 0 0 0
4 5 2 0 0 0
4 21 1 0 0 0
5 6 1 0 0 0
5 13 1 0 0 0
6 7 1 0 0 0
6 11 2 0 0 0
7 8 2 0 0 0
7 22 1 0 0 0
8 9 1 0 0 0
8 23 1 0 0 0
9 10 2 0 0 0
9 24 1 0 0 0
10 11 1 0 0 0
10 25 1 0 0 0
11 12 1 0 0 0
12 13 1 0 0 0
12 14 1 0 0 0
14 15 1 0 0 0
14 26 1 0 0 0
14 27 1 0 0 0
15 28 1 0 0 0
15 29 1 0 0 0
15 30 1 0 0 0
16 17 1 0 0 0
16 31 1 0 0 0
16 32 1 0 0 0
17 18 1 0 0 0
17 33 1 0 0 0
17 34 1 0 0 0
18 35 1 0 0 0
18 36 1 0 0 0
18 37 1 0 0 0
M CHG 1 17 1
M END
$$$$
Here is the command:
python -u sample_frag.py --ckpt ckpt/500.pt --pdb_path 2VUK_ligand_pocket10.pdb --mol_file 2VUK_ligand.sdf --keep_index 5 6 11 12 13 14 15 --num_atom 18 --num_samples 20 --sampling_type generalized
Lumen97
commented
2 months ago +1, I've encountered the same issue.
Layne-Huang
commented
2 months ago Hi,
Thanks for your feedback. There is a bug in the molecule visualization code. The idx of atom should start from 0. Please use the updated visualization code.
from rdkit import Chem
mol = Chem.SDMolSupplier(f)[0]
smiles = Chem.MolToSmiles(mol)
print(smiles)
mol.RemoveAllConformers()
for i, atom in enumerate(mol.GetAtoms()):
atom.SetProp('molAtomMapNumber', str(i))
Draw.MolToImage(mol, size=(1000,1000))The visualization of the 2vuk ligand should be like this:
And you should use 4 5 10 11 12 13 14 as the keep index.
The generated sample is shown as:
BLEACH366
commented
2 months ago OK, it works. Thank you for your help.
BLEACH366
commented
2 months ago Hi,
I meet another problem for sample frag(maybe not a bug).
I set the seed_frag like this:
And I sample a molecule like this:
We can see that although the atom type and position don't change, the bond type for the red atom has changed(from double bond to single bond, which makes the aromaticity disappeared). Maybe consider the bond type could improve it?
Layne-Huang
commented
2 months ago Thank you very much for your feedback! Unfortunately, PMDM does not 100% support remaining the edges of the fragment for this version. But we are working on improving it by predicting the edge as well as the atom types and atom coordinates. We will let you know the new version is released. Thanks for your interests!
My input molecular and fixed segment is as followed:
For some sample results, the atom type changed.
And others may not have the seed frag.
What can I do to fix it?