How can ligand atom names and/or order be matched to the CIF format?

[kirmedvedev]

Is there any way to match names and/or order of ligand's atoms in the output structure to CIF or SDF format of the ligand file?
Output:

ATOM 1949 N N_1 . LIG . 1 ? B 1.644 -8.467 17.946 1.000 2 B LIG 79.648 1
ATOM 1950 C C_1 . LIG . 1 ? B 0.784 -9.476 17.979 1.000 2 B LIG 82.140 1
ATOM 1951 N N_2 . LIG . 1 ? B 1.049 -10.542 18.752 1.000 2 B LIG 82.164 1
ATOM 1952 C C_2 . LIG . 1 ? B 0.173 -11.557 18.777 1.000 2 B LIG 81.894 1
ATOM 1953 N N_3 . LIG . 1 ? B -0.953 -11.599 18.095 1.000 2 B LIG 81.778 1
ATOM 1954 C C_3 . LIG . 1 ? B -1.246 -10.551 17.312 1.000 2 B LIG 84.079 1
ATOM 1955 C C_4 . LIG . 1 ? B -0.398 -9.456 17.224 1.000 2 B LIG 83.583 1
ATOM 1956 N N_4 . LIG . 1 ? B -0.968 -8.562 16.364 1.000 2 B LIG 82.189 1
ATOM 1957 C C_5 . LIG . 1 ? B -2.066 -9.108 15.957 1.000 2 B LIG 82.683 1
ATOM 1958 N N_5 . LIG . 1 ? B -2.263 -10.304 16.511 1.000 2 B LIG 86.551 1
ATOM 1959 C C_6 . LIG . 1 ? B -3.438 -11.201 16.289 1.000 2 B LIG 83.855 1
ATOM 1960 O O_1 . LIG . 1 ? B -3.525 -11.492 14.916 1.000 2 B LIG 83.025 1
ATOM 1961 C C_7 . LIG . 1 ? B -4.897 -11.534 14.578 1.000 2 B LIG 84.940 1
ATOM 1962 C C_8 . LIG . 1 ? B -5.130 -10.602 13.440 1.000 2 B LIG 81.968 1
ATOM 1963 O O_2 . LIG . 1 ? B -4.725 -9.323 13.857 1.000 2 B LIG 83.554 1
ATOM 1964 P P_1 . LIG . 1 ? B -4.721 -8.194 12.771 1.000 2 B LIG 89.003 1
ATOM 1965 O O_3 . LIG . 1 ? B -4.034 -8.622 11.558 1.000 2 B LIG 77.465 1
ATOM 1966 O O_4 . LIG . 1 ? B -4.147 -6.973 13.425 1.000 2 B LIG 77.723 1
ATOM 1967 O O_5 . LIG . 1 ? B -6.240 -7.865 12.424 1.000 2 B LIG 85.966 1
ATOM 1968 P P_2 . LIG . 1 ? B -6.685 -6.575 11.739 1.000 2 B LIG 88.616 1
ATOM 1969 O O_6 . LIG . 1 ? B -7.991 -6.827 11.083 1.000 2 B LIG 74.573 1
ATOM 1970 O O_7 . LIG . 1 ? B -5.639 -6.146 10.820 1.000 2 B LIG 75.176 1
ATOM 1971 O O_8 . LIG . 1 ? B -6.899 -5.505 12.865 1.000 2 B LIG 82.207 1
ATOM 1972 P P_3 . LIG . 1 ? B -7.007 -3.977 12.589 1.000 2 B LIG 85.246 1
ATOM 1973 O O_9 . LIG . 1 ? B -5.709 -3.617 11.896 1.000 2 B LIG 70.253 1
ATOM 1974 O O_10 . LIG . 1 ? B -7.101 -3.294 13.872 1.000 2 B LIG 70.072 1
ATOM 1975 O O_11 . LIG . 1 ? B -8.187 -3.761 11.713 1.000 2 B LIG 70.465 1
ATOM 1976 C C_9 . LIG . 1 ? B -5.713 -11.078 15.743 1.000 2 B LIG 83.223 1
ATOM 1977 O O_12 . LIG . 1 ? B -6.380 -12.179 16.293 1.000 2 B LIG 78.227 1
ATOM 1978 C C_10 . LIG . 1 ? B -4.718 -10.494 16.676 1.000 2 B LIG 82.254 1
ATOM 1979 O O_13 . LIG . 1 ? B -5.053 -10.779 18.010 1.000 2 B LIG 78.602 1

CIF:

ATP  O1G     O1G   O  0  1  N  N  N  45.779  46.330  56.052   1.740   1.140  -6.672  O1G     ATP   2  
ATP  O2G     O2G   O  0  1  N  N  N  47.382  44.497  56.626   2.123  -1.036  -7.891  O2G     ATP   3  
ATP  O3G     O3G   O  0  1  N  N  N  45.972  45.530  58.375  -0.302  -0.139  -7.421  O3G     ATP   4  
ATP  PB      PB    P  0  1  N  N  R  43.911  43.740  55.655   0.255  -0.130  -4.446  PB      ATP   5  
ATP  O1B     O1B   O  0  1  N  N  N  42.975  42.722  55.986   0.810   1.234  -4.304  O1B     ATP   6  
ATP  O2B     O2B   O  0  1  N  N  N  43.603  44.767  54.678  -1.231  -0.044  -5.057  O2B     ATP   7  
ATP  O3B     O3B   O  0  1  N  N  N  45.041  44.015  56.738   1.192  -0.990  -5.433  O3B     ATP   8  
ATP  PA      PA    P  0  1  N  N  R  45.228  42.669  53.257  -0.745   0.068  -2.071  PA      ATP   9  
ATP  O1A     O1A   O  0  1  N  N  N  46.380  43.396  52.788  -2.097   0.143  -2.669  O1A     ATP  10  
ATP  O2A     O2A   O  0  1  N  N  N  44.183  42.190  52.351  -0.125   1.549  -1.957  O2A     ATP  11  
ATP  O3A     O3A   O  0  1  N  N  N  44.917  42.716  54.789   0.203  -0.840  -3.002  O3A     ATP  12  
ATP  "O5'"   O5*   O  0  1  N  N  N  46.172  41.568  53.302  -0.844  -0.587  -0.604  "O5'"   ATP  13  
ATP  "C5'"   C5*   C  0  1  N  N  N  46.609  40.422  53.542  -1.694   0.260   0.170  "C5'"   ATP  14  
ATP  "C4'"   C4*   C  0  1  N  N  R  46.520  38.989  53.364  -1.831  -0.309   1.584  "C4'"   ATP  15  
ATP  "O4'"   O4*   O  0  1  N  N  N  46.785  38.908  51.948  -0.542  -0.355   2.234  "O4'"   ATP  16  
ATP  "C3'"   C3*   C  0  1  N  N  S  47.808  38.874  54.112  -2.683   0.630   2.465  "C3'"   ATP  17  
ATP  "O3'"   O3*   O  0  1  N  N  N  47.713  38.357  55.423  -4.033   0.165   2.534  "O3'"   ATP  18  
ATP  "C2'"   C2*   C  0  1  N  N  R  48.719  38.116  53.139  -2.011   0.555   3.856  "C2'"   ATP  19  
ATP  "O2'"   O2*   O  0  1  N  N  N  48.632  36.737  53.425  -2.926   0.043   4.827  "O2'"   ATP  20  
ATP  "C1'"   C1*   C  0  1  N  N  R  48.133  38.409  51.721  -0.830  -0.418   3.647  "C1'"   ATP  21  
ATP  N9      N9    N  0  1  Y  N  N  48.846  39.464  50.986   0.332   0.015   4.425  N9      ATP  22  
ATP  C8      C8    C  0  1  Y  N  N  48.616  40.842  50.945   1.302   0.879   4.012  C8      ATP  23  
ATP  N7      N7    N  0  1  Y  N  N  49.425  41.489  50.165   2.184   1.042   4.955  N7      ATP  24  
ATP  C5      C5    C  0  1  Y  N  N  50.232  40.470  49.664   1.833   0.300   6.033  C5      ATP  25  
ATP  C6      C6    C  0  1  Y  N  N  51.308  40.466  48.731   2.391   0.077   7.303  C6      ATP  26  
ATP  N6      N6    N  0  1  N  N  N  51.721  41.568  48.129   3.564   0.706   7.681  N6      ATP  27  
ATP  N1      N1    N  0  1  Y  N  N  51.912  39.274  48.447   1.763  -0.747   8.135  N1      ATP  28  
ATP  C2      C2    C  0  1  Y  N  N  51.493  38.151  49.029   0.644  -1.352   7.783  C2      ATP  29  
ATP  N3      N3    N  0  1  Y  N  N  50.491  38.016  49.900   0.088  -1.178   6.602  N3      ATP  30  
ATP  C4      C4    C  0  1  Y  N  N  49.892  39.253  50.171   0.644  -0.371   5.704  C4      ATP  31  

Thank you!

[wukevin]

Unfortunately, there's no easy way to do this that I am aware of since Chai1 works on the level of SMILES inputs; you might consider doing some sort of graph alignment similar to what DockQ does here:
https://github.com/bjornwallner/DockQ/blob/13c9dcc84ef2751ecf6b958c6f55dc1981457b16/src/DockQ/DockQ.py#L245-L260

After aligning the graphs you could transfer the atom names that way.

[kirmedvedev]

Unfortunately, there's no easy way to do this that I am aware of since Chai1 works on the level of SMILES inputs; you might consider doing some sort of graph alignment similar to what DockQ does here: https://github.com/bjornwallner/DockQ/blob/13c9dcc84ef2751ecf6b958c6f55dc1981457b16/src/DockQ/DockQ.py#L245-L260

After aligning the graphs you could transfer the atom names that way.

Thank you! I will try it

[arogozhnikov]

@kirmedvedev I previously observed that ordering returned by rdkit coincided with first appearance in smiles, but you'd better double check this.