scrup.py changes the atom order in the produced file

[hima111997]

i was trying to perform redocking step on a molecule in an sdf format. this is the original atom order from cocrystalized structure:
It start with C - C atoms

  -13.5510  -32.6490   95.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4140  -31.7060   95.4280 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2110  -32.2340   94.8890 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3340  -31.5830   96.9530 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2750  -30.6770   97.3000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6530  -31.0540   97.4960 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5830  -30.9780   98.9190 O   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8190  -31.9400   97.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.7610  -32.1690   95.6430 N   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1790  -31.3590   97.4740 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.3770  -30.0750   96.8790 O   0  0  0  0  0  0  0  0  0  0  0  0

However after performing this command:

!scrub.py lig.sdf -o lig_H.sdf --ff uff --ph 7.4

the new file has different atom order (it added hydrogen which is not a problem here):

1.2781   -1.4038    0.5206 C   0  0  0  0  0  0  0  0  0  0  0  0
 -0.1118   -1.4998    0.0478 N   0  0  0  0  0  0  0  0  0  0  0  0
 -0.8928   -0.3005    0.4175 C   0  0  1  0  0  0  0  0  0  0  0  0
  1.9868   -0.1800   -0.0899 C   0  0  2  0  0  0  0  0  0  0  0  0
  3.3165   -0.1016    0.3603 O   0  0  0  0  0  0  0  0  0  0  0  0
  1.2182    1.1133    0.2389 C   0  0  1  0  0  0  0  0  0  0  0  0
  1.8199    2.1887   -0.4349 O   0  0  0  0  0  0  0  0  0  0  0  0
 -0.2578    0.9778   -0.1953 C   0  0  2  0  0  0  0  0  0  0  0  0
 -0.9849    2.1269    0.1652 O   0  0  0  0  0  0  0  0  0  0  0  0
 -2.3687   -0.4645   -0.0038 C   0  0  0  0  0  0  0  0  0  0  0  0
 -2.4876   -0.6385   -1.3915 O   0  0  0  0  0  0  0  0  0  0  0  0
  1.8304   -2.3237    0.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
  1.2979   -1.3443    1.6326 H   0  0  0  0  0  0  0  0  0  0  0  0
 -0.1145   -1.6322   -0.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
 -0.5458   -2.3450    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
 -0.8870   -0.1974    1.5278 H   0  0  0  0  0  0  0  0  0  0  0  0
  2.0113   -0.3084   -1.1949 H   0  0  0  0  0  0  0  0  0  0  0  0
  3.2955    0.0036    1.3476 H   0  0  0  0  0  0  0  0  0  0  0  0
  1.2641    1.2824    1.3416 H   0  0  0  0  0  0  0  0  0  0  0  0
  1.5426    3.0166    0.0377 H   0  0  0  0  0  0  0  0  0  0  0  0
 -0.2820    0.8941   -1.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
 -0.9682    2.1947    1.1558 H   0  0  0  0  0  0  0  0  0  0  0  0
 -2.7912   -1.3604    0.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
 -2.9706    0.4076    0.3420 H   0  0  0  0  0  0  0  0  0  0  0  0
 -2.6001    0.2647   -1.7873 H   0  0  0  0  0  0  0  0  0  0  0  0

It now starts with C - N atoms.

This makes a problem when i try to calculate the RMSD between the docked pose and the cocrytalized structure

[diogomart]

You can use RDKit to map the indices, as here: https://github.com/rdkit/rdkit/blob/master/Contrib/CalcLigRMSD/CalcLigRMSD.py

Keeping indices is currently not planned, i'll keep the issue open in case someone wants to implement that.