mk_export.py not parsing PDBQT scores

tlhr commented 1 year ago

It seems mk_export.py can no longer parse scores from PDBQT files and insert them as properties in SDF files. Here's a simple example file:

MODEL 1
REMARK VINA RESULT:      -2.7      0.000      0.000
REMARK SMILES CCO
REMARK SMILES IDX 1 1 2 2 3 3
REMARK H PARENT 3 4
REMARK Flexibility Score: inf
ROOT
ATOM      1  C   UNL     1      -0.667  11.713  24.654  1.00  0.00     0.034 C 
ATOM      2  C   UNL     1      -2.004  11.017  24.423  1.00  0.00     0.152 C 
ENDROOT
BRANCH   2   3
ATOM      3  O   UNL     1      -2.705  11.640  23.381  1.00  0.00    -0.397 OA
ATOM      4  H   UNL     1      -3.199  12.399  23.786  1.00  0.00     0.210 HD
ENDBRANCH   2   3
TORSDOF 1
ENDMDL

The output of mk_export.py <file>.pdbqt - is:


     RDKit          3D

  9  8  0  0  0  0  0  0  0  0999 V2000
   -0.6670   11.7130   24.6540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0040   11.0170   24.4230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7050   11.6400   23.3810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   11.8078   25.7347 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1389   11.1200   24.1970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6906   12.7133   24.1970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8240    9.9641   24.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6028   11.0794   25.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1990   12.3990   23.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  1  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
M  END
$$$$

Meeko 0.4.0 does not have this problem, and successfully adds the docking free energy as a property:


     RDKit          3D

  9  8  0  0  0  0  0  0  0  0999 V2000
   -0.6670   11.7130   24.6540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0040   11.0170   24.4230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7050   11.6400   23.3810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   11.8078   25.7347 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1389   11.1200   24.1970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6906   12.7133   24.1970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8240    9.9641   24.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6028   11.0794   25.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1990   12.3990   23.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  1  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
M  END
>  <meeko>  (1) 
{"free_energy": -2.7}

$$$$

diogomart commented 1 year ago

Thanks for finding and reporting this!

diogomart commented 1 year ago

fixed in the develop branch for vina: e03f9394f56d1aa6bbed670ab395a20cfe0765dc and ad-gpu: 8c0fcadae2b2546a9083414c99284ec23e565592

tlhr commented 1 year ago

Thank you for the super quick fix, it works now :)

forlilab / Meeko

mk_export.py not parsing PDBQT scores #65