forlilab / Meeko

Interfacing RDKit and AutoDock
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Missing name line in REMARK lines #50

Open gkxiao opened 1 year ago

gkxiao commented 1 year ago

The name of a molecule is a very important information. But the output file of meeko did not include the name line.

test.sdf: an example of input file with molecular name "test"

test
 OpenBabel06272315433D

  4  3  0  0  0  0  0  0  0  0999 V2000
    1.0507    0.0872   -0.0485 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2754    0.0872   -0.0485 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4632    0.7434   -0.7103 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4632   -0.5690    0.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
M  END
$$$$

test.pdbqt: the output PDBQT file prepared with meeko command:

mk_prepare_ligand.py -i test.sdf -o test.pdbqt

Here is the output.

REMARK SMILES C=O
REMARK SMILES IDX 1 1 2 2
REMARK H PARENT
REMARK Flexibility Score: inf
ROOT
ATOM      1  C   UNL     1       1.051   0.087  -0.049  1.00  0.00     0.307 C
ATOM      2  O   UNL     1       2.275   0.087  -0.049  1.00  0.00    -0.307 OA
ENDROOT
TORSDOF 0

There is no name line in the REMARK lines. Here is an example with Name line:

REMARK  Name = test
REMARK  0 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK                            x       y       z     vdW  Elec       q    Type
REMARK                         _______ _______ _______ _____ _____    ______ ____
ROOT
ATOM      1  C   UNL     1       1.051   0.087  -0.049  0.00  0.00    +0.000 C
ATOM      2  O   UNL     1       2.275   0.087  -0.049  0.00  0.00    +0.000 OA
ENDROOT
TORSDOF 0
gkxiao commented 1 year ago

The sdf file generated by mk_export.py is also missing the molecule name.