Re: [Rdkit-discuss] can't kekulize molecule

Francois BERENGER Wed, 16 Aug 2017 00:56:47 -0700

On 08/16/2017 03:36 PM, Greg Landrum wrote:

Hi Shuai,
The RDKit Mol2 parser is really only validated for the atom typesgenerated by corina. I'm not surprised that the ouput from open babelwould not be understood. This is documented:
http://rdkit.org/docs/api/rdkit.Chem.rdmolfiles-module.html#MolFromMol2File


It would be really nice if open babel MOL2 output could directly be read
in by rdkit.

I often find myself running
$ obabel in.mol2 -O out.sdf
just for that purpose.

An aside: If you have an SDF file you can read that directly into theRDKit. It seems like you shouldn't need the openbabel translation stepat all.


-greg

On Wed, Aug 16, 2017 at 12:13 AM, David Liu <sdhsm1...@gmail.com<mailto:sdhsm1...@gmail.com>> wrote:


    Dear all,

    I have troubles to kekulize molecule using rdkit, below is an example:

    The example.mol2 file looks like below:

    @MOLECULE
    example
    46 49 0 0 0
    SMALL
    GASTEIGER

    @ATOM
    1 C -4.5556 -0.2844 1.1718 C.3 1 LIG1 -0.0109
    2 C -6.0291 -0.7271 1.2334 C.3 1 LIG1 0.0493
    3 C -6.4413 -0.5958 -1.0493 C.3 1 LIG1 0.0493
    4 C -5.1977 0.3130 -1.1927 C.3 1 LIG1 -0.0109
    5 C 5.5992 -2.5640 -0.8780 C.ar 1 LIG1 -0.0253
    6 O -6.3822 -1.4588 0.0764 O.3 1 LIG1 -0.3796
    7 C 2.8943 1.6722 0.9911 C.ar 1 LIG1 0.2664
    8 C 5.1745 -2.0407 0.3480 C.ar 1 LIG1 0.1371
    9 C -1.6179 0.4017 0.1577 C.ar 1 LIG1 0.2173
    10 C -4.0573 -0.1702 -0.2838 C.3 1 LIG1 0.0275
    11 C 0.8767 -0.2307 1.1489 C.ar 1 LIG1 0.0370
    12 C 2.1438 -0.5325 1.6439 C.ar 1 LIG1 -0.0306
    13 C 6.1958 -1.7294 -1.8279 C.ar 1 LIG1 -0.0590
    14 C 6.3717 -0.3702 -1.5525 C.ar 1 LIG1 -0.0605
    15 C 5.9487 0.1564 -0.3282 C.ar 1 LIG1 -0.0452
    16 C 0.6358 1.0320 0.5744 C.ar 1 LIG1 0.1483
    17 C -0.1716 -1.1537 1.2042 C.ar 1 LIG1 0.0418
    18 C 3.1618 0.4153 1.5592 C.ar 1 LIG1 0.0780
    19 C 5.3424 -0.6749 0.6231 C.ar 1 LIG1 0.0480
    20 C 1.3530 3.2786 -0.1013 C.3 1 LIG1 0.0167
    21 F 4.6032 -2.8623 1.2640 F 1 LIG1 -0.2043
    22 S 4.7969 0.0115 2.1898 S.3 1 LIG1 -0.0812
    23 N -1.3906 -0.8211 0.7091 N.ar 1 LIG1 -0.2222
    24 O 3.8206 2.5277 0.9363 O.2 1 LIG1 -0.2664
    25 N 1.6412 1.9659 0.5033 N.ar 1 LIG1 -0.2949
    26 N -0.6088 1.3106 0.0937 N.ar 1 LIG1 -0.1964
    27 N -2.9091 0.7394 -0.3655 N.pl3 1 LIG1 -0.3104
    28 H -3.9262 -1.0225 1.7144 H 1 LIG1 0.0305
    29 H -4.4544 0.6942 1.6907 H 1 LIG1 0.0305
    30 H -6.1785 -1.3738 2.1237 H 1 LIG1 0.0560
    31 H -6.6965 0.1565 1.3647 H 1 LIG1 0.0560
    32 H -7.3658 0.0220 -1.0063 H 1 LIG1 0.0560
    33 H -6.5227 -1.2302 -1.9574 H 1 LIG1 0.0560
    34 H -4.8575 0.3261 -2.2513 H 1 LIG1 0.0305
    35 H -5.4753 1.3532 -0.9112 H 1 LIG1 0.0305
    36 H 5.4676 -3.6168 -1.0922 H 1 LIG1 0.0646
    37 H -3.7461 -1.1771 -0.6436 H 1 LIG1 0.0500
    38 H 2.3428 -1.4998 2.0895 H 1 LIG1 0.0638
    39 H 6.5237 -2.1362 -2.7758 H 1 LIG1 0.0618
    40 H 6.8363 0.2748 -2.2870 H 1 LIG1 0.0618
    41 H 6.0904 1.2094 -0.1219 H 1 LIG1 0.0630
    42 H -0.0243 -2.1352 1.6372 H 1 LIG1 0.0838
    43 H 2.2342 3.9528 -0.1073 H 1 LIG1 0.0457
    44 H 0.5450 3.7853 0.4685 H 1 LIG1 0.0457
    45 H 1.0258 3.1432 -1.1544 H 1 LIG1 0.0457
    46 H -3.0166 1.6655 -0.8392 H 1 LIG1 0.1492
    @BOND
    1 1 2 1
    2 1 10 1
    3 2 6 1
    4 3 4 1
    5 3 6 1
    6 4 10 1
    7 5 8 ar
    8 5 13 ar
    9 7 18 ar
    10 7 24 2
    11 7 25 ar
    12 8 19 ar
    13 8 21 1
    14 9 23 ar
    15 9 26 ar
    16 9 27 1
    17 10 27 1
    18 11 12 ar
    19 11 16 ar
    20 11 17 ar
    21 12 18 ar
    22 13 14 ar
    23 14 15 ar
    24 15 19 ar
    25 16 25 ar
    26 16 26 ar
    27 17 23 ar
    28 18 22 1
    29 19 22 1
    30 20 25 1
    31 1 28 1
    32 1 29 1
    33 2 30 1
    34 2 31 1
    35 3 32 1
    36 3 33 1
    37 4 34 1
    38 4 35 1
    39 5 36 1
    40 10 37 1
    41 12 38 1
    42 13 39 1
    43 14 40 1
    44 15 41 1
    45 17 42 1
    46 20 43 1
    47 20 44 1
    48 20 45 1
    49 27 46 1

    And the example.py code looks like

    from rdkit.Chem import AllChem
    from rdkit import Chem

    rdkit_mol = Chem.MolFromMol2File("example.mol2", sanitize=False,
    removeHs=False)
    mol = AllChem.RemoveHs(rdkit_mol)

    If running the example.py, it returns an error as below:

    ValueError: Sanitization error: Can't kekulize mol. Unkekulized
    atoms: 8 10 11 15 16 17 22 24 25

    It seems rdkit cannot understand the molecules when it try to remove
    the hydrogens, probably related to the format of the mol2 file I
    used here? I use openbabel to convert the mol2 file from an sdf
    file. So I wonder if there is a plan to parse the mol2 file like
    this or I need to further cook the mol2 file. I appreciate for any
    advices!


    Thanks,

    Shuai


    
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Re: [Rdkit-discuss] can't kekulize molecule

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