Hi RDKiters,
Hope you are well. I'm having trouble loading these molecules. Do you know
any walk around??
Bests,
Eduardo
In: rdkit.__version__
Out: '2020.09.5'
In: Chem.MolFromMOL2File('file.mol2')
Out: None
In:Chem.MolFromPDBBlock(pdb_block)
Out: (Molecule successfully loaded but missing connections)
*file.mol2*
>
@<TRIPOS>MOLECULE
> pdb3b3b.ent_out_ok
> 26 27 0 0 0
> SMALL
> GASTEIGER
> @<TRIPOS>ATOM
> 1 N 56.3038 -19.9123 38.1221 N.3 1 LIG -0.3224
> 2 CA 55.7546 -19.8386 36.7785 C.3 1 LIG 0.0489
> 3 C 56.6780 -19.0176 35.8775 C.2 1 LIG 0.0588
> 4 O 56.8003 -17.8103 36.1384 O.co2 1 LIG -0.5482
> 5 CB 54.3375 -19.2367 36.7831 C.3 1 LIG -0.0052
> 6 CG 53.2279 -20.0619 37.3598 C.ar 1 LIG -0.0205
> 7 CD1 52.5022 -20.9701 36.6718 C.ar 1 LIG 0.0060
> 8 CD2 52.6251 -19.9979 38.6870 C.ar 1 LIG 0.0029
> 9 CE2 51.4779 -20.8441 38.7046 C.ar 1 LIG 0.0467
> 10 CE3 52.8995 -19.2788 39.8677 C.ar 1 LIG -0.0523
> 11 NE1 51.4807 -21.4416 37.4637 N.ar 1 LIG -0.3604
> 12 CZ2 50.6116 -20.9179 39.8080 C.ar 1 LIG -0.0378
> 13 CZ3 52.0516 -19.3528 40.9911 C.ar 1 LIG -0.0611
> 14 CH2 50.8981 -20.1559 40.9548 C.ar 1 LIG -0.0598
> 15 OXT 57.2414 -19.5929 34.9256 O.co2 1 LIG -0.5482
> 16 HA 55.6995 -20.8519 36.3812 H 1 LIG 0.0523
> 17 HB1 54.3326 -18.2711 37.2871 H 1 LIG 0.0332
> 18 HB2 54.0496 -19.0290 35.7533 H 1 LIG 0.0332
> 19 HD1 52.6579 -21.2317 35.6382 H 1 LIG 0.0810
> 20 HE1 50.7760 -22.0861 37.1266 H 1 LIG 0.1653
> 21 HE3 53.7741 -18.6562 39.8800 H 1 LIG 0.0624
> 22 HZ2 49.7440 -21.5583 39.7776 H 1 LIG 0.0638
> 23 HZ3 52.2783 -18.7898 41.8812 H 1 LIG 0.0618
> 24 HH2 50.2483 -20.2108 41.8156 H 1 LIG 0.0618
> 25 H1 55.7027 -20.4381 38.7435 H 1 LIG 0.1188
> 26 H2 57.1830 -20.4155 38.1180 H 1 LIG 0.1188
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 25 1
> 3 1 26 1
> 4 2 3 1
> 5 2 5 1
> 6 2 16 1
> 7 3 4 ar
> 8 3 15 ar
> 9 5 6 1
> 10 5 17 1
> 11 5 18 1
> 12 6 7 ar
> 13 6 8 ar
> 14 7 11 ar
> 15 7 19 1
> 16 8 9 ar
> 17 8 10 ar
> 18 9 12 ar
> 19 10 13 ar
> 20 10 21 1
> 21 9 11 ar
> 22 11 20 1
> 23 12 14 ar
> 24 12 22 1
> 25 13 14 ar
> 26 13 23 1
> 27 14 24 1
*pdb_block*
> REMARK 4 active torsions:
> REMARK status: ('A' for Active; 'I' for Inactive)
> REMARK 1 A between atoms: N_1 and CA_2
> REMARK 2 A between atoms: CA_2 and C_3
> REMARK 3 A between atoms: CA_2 and CB_5
> REMARK 4 A between atoms: CB_5 and CG_6
> ATOM 1 CG LIG d 1 53.228 -20.062 37.360 0.00 0.00
> ATOM 2 CD1 LIG d 1 52.502 -20.970 36.672 0.00 0.00
> ATOM 3 CD2 LIG d 1 52.625 -19.998 38.687 0.00 0.00
> ATOM 4 CE2 LIG d 1 51.478 -20.844 38.705 0.00 0.00
> ATOM 5 CE3 LIG d 1 52.900 -19.279 39.868 0.00 0.00
> ATOM 6 NE1 LIG d 1 51.481 -21.442 37.464 0.00 0.00
> ATOM 7 CZ2 LIG d 1 50.612 -20.918 39.808 0.00 0.00
> ATOM 8 CZ3 LIG d 1 52.052 -19.353 40.991 0.00 0.00
> ATOM 9 CH2 LIG d 1 50.898 -20.156 40.955 0.00 0.00
> ATOM 10 HE1 LIG d 1 50.776 -22.086 37.127 0.00 0.00
> ATOM 11 CB LIG d 1 54.337 -19.237 36.783 0.00 0.00
> ATOM 12 CA LIG d 1 55.755 -19.839 36.779 0.00 0.00
> ATOM 13 N LIG d 1 56.304 -19.912 38.122 0.00 0.00
> ATOM 14 H1 LIG d 1 55.703 -20.438 38.743 0.00 0.00
> ATOM 15 H2 LIG d 1 57.183 -20.416 38.118 0.00 0.00
> ATOM 16 C LIG d 1 56.678 -19.018 35.877 0.00 0.00
> ATOM 17 O LIG d 1 56.800 -17.810 36.138 0.00 0.00
> ATOM 18 OXT LIG d 1 57.241 -19.593 34.926 0.00 0.00
>
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