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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