Comments (4)
What SMILES string did the code generate and how long does it take to make it?
from xyz2mol.
I couldn't get SMILES string from the code since it took too much time.
SMILES generated from the original SDF file by RDKit (with option isomericSmiles=False
) is Cc1cn(C2CC(O)C(COP(=O)([O-])OP(=O)([O-])OC3OC(C)C([NH3+])C(O)C3O)O2)c(=O)[nH]c1=O
.
Original SDF:
0FX_3VBL_A
frProtoss 02171720243D 1 1.00000 0.00000 0
Protoss
61 63 0 0 0 0 999 V2000
-10.5130 36.5570 -27.2740 O 0 0 0 0 0 0 0 0 0 0 0 0
-11.2500 35.5440 -26.4350 P 0 0 0 0 0 0 0 0 0 0 0 0
-10.7820 34.1390 -26.1530 O 0 5 0 0 0 0 0 0 0 0 0 0
-12.6550 35.2460 -27.1540 O 0 0 0 0 0 0 0 0 0 0 0 0
-13.5190 36.3060 -27.5670 C 0 0 2 0 0 0 0 0 0 0 0 0
-14.9380 36.1250 -27.0400 C 0 0 2 0 0 0 0 0 0 0 0 0
-14.9050 35.7870 -25.6490 O 0 0 0 0 0 0 0 0 0 0 0 0
-15.4420 34.9070 -27.8090 C 0 0 1 0 0 0 0 0 0 0 0 0
-16.7510 34.5310 -27.3550 O 0 0 0 0 0 0 0 0 0 0 0 0
-15.2980 35.1000 -29.3220 C 0 0 2 0 0 0 0 0 0 0 0 0
-15.6460 33.8700 -30.0130 N 0 3 0 0 0 0 0 0 0 0 0 0
-13.8780 35.5310 -29.7080 C 0 0 1 0 0 0 0 0 0 0 0 0
-13.5980 35.6000 -31.2120 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.4810 36.6850 -28.9450 O 0 0 0 0 0 0 0 0 0 0 0 0
-11.6530 36.1670 -25.0090 O 0 0 0 0 0 0 0 0 0 0 0 0
-10.5810 36.9380 -24.0850 P 0 0 0 0 0 0 0 0 0 0 0 0
-9.2600 36.1800 -24.1260 O 0 0 0 0 0 0 0 0 0 0 0 0
-11.3360 37.1730 -22.8000 O 0 5 0 0 0 0 0 0 0 0 0 0
-10.3670 38.3950 -24.7190 O 0 0 0 0 0 0 0 0 0 0 0 0
-11.5020 39.2260 -24.9770 C 0 0 0 0 0 0 0 0 0 0 0 0
-11.0750 40.6710 -25.2160 C 0 0 1 0 0 0 0 0 0 0 0 0
-10.5170 41.2200 -24.0210 O 0 0 0 0 0 0 0 0 0 0 0 0
-9.9190 40.6770 -26.2160 C 0 0 1 0 0 0 0 0 0 0 0 0
-10.4450 40.7660 -27.5430 O 0 0 0 0 0 0 0 0 0 0 0 0
-9.0910 41.8900 -25.8100 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.3240 41.9660 -24.3050 C 0 0 2 0 0 0 0 0 0 0 0 0
-8.1600 41.4700 -23.5610 N 0 0 0 0 0 0 0 0 0 0 0 0
-8.1730 40.2310 -23.0310 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.0730 39.7670 -22.3250 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.0110 38.3940 -21.6940 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.0900 42.2640 -23.4520 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.0980 43.4130 -23.9620 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.9990 41.8580 -22.7760 N 0 0 0 0 0 0 0 0 0 0 0 0
-5.9930 40.6250 -22.2180 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.9790 40.2560 -21.6000 O 0 0 0 0 0 0 0 0 0 0 0 0
-13.1751 37.1090 -27.0802 H 0 0 0 0 0 0 0 0 0 0 0 0
-15.5031 36.9319 -27.2121 H 0 0 0 0 0 0 0 0 0 0 0 0
-14.0646 35.2836 -25.4481 H 0 0 0 0 0 0 0 0 0 0 0 0
-14.8341 34.1515 -27.5648 H 0 0 0 0 0 0 0 0 0 0 0 0
-17.4419 35.0114 -27.8952 H 0 0 0 0 0 0 0 0 0 0 0 0
-15.9344 35.8152 -29.6109 H 0 0 0 0 0 0 0 0 0 0 0 0
-15.5498 34.0032 -30.9994 H 0 0 0 0 0 0 0 0 0 0 0 0
-15.0359 33.1360 -29.7147 H 0 0 0 0 0 0 0 0 0 0 0 0
-13.2906 34.7934 -29.3750 H 0 0 0 0 0 0 0 0 0 0 0 0
-12.6523 35.8882 -31.3621 H 0 0 0 0 0 0 0 0 0 0 0 0
-13.7401 34.6978 -31.6193 H 0 0 0 0 0 0 0 0 0 0 0 0
-14.2187 36.2590 -31.6367 H 0 0 0 0 0 0 0 0 0 0 0 0
-12.1181 39.1925 -24.1900 H 0 0 0 0 0 0 0 0 0 0 0 0
-11.9786 38.8869 -25.7881 H 0 0 0 0 0 0 0 0 0 0 0 0
-11.8403 41.2243 -25.5449 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.3762 39.8429 -26.1176 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.6916 40.7702 -28.2006 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.4157 42.7178 -26.2675 H 0 0 0 0 0 0 0 0 0 0 0 0
-8.1228 41.7519 -26.0185 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.4786 42.9217 -24.0544 H 0 0 0 0 0 0 0 0 0 0 0 0
-8.9758 39.6461 -23.1468 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.1284 38.2758 -21.2390 H 0 0 0 0 0 0 0 0 0 0 0 0
-7.7468 38.3019 -21.0231 H 0 0 0 0 0 0 0 0 0 0 0 0
-7.1168 37.6964 -22.4026 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.2045 42.4587 -22.6874 H 0 0 0 0 0 0 0 0 0 0 0 0
-16.5918 33.6244 -29.8005 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 15 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
5 14 1 0 0 0 0
6 7 1 0 0 0 0
6 8 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
12 13 1 0 0 0 0
12 14 1 0 0 0 0
15 16 1 0 0 0 0
16 17 2 0 0 0 0
16 18 1 0 0 0 0
16 19 1 0 0 0 0
19 20 1 0 0 0 0
20 21 1 0 0 0 0
21 22 1 0 0 0 0
21 23 1 0 0 0 0
22 26 1 0 0 0 0
23 24 1 0 0 0 0
23 25 1 0 0 0 0
25 26 1 0 0 0 0
26 27 1 0 0 0 0
27 28 1 0 0 0 0
27 31 1 0 0 0 0
28 29 2 0 0 0 0
29 30 1 0 0 0 0
29 34 1 0 0 0 0
31 32 2 0 0 0 0
31 33 1 0 0 0 0
33 34 1 0 0 0 0
34 35 2 0 0 0 0
33 60 1 0 0 0 0
5 36 1 0 0 0 0
6 37 1 0 0 0 0
7 38 1 0 0 0 0
8 39 1 0 0 0 0
9 40 1 0 0 0 0
10 41 1 0 0 0 0
11 42 1 0 0 0 0
11 43 1 0 0 0 0
12 44 1 0 0 0 0
13 45 1 0 0 0 0
13 46 1 0 0 0 0
13 47 1 0 0 0 0
11 61 1 0 0 0 0
20 48 1 0 0 0 0
20 49 1 0 0 0 0
21 50 1 0 0 0 0
23 51 1 0 0 0 0
24 52 1 0 0 0 0
25 53 1 0 0 0 0
25 54 1 0 0 0 0
26 55 1 0 0 0 0
28 56 1 0 0 0 0
30 57 1 0 0 0 0
30 58 1 0 0 0 0
30 59 1 0 0 0 0
M CHG 3 3 -1 11 1 18 -1
M END
$$$$
from xyz2mol.
I've made a new version that is much faster. It works for your example as long as you specify the correct charge. Let me know if you find more problems.
from xyz2mol.
It worked! Thank you for your modification.
from xyz2mol.
Related Issues (20)
- Purpose of 1.3 multiplier in checking covalent bonds HOT 2
- Stranger case when convert xyz file to mol HOT 5
- missing support for boron atoms HOT 1
- Problem with assignment of charges HOT 4
- 'charge_OK' referenced before assignment HOT 1
- Exceptionally long runtime for a few organic structures from materials project HOT 7
- Failure for Ruthenium complexes HOT 2
- `--sdf` argument HOT 1
- Release on conda HOT 25
- Valence greater than 4 HOT 1
- typo? HOT 2
- NameError: name 'defaultdict' is not defined HOT 5
- Parsing nciatlas geometries HOT 1
- Add UserWarning for incorrect charge?
- atomic valence of O atom inconsistent with RDkit HOT 2
- Convert xyz file with several structures in it (different molecules or same molecule, conformers) HOT 2
- how does this relate to rdkit.Chem.rdmolfiles.MolFromXYZBlock and rdkit.Chem.rdmolfiles.MolFromXYZFile ? HOT 1
- Propyl radical gives empty list of molecules HOT 4
- sdf file is empty while converting from xyz file HOT 12
- Comparison with OpenBabel?
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from xyz2mol.