Comments (4)
jhjensen2
commented on August 28, 2024
What SMILES string did the code generate and how long does it take to make it?
from xyz2mol.
n-yoshikawa
commented on August 28, 2024
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
$$$$
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jhjensen2
commented on August 28, 2024
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.
n-yoshikawa
commented on August 28, 2024
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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