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openbabel --gen3d报错
待办的
#I6H1TN
chenqian
创建于
2023-02-22 18:24
``` sdf文件如下: csCF1400/ 01010917432D 27 32 0 0 0 0 0 0 0 0999 V2000 4.6417 -3.9125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.8542 -2.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6417 -2.5750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8542 -3.6542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9000 -4.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1292 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1375 -2.4167 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0 4.9000 -1.7875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7167 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9625 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7042 -1.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1375 -4.0792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9125 -5.6542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4125 -0.2042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7292 -0.4625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3292 -5.3250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8417 0.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7167 -3.1375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4250 -2.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6250 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4292 -4.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3417 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7292 -5.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0625 -4.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5917 -0.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5167 -3.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4250 -3.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 4 1 0 0 3 6 1 0 0 4 1 1 0 0 5 1 1 0 0 6 1 1 0 0 2 7 1 6 0 3 8 1 6 0 9 5 1 0 0 10 11 1 0 0 11 8 2 0 0 4 12 1 6 0 13 9 1 0 0 14 25 1 0 0 15 10 1 0 0 16 5 2 0 0 17 14 1 0 0 18 26 1 0 0 19 27 1 0 0 20 15 1 0 0 21 9 2 0 0 22 8 1 0 0 23 13 1 0 0 24 21 1 0 0 25 22 2 0 0 26 12 1 0 0 27 12 1 0 0 3 2 1 0 0 24 23 2 0 0 19 7 1 0 0 7 18 1 0 0 14 10 2 0 0 20 17 1 0 0 M END > <ID> (5,298) CL01883737 $$$$ csCF1400/ 01010917432D 26 29 0 0 0 0 0 0 0 0999 V2000 ``` 输入命令: ``` obabel *.sdf -omol2 -O *.mol2 -p --gen3d ``` 会出现警告和报错 警告: WARNING: Problems reading a MDL file Missing data following atom specification in atom block 报错: openbabel Error in Do 3D coordinate generation failed 2023.2.24 运行collect_error_sdfs.py后bad/文件夹里的小分子sdf csCF1400/ 01010917432D 26 30 0 0 0 0 0 0 0 0999 V2000 4.0792 -8.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4875 -9.5417 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6667 -9.5417 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0792 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9042 -10.2542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2542 -10.2542 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.2375 -5.8542 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.5667 -6.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7917 -7.5875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0500 -10.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2375 -6.7625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4042 -5.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9542 -7.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3667 -7.5917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3792 -6.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6667 -10.9542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4917 -10.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5125 -8.0042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7917 -6.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2292 -7.5875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5167 -6.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6417 -5.1417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2292 -4.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2292 -3.0042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6417 -3.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6417 -2.2875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 3 1 1 1 0 1 4 1 6 0 5 2 1 0 0 6 3 1 0 0 7 12 1 0 0 8 13 1 0 0 9 4 1 0 0 6 10 1 1 0 11 21 1 0 0 12 11 1 0 0 13 11 1 0 0 14 4 2 0 0 15 8 2 0 0 16 6 1 0 0 17 5 1 0 0 18 9 1 0 0 19 9 1 0 0 20 18 1 0 0 21 19 1 0 0 22 7 1 0 0 23 22 1 0 0 24 25 1 0 0 25 23 1 0 0 26 24 1 0 0 2 3 1 0 0 5 10 1 1 0 17 16 1 0 0 20 11 1 0 0 8 7 1 0 0 M END > <ID> (40,075) CL01972391 $$$$ csCF1400/ 01010917432D 28 31 0 0 0 0 0 0 0 0999 V2000 collect_error_sdfs.py
``` sdf文件如下: csCF1400/ 01010917432D 27 32 0 0 0 0 0 0 0 0999 V2000 4.6417 -3.9125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.8542 -2.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6417 -2.5750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8542 -3.6542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9000 -4.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1292 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1375 -2.4167 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0 4.9000 -1.7875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7167 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9625 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7042 -1.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1375 -4.0792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9125 -5.6542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4125 -0.2042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7292 -0.4625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3292 -5.3250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8417 0.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7167 -3.1375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4250 -2.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6250 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4292 -4.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3417 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7292 -5.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0625 -4.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5917 -0.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5167 -3.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4250 -3.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 4 1 0 0 3 6 1 0 0 4 1 1 0 0 5 1 1 0 0 6 1 1 0 0 2 7 1 6 0 3 8 1 6 0 9 5 1 0 0 10 11 1 0 0 11 8 2 0 0 4 12 1 6 0 13 9 1 0 0 14 25 1 0 0 15 10 1 0 0 16 5 2 0 0 17 14 1 0 0 18 26 1 0 0 19 27 1 0 0 20 15 1 0 0 21 9 2 0 0 22 8 1 0 0 23 13 1 0 0 24 21 1 0 0 25 22 2 0 0 26 12 1 0 0 27 12 1 0 0 3 2 1 0 0 24 23 2 0 0 19 7 1 0 0 7 18 1 0 0 14 10 2 0 0 20 17 1 0 0 M END > <ID> (5,298) CL01883737 $$$$ csCF1400/ 01010917432D 26 29 0 0 0 0 0 0 0 0999 V2000 ``` 输入命令: ``` obabel *.sdf -omol2 -O *.mol2 -p --gen3d ``` 会出现警告和报错 警告: WARNING: Problems reading a MDL file Missing data following atom specification in atom block 报错: openbabel Error in Do 3D coordinate generation failed 2023.2.24 运行collect_error_sdfs.py后bad/文件夹里的小分子sdf csCF1400/ 01010917432D 26 30 0 0 0 0 0 0 0 0999 V2000 4.0792 -8.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4875 -9.5417 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6667 -9.5417 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0792 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9042 -10.2542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2542 -10.2542 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.2375 -5.8542 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.5667 -6.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7917 -7.5875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0500 -10.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2375 -6.7625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4042 -5.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9542 -7.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3667 -7.5917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3792 -6.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6667 -10.9542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4917 -10.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5125 -8.0042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7917 -6.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2292 -7.5875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5167 -6.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6417 -5.1417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2292 -4.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2292 -3.0042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6417 -3.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6417 -2.2875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 3 1 1 1 0 1 4 1 6 0 5 2 1 0 0 6 3 1 0 0 7 12 1 0 0 8 13 1 0 0 9 4 1 0 0 6 10 1 1 0 11 21 1 0 0 12 11 1 0 0 13 11 1 0 0 14 4 2 0 0 15 8 2 0 0 16 6 1 0 0 17 5 1 0 0 18 9 1 0 0 19 9 1 0 0 20 18 1 0 0 21 19 1 0 0 22 7 1 0 0 23 22 1 0 0 24 25 1 0 0 25 23 1 0 0 26 24 1 0 0 2 3 1 0 0 5 10 1 1 0 17 16 1 0 0 20 11 1 0 0 8 7 1 0 0 M END > <ID> (40,075) CL01972391 $$$$ csCF1400/ 01010917432D 28 31 0 0 0 0 0 0 0 0999 V2000 collect_error_sdfs.py
评论 (
0
)
chenqian
创建了
任务
chenqian
修改了
描述
原值
新值
``` sdf文件如下:
csCF1400/ 01010917432D
27 32 0 0 0 0 0 0 0 0999 V2000
4.6417 -3.9125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.8542 -2.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.6417 -2.5750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
3.8542 -3.6542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.9000 -4.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1292 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1375 -2.4167 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0
4.9000 -1.7875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7167 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9625 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7042 -1.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1375 -4.0792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
5.9125 -5.6542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.4125 -0.2042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7292 -0.4625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3292 -5.3250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8417 0.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7167 -3.1375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4250 -2.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6250 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4292 -4.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3417 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7292 -5.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0625 -4.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5917 -0.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5167 -3.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4250 -3.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 4 1 0 0
3 6 1 0 0
4 1 1 0 0
5 1 1 0 0
6 1 1 0 0
2 7 1 6 0
3 8 1 6 0
9 5 1 0 0
10 11 1 0 0
11 8 2 0 0
4 12 1 6 0
13 9 1 0 0
14 25 1 0 0
15 10 1 0 0
16 5 2 0 0
17 14 1 0 0
18 26 1 0 0
19 27 1 0 0
20 15 1 0 0
21 9 2 0 0
22 8 1 0 0
23 13 1 0 0
24 21 1 0 0
25 22 2 0 0
26 12 1 0 0
27 12 1 0 0
3 2 1 0 0
24 23 2 0 0
19 7 1 0 0
7 18 1 0 0
14 10 2 0 0
20 17 1 0 0
M END
> <ID> (5,298)
CL01883737
$$$$
csCF1400/ 01010917432D
26 29 0 0 0 0 0 0 0 0999 V2000
```
输入命令:
```
obabel *.sdf -omol2 -O *.mol2 -p --gen3d
```
会出现警告和报错
警告:
WARNING: Problems reading a MDL file
Missing data following atom specification in atom block
报错:
openbabel Error in Do
3D coordinate generation failed
chenqian
修改了
描述
原值
``` sdf文件如下:
csCF1400/ 01010917432D
27 32 0 0 0 0 0 0 0 0999 V2000
4.6417 -3.9125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.8542 -2.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.6417 -2.5750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
3.8542 -3.6542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.9000 -4.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1292 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1375 -2.4167 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0
4.9000 -1.7875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7167 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9625 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7042 -1.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1375 -4.0792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
5.9125 -5.6542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.4125 -0.2042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7292 -0.4625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3292 -5.3250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8417 0.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7167 -3.1375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4250 -2.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6250 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4292 -4.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3417 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7292 -5.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0625 -4.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5917 -0.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5167 -3.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4250 -3.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 4 1 0 0
3 6 1 0 0
4 1 1 0 0
5 1 1 0 0
6 1 1 0 0
2 7 1 6 0
3 8 1 6 0
9 5 1 0 0
10 11 1 0 0
11 8 2 0 0
4 12 1 6 0
13 9 1 0 0
14 25 1 0 0
15 10 1 0 0
16 5 2 0 0
17 14 1 0 0
18 26 1 0 0
19 27 1 0 0
20 15 1 0 0
21 9 2 0 0
22 8 1 0 0
23 13 1 0 0
24 21 1 0 0
25 22 2 0 0
26 12 1 0 0
27 12 1 0 0
3 2 1 0 0
24 23 2 0 0
19 7 1 0 0
7 18 1 0 0
14 10 2 0 0
20 17 1 0 0
M END
> <ID> (5,298)
CL01883737
$$$$
csCF1400/ 01010917432D
26 29 0 0 0 0 0 0 0 0999 V2000
```
输入命令:
```
obabel *.sdf -omol2 -O *.mol2 -p --gen3d
```
会出现警告和报错
警告:
WARNING: Problems reading a MDL file
Missing data following atom specification in atom block
报错:
openbabel Error in Do
3D coordinate generation failed
新值
``` sdf文件如下:
csCF1400/ 01010917432D
27 32 0 0 0 0 0 0 0 0999 V2000
4.6417 -3.9125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.8542 -2.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.6417 -2.5750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
3.8542 -3.6542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.9000 -4.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1292 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1375 -2.4167 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0
4.9000 -1.7875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7167 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9625 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7042 -1.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1375 -4.0792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
5.9125 -5.6542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.4125 -0.2042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7292 -0.4625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3292 -5.3250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8417 0.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7167 -3.1375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4250 -2.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6250 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4292 -4.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3417 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7292 -5.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0625 -4.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5917 -0.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5167 -3.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4250 -3.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 4 1 0 0
3 6 1 0 0
4 1 1 0 0
5 1 1 0 0
6 1 1 0 0
2 7 1 6 0
3 8 1 6 0
9 5 1 0 0
10 11 1 0 0
11 8 2 0 0
4 12 1 6 0
13 9 1 0 0
14 25 1 0 0
15 10 1 0 0
16 5 2 0 0
17 14 1 0 0
18 26 1 0 0
19 27 1 0 0
20 15 1 0 0
21 9 2 0 0
22 8 1 0 0
23 13 1 0 0
24 21 1 0 0
25 22 2 0 0
26 12 1 0 0
27 12 1 0 0
3 2 1 0 0
24 23 2 0 0
19 7 1 0 0
7 18 1 0 0
14 10 2 0 0
20 17 1 0 0
M END
> <ID> (5,298)
CL01883737
$$$$
csCF1400/ 01010917432D
26 29 0 0 0 0 0 0 0 0999 V2000
```
输入命令:
```
obabel *.sdf -omol2 -O *.mol2 -p --gen3d
```
会出现警告和报错
警告:
WARNING: Problems reading a MDL file
Missing data following atom specification in atom block
报错:
openbabel Error in Do
3D coordinate generation failed
2023.2.24
运行collect_error_sdfs.py后bad/文件夹里的小分子sdf
csCF1400/ 01010917432D
26 30 0 0 0 0 0 0 0 0999 V2000
4.0792 -8.8292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.4875 -9.5417 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
3.6667 -9.5417 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.0792 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9042 -10.2542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
3.2542 -10.2542 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7.2375 -5.8542 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.5667 -6.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7917 -7.5875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.0500 -10.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2375 -6.7625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4042 -5.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9542 -7.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3667 -7.5917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.3792 -6.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.6667 -10.9542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4917 -10.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5125 -8.0042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7917 -6.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2292 -7.5875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5167 -6.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6417 -5.1417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2292 -4.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2292 -3.0042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.6417 -3.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6417 -2.2875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1 0
3 1 1 1 0
1 4 1 6 0
5 2 1 0 0
6 3 1 0 0
7 12 1 0 0
8 13 1 0 0
9 4 1 0 0
6 10 1 1 0
11 21 1 0 0
12 11 1 0 0
13 11 1 0 0
14 4 2 0 0
15 8 2 0 0
16 6 1 0 0
17 5 1 0 0
18 9 1 0 0
19 9 1 0 0
20 18 1 0 0
21 19 1 0 0
22 7 1 0 0
23 22 1 0 0
24 25 1 0 0
25 23 1 0 0
26 24 1 0 0
2 3 1 0 0
5 10 1 1 0
17 16 1 0 0
20 11 1 0 0
8 7 1 0 0
M END
> <ID> (40,075)
CL01972391
$$$$
csCF1400/ 01010917432D
28 31 0 0 0 0 0 0 0 0999 V2000
collect_error_sdfs.py
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