PCQM4Mv2是OGB的一个量化benchmark数据集。该数据集包含3378606个.xyz文件。所有的.xyz文件都集中在pcqm4m-v2-train.sdf文件里。
.sdf文件的部分内容如下:
/Volumes/PubChemQCDataBaseWork/pubchemqc2017database/xyz/00000000_00009999/0.xyz
OpenBabel02162213453D
30 32 0 0 1 0 0 0 0 0999 V2000
4.9919 -5.2514 4.0126 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1051 -3.0257 3.5200 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5521 -3.9001 1.9140 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3372 -1.9217 2.7029 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7751 -2.7953 1.0929 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8586 1.2252 -1.7853 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8118 0.8707 -3.0956 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7890 -0.8350 -0.8455 C 0 0 0 0 0 3 0 0 0 0 0 0
4.6658 -0.4760 -3.0127 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2150 -4.0391 3.1392 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6770 -1.7955 1.4745 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8499 -0.2104 -1.5946 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9121 -0.5519 0.6130 C 0 0 2 0 0 0 0 0 0 0 0 0
3.9134 0.7241 -0.9340 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0405 0.6404 1.1008 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7160 0.0207 -3.7371 N 0 0 0 0 0 0 0 0 0 0 0 0
3.9796 1.1019 0.3172 N 0 0 0 0 0 2 0 0 0 0 0 0
5.2985 1.1457 2.1772 O 0 0 0 0 0 0 0 0 0 0 0 0
5.1819 -5.0262 5.0671 H 0 0 0 0 0 0 0 0 0 0 0 0
5.6619 -6.0746 3.7296 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9660 -5.6247 3.9250 H 0 0 0 0 0 0 0 0 0 0 0 0
6.6247 -3.1010 4.4725 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8445 -4.6636 1.5979 H 0 0 0 0 0 0 0 0 0 0 0 0
7.0168 -1.1395 3.0281 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2336 -2.7113 0.1540 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1303 1.9004 -1.3493 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0282 1.2549 -3.7434 H 0 0 0 0 0 0 0 0 0 0 0 0
6.4528 -1.5789 -1.2859 H 0 0 0 0 0 0 0 0 0 0 0 0
5.3755 -1.1468 -3.5021 H 0 0 0 0 0 0 0 0 0 0 0 0
6.9467 -0.2303 0.8014 H 0 0 0 0 0 0 0 0 0 0 0 0
1 19 1 0 0 0 0
2 22 1 0 0 0 0
3 10 2 0 0 0 0
4 24 1 0 0 0 0
4 2 2 0 0 0 0
5 11 2 0 0 0 0
5 3 1 0 0 0 0
6 26 1 0 0 0 0
6 14 1 0 0 0 0
7 6 2 0 0 0 0
8 13 1 0 0 0 0
9 12 1 0 0 0 0
10 2 1 0 0 0 0
10 1 1 0 0 0 0
11 4 1 0 0 0 0
12 14 2 0 0 0 0
12 8 1 0 0 0 0
13 30 1 1 0 0 0
13 15 1 0 0 0 0
13 11 1 0 0 0 0
14 17 1 0 0 0 0
15 18 2 0 0 0 0
16 7 1 0 0 0 0
16 9 2 0 0 0 0
17 15 1 0 0 0 0
20 1 1 0 0 0 0
21 1 1 0 0 0 0
23 3 1 0 0 0 0
25 5 1 0 0 0 0
27 7 1 0 0 0 0
28 8 1 0 0 0 0
29 9 1 0 0 0 0
M END
$$$$
/Volumes/PubChemQCDataBaseWork/pubchemqc2017database/xyz/00000000_00009999/1.xyz
OpenBabel02162213453D
34 34 0 0 0 0 0 0 0 0999 V2000
7.0068 1.8970 3.2727 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4650 -0.2257 1.3353 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4432 2.1011 9.5057 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3366 -2.5350 5.1551 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6396 1.6000 5.9257 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9474 1.8190 7.1190 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1830 0.2123 3.8873 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3870 0.7439 3.5935 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7754 -0.2729 6.7631 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3568 1.0842 2.1622 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4537 0.4611 5.1348 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0098 0.8730 7.5380 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4835 -0.4763 5.5827 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0856 0.5626 2.3959 N 0 0 0 0 0 0 0 0 0 0 0 0
6.9369 0.8984 1.1006 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2593 0.9658 8.6759 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3108 -1.5731 4.7848 O 0 0 0 0 0 0 0 0 0 0 0 0
7.1466 1.3059 4.1845 H 0 0 0 0 0 0 0 0 0 0 0 0
6.4174 2.7835 3.5327 H 0 0 0 0 0 0 0 0 0 0 0 0
7.9816 2.2170 2.9038 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3066 -1.2574 1.6696 H 0 0 0 0 0 0 0 0 0 0 0 0
5.1340 -0.2156 0.4776 H 0 0 0 0 0 0 0 0 0 0 0 0
3.4967 0.2086 1.0638 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2404 1.9714 10.3469 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1957 3.0318 8.9780 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4730 2.1641 9.8816 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3625 -3.3009 4.3776 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6682 -2.0951 5.1999 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5723 -2.9938 6.1242 H 0 0 0 0 0 0 0 0 0 0 0 0
3.3352 2.3628 5.5870 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1307 2.7235 7.6863 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7052 -0.4677 3.1921 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8961 1.3664 4.3173 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0389 -0.9814 7.1205 H 0 0 0 0 0 0 0 0 0 0 0 0
1 19 1 0 0 0 0
1 18 1 0 0 0 0
2 21 1 0 0 0 0
2 14 1 0 0 0 0
3 26 1 0 0 0 0
3 24 1 0 0 0 0
4 28 1 0 0 0 0
4 29 1 0 0 0 0
5 6 1 0 0 0 0
6 12 2 0 0 0 0
6 31 1 0 0 0 0
7 11 1 0 0 0 0
8 7 2 0 0 0 0
8 33 1 0 0 0 0
9 34 1 0 0 0 0
9 12 1 0 0 0 0
10 14 1 0 0 0 0
10 1 1 0 0 0 0
11 13 1 0 0 0 0
11 5 2 0 0 0 0
12 16 1 0 0 0 0
13 9 2 0 0 0 0
14 8 1 0 0 0 0
15 10 2 0 0 0 0
16 3 1 0 0 0 0
17 4 1 0 0 0 0
17 13 1 0 0 0 0
20 1 1 0 0 0 0
22 2 1 0 0 0 0
23 2 1 0 0 0 0
25 3 1 0 0 0 0
27 4 1 0 0 0 0
30 5 1 0 0 0 0
32 7 1 0 0 0 0
M END
$$$$