Hi,
In CCGnet-OB directory, I was trying to execute predict.py. However, I got the following error:
File "predict.py", line 99, in make_graph_dataset
self.data_attr_names = D[0].keys()
AttributeError: 'NoneType' object has no attribute 'keys'

Also, I am using ccgnet-main/data/Test/Test_Table.tab and ccgnet-main/data/Test/coformers as pwd of input files.
If you could please suggest probable solution.
Thanks.

自己数据集的sdf文件格式如果不优化的话是会报错吗?
还有用制表符去连接的sdf-sdf-1-refcode 最后的refcode码是不需要的嘛?

Hi Saoge123,

We appriciate your valuable work and code for co-crystal prediction.

While I use the example command to run predict.py, the python code reports an error message as following. It seems that I don't have ccdc module. However, there is no further instruction in this blog and README.md. Could you please figure out how to fix it?

============
Traceback (most recent call last):
File "predict.py", line 4, in
from Featurize import *
File "D:\QSAR\ccgnet-main\Featurize_init_.py", line 7, in
from .Change_Hbond_Criterion import Change_Hbond_Criterion
File "D:\QSAR\ccgnet-main\Featurize\Change_Hbond_Criterion.py", line 2, in
import ccdc
ModuleNotFoundError: No module named 'ccdc'

Many thanks.

1. 我在源码中\data\Test\coformers中看到148个sdf文件，请教作者是如何生成sdf文件的？
2. 请教作者，如何根据文章中的限制条件，在剑桥数据库中筛选出合适的化合物？

About problems in predict.py: I tried to predict whether two compounds could form a cocrystal with predict.py, but results are very bad.
this is my sdf 3d format for a compound：

`

OpenBabel05042118463D

17 17 0 0 0 0 0 0 0 0999 V2000
-1.9173 0.6874 0.0034 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7014 1.3857 0.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4874 0.6703 0.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4593 -0.7218 0.0008 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7428 -1.4247 -0.0091 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9529 -0.7231 -0.0142 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2967 -1.3795 -0.0408 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3301 -0.7249 -0.0461 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.3233 -2.7270 -0.0626 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6235 -1.4382 0.0038 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7056 1.2887 0.0036 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8489 1.2545 0.0063 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7112 2.4716 0.0294 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6827 -2.5043 -0.0137 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4804 -3.2086 -0.0612 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3380 -0.7700 0.0138 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5637 2.2521 -0.0092 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 6 1 0 0 0 0
1 12 1 0 0 0 0
2 3 1 0 0 0 0
2 13 1 0 0 0 0
3 4 2 0 0 0 0
3 11 1 0 0 0 0
4 5 1 0 0 0 0
4 10 1 0 0 0 0
5 6 2 0 0 0 0
5 14 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
7 9 1 0 0 0 0
9 15 1 0 0 0 0
10 16 1 0 0 0 0
11 17 1 0 0 0 0
M END
$$$$
`

and this is my 2d sdf format:

`

OpenBabel05042116122D

7 6 0 0 0 0 0 0 0 0999 V2000
-1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
6 7 1 0 0 0 0
M END
$$$$
`

I tried with these two formats, my test set has about 150 samples, and the results predicted by ccgnet is very bad, most samples are tagged as 1 (YES), and only few samples are tagged as 0. This is completely different from our own labels.

Any ideas? Is our format of files wrong?

因为看您的论文是在四川大学发表的，所以请原谅我直接使用中文向您提问。

我是来自上海大学的计算机研究生新生，我对您的论文计算机实现方法非常感兴趣。在读您的论文时，是我第一次感受到论文可以这么清晰和高效的表达，您的论文每一个细节都非常详尽，我在此想先向您表达我深深的敬佩之意！！！

在读到您的Method部分，因为我英语水平不高，在借助翻译软件之后也没办法理解Node update function Φv中的h(c)的定义，h(c) is a scalar corresponding to a given input feature and a given slice of Al. 我理解是h也是训练的参数，类似W，所以特此向您求证。

我刚阅读完您的论文，马上会尽力理解您的代码，我看您在另一个问题回答了您的邮箱，如果您允许的话，我也想和您交流一些关于这篇论文的问题。