About reproduction of evaluation

[tolearnmuch]

Good work, the details on evaluation are lack, when using
bash ./evaluation/batch_eval.sh 1 0 0
to do evaluation, the affinity calculation would produce errors by ourselves. We'd like to ask if convenient to release some information on evaluation.

[RuizhiZhu]

We have also been trying to work on the evaluation part recently, and we found that the env_adt.yml file specifies some package versions but is not complete, for example, the version of rdkit is not given. And we noticed that the env_adt.yml file specifies python=2.7.18, which should be because autodock only supports python2.7, but there is no calrmsd function in python2.7 . We would also like to get more information about the evaluation section.

[pengxingang]

Hi, thanks for your interest in our work. The file env_adt.yml only defines the environment for docking with qvina2. As you can see in line 135 in evaluation/docking.py, the code will execute commands that activate the adt environment to run qvina2. For evaluation, you do not need to explicitly change to the adt environment to run evaluation scripts.

Besides, to make sure adt environment is installed successfully, you can first activate the environment in a terminal and
manually execute the comments defined in line 135. For example, type qvina2 in the terminal in the adt environment to see whether it prints meaningful information. If the adt environment is successfully installed, you can just run the evaluation scripts in your normal environment (not the adt environment).

[tolearnmuch]

Thanks for your replies, they are very helpful. All scripts in around line 135 in docking.py could be okay, except qvina2. After we have created the env adt, the qvina2 command could not be found. qvina2 seems not in env_adt.yml. So we'd like to ask if qvina2 is installed by some other way and please provide some help if convenient.

[pengxingang]

Hi, maybe you need to download and install qvina2 separately. Refer to the qvina2 website or conda-forge website, and check by typing qvina2 (or qvina, depending on the version) in the terminal.