Hi,
There a a few things to correct in your readme file:
"Note: PyG subgraph function has been put to another place, therefore, replace the following command at ./utils/transform.py"
should be:
"Note: PyG subgraph function has been put to another place, therefore, replace the following command at ./utils/transforms.py"
"Please follow the instructions in ./data/surf_maker for this process. Alternatively, to test the successful configuration of your environment, you can execute the ./data/surf_maker/surf_maker_test.py script."
should be:
"Please follow the instructions in ./data/surface_maker for this process. Alternatively, to test the successful configuration of your environment, you can execute the ./data/surface_maker/surface_maker_test.py script."
Trying to create a surf_maker environment with:
mamba create -n surf_maker pymesh2 jupyter scipy joblib biopython rdkit plyfile -c conda-forge
gets stuck at some point even with mamba.
The alternative:
conda env create -f surf_maker_environment.yml
does not work as surf_maker_environment.yml does not contain the definition for an environment
To be able to create the environment, you start with creating the surf_maker only with pymesh2, you activate the environment with conda activate surf_maker and then install the remaining packages but you do not need scipy as it is already installed along pymesh2. However, you need to add ipython, which is not indicated in the readme file. If you try to do everything at once, it never resolves it.
One problematic thing... is the hard-coded PATHs to your system. I'll install apbs, pdb2pqr, msms and multivalue, within the python environment folder and modify the scripts to set PATHs relative to the environment.
best
Hi,
There a a few things to correct in your readme file:
"Note: PyG subgraph function has been put to another place, therefore, replace the following command at ./utils/transform.py"
should be:
"Note: PyG subgraph function has been put to another place, therefore, replace the following command at ./utils/transforms.py"
"Please follow the instructions in ./data/surf_maker for this process. Alternatively, to test the successful configuration of your environment, you can execute the ./data/surf_maker/surf_maker_test.py script."
should be:
"Please follow the instructions in ./data/surface_maker for this process. Alternatively, to test the successful configuration of your environment, you can execute the ./data/surface_maker/surface_maker_test.py script."
Trying to create a surf_maker environment with:
mamba create -n surf_maker pymesh2 jupyter scipy joblib biopython rdkit plyfile -c conda-forge
gets stuck at some point even with mamba.
The alternative:
conda env create -f surf_maker_environment.yml
does not work as surf_maker_environment.yml does not contain the definition for an environment
To be able to create the environment, you start with creating the surf_maker only with pymesh2, you activate the environment with conda activate surf_maker and then install the remaining packages but you do not need scipy as it is already installed along pymesh2. However, you need to add ipython, which is not indicated in the readme file. If you try to do everything at once, it never resolves it.
One problematic thing... is the hard-coded PATHs to your system. I'll install apbs, pdb2pqr, msms and multivalue, within the python environment folder and modify the scripts to set PATHs relative to the environment.
best