findClusterCenters

[mmuratyas]

Hello; I applied the casestudy2 commands in the watfinder tutorial for my own molecule. It gave an error like "NameError: name 'findClusterCenters' is not defined". Can you help me with this?

[karolamik13]

Hello, you need to download the most current version of ProDy from GitHub (https://github.com/prody/ProDy) and install it to have this function.

[mmuratyas]

The currently installed version is ProDy-2.4.1. But it still gives the same error.

[jamesmkrieger]

The github version should already say 2.5.0

There is no watfinder in 2.4.1

[jamesmkrieger]

or rather, there isn't the full watfinder toolkit in prody 2.4.1, just some earlier parts of it

[jamesmkrieger]

If you're using windows then you can't install from github but you can download this release candidate wheel and install from that: https://github.com/jamesmkrieger/ProDy/releases/download/v2.5rc1/ProDy-2.5.0rc1-cp38-cp38-win_amd64.whl
pip install ProDy-2.5.0rc1-cp38-cp38-win_amd64.whl

[mmuratyas]

I will try it. thank you so much

[mmuratyas]

If you're using windows then you can't install from github but you can download this release candidate wheel and install from that: https://github.com/jamesmkrieger/ProDy/releases/download/v2.5rc1/ProDy-2.5.0rc1-cp38-cp38-win_amd64.whl pip install ProDy-2.5.0rc1-cp38-cp38-win_amd64.whl

I tried this but it gave me an error like “ERROR: ProDy-2.5.0rc1-cp38-cp38-win_amd64.whl is not a supported wheel on this platform.”

[jamesmkrieger]

ok, sorry your platform doesn't match mine. You could try using git bash and installing compiler tools there, which I think is what I ended up doing to build that wheel.

If you can, I'd recommend you to try wsl instead though

[mmuratyas]

ok, sorry your platform doesn't match mine. You could try using git bash and installing compiler tools there, which I think is what I ended up doing to build that wheel.

If you can, I'd recommend you to try wsl instead though

Thank you for your interest. If there is a linux version of Prody-2.5.0 can you share the link? I usually use linux.

[jamesmkrieger]

You should just be able to install from github on linux using the main branch

[email protected]:prody/ProDy.git
cd ProDy
python setup.py build_ext --inplace --force
pip install -Ue .

[jamesmkrieger]

why did you reply about the windows wheel if you're using linux?

[mmuratyas]

why did you reply about the windows wheel if you're using linux?

First I wrote about the error I got in linux, but I was offered the windows version of Prody-2.5.0. I thought there was no linux version, so I tried to install it on windows.

[jamesmkrieger]

ok, sorry for the confusion. The reason I offered a windows version is because windows can't install it itself. Linux doesn't need an installed version because it can install it.

[jamesmkrieger]

We are planning to make a proper release once everything is ready with InSty too, but we haven't got there yet. We have also had some requests to support later versions of numpy, scipy and python, and we'll hopefully be able to include that in the release too

[mmuratyas]

We are planning to make a proper release once everything is ready with InSty too, but we haven't got there yet. We have also had some requests to support later versions of numpy, scipy and python, and we'll hopefully be able to include that in the release too

Thank you for your efforts and help.