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jamesgleave / DD_protocol

Official repository for the Deep Docking protocol
MIT License
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conda requirements #7

Closed ghost closed 8 months ago

ghost commented 1 year ago

Hi Can you mention how to install the dependencies for DD protocol? Also I have a 3 million small molecule library in sdf format, can I use it as a test for docking? Thanks Deb

fgentile89 commented 1 year ago

https://github.com/jamesgleave/DD_protocol/blob/main/utilities/environment.yml should help with installing the dependencies. SDF files should be good for docking, depending on what program you are going to use. Best,

Francesco

julmarci commented 1 year ago

Hello Francesco.

Keras dependency is missing in https://github.com/jamesgleave/DD_protocol/blob/main/utilities/environment.yml. The version that is automatically installed in conda, based on the rest of the requirements, has this problem when loading the models.

"AttributeError: 'str' object has no attribute 'decode'"

https://stackoverflow.com/questions/53740577/does-any-one-got-attributeerror-str-object-has-no-attribute-decode-whi

What version of Keras should we install?

Thank you so much.

fgentile89 commented 1 year ago

Hi, Have you tried to reinstall the h5py package as they suggested in that post? In our machines, we have keras 2.6.0 and h5py 3.1.0

julmarci commented 1 year ago

Installing a previous version of h5py solves the issue.

However, I wasn't able to install keras 2.6.0 together with tensorflow 1, so I'm wondering if this tool works with tensorflow 2 libraries.

ghost commented 1 year ago

hola, yo tengo el mismo problema con conda, podrías proporcionarnos un listado de las dependencias necesarias e instaladas en tu sistema con su respectiva versión, de ante mano te agradezco