Comments (2)
The class label, affinity, and RMSD fields are not actually used for the default model architectures in this project. They are a holdover from using the same data file format we use for other projects in Koes Group. You can just set them to zero if you do not know what values to put in those fields in the data file.
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Regarding your first point: It's ok to use only part of the receptor structure as long as the cutoff size is greater than the grid size, otherwise you might see weird boundary effects in the generated ligands in the regions where the receptor was split.
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Related Issues (20)
- feedback about generated molecules HOT 2
- AttributeError when using generate.py HOT 2
- Aborted (core dumped) when generate molecules HOT 7
- AttributeError: type object 'object' has no attribute 'dtype' HOT 9
- where is the output for generated molecules and matrix? HOT 4
- gnina minmize problem HOT 2
- Can not access to https://bits.csb.pitt.edu/files/ to download those files HOT 2
- Segmentation Fault when running tests HOT 1
- tests ValueError: File does not exist: data/test_pockets/xxx HOT 3
- change configuration file for prior (no lig) sampling HOT 1
- Error when run cmake of libmogrid HOT 4
- Errors when run pytest tests HOT 12
- how I can export embeddings HOT 3
- Get Stuck when runing generate.py HOT 2
- Train_file and test_file are missing HOT 1
- CUDNN Error (out of memory?): CUDNN_STATUS_EXECUTION_FAILED HOT 2
- Get killed when running generate.py HOT 5
- Cannot use model with `fit_atoms: True` HOT 8
- Changing parameters while testing the model HOT 6
- KeyError: 'minimizedAffinity' in tests HOT 6
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