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29 lines
2.0 KiB
Python
29 lines
2.0 KiB
Python
# List of paths to folders and binaries. All folder paths should finish with slash (/)
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# Paths required for prediction.
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library_folder = '' # Where the Github Repo is located.
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structures_folder = library_folder + 'PDB/' # Where pdb/mmCIF structures files are stored.
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predictions_folder = library_folder + 'predictions/' # Output folder.
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model_folder = library_folder + 'models/' # Where the networks as stored as pairs of files (.h5,.data).
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# Additional paths required for prediction with evolutionary information.
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MSA_folder = library_folder + 'MSA/' # Where multiple sequence alignments are stored.
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path2hhblits = None # Path to hhblits binary. Not required if using ScanNet_noMSA networks.
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path2sequence_database = None # Path to sequence database Not required if using ScanNet_noMSA networks. Example:
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# path2hhblits = '/path/to/hh-suite/build/bin/hhblits' # Path to hhblits binary. Not required if using ScanNet_noMSA networks.
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# path2sequence_database = '/path/to/uniclust30_2018_08/uniclust30_2018_08' # Path to sequence database Not required if using ScanNet_noMSA networks.
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# Additional paths required for training models.
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pipeline_folder = library_folder + 'pipelines/' # Where preprocessed datasets are stored.
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initial_values_folder = model_folder + 'initial_values/' # Where initial values of the parameters for the gaussian kernels and residue-residue graph edges are stored.
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# Path to visualizations folder.
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visualization_folder = library_folder + 'visualizations/'
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# Additional paths for reproducing baselines.
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path_to_dssp = '/path/to/mkdssp' # Path to dssp binary. Only for reproducing handcrafted features baseline performance.
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path_to_msms = '/path/to/msms.x86_64Linux2.2.6.1' # Path to msms binary. Only for reproducing handcrafted features baseline performance.
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path_to_multiprot = library_folder + 'baselines/homology/' + 'multiprot.Linux' # Path to multiprot executable. Only relevant for homology baseline.
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homology_folder = library_folder + 'baselines/homology/' # Where files are stored for homology baseline. |