mirror of
https://github.com/jertubiana/ScanNet.git
synced 2026-06-04 13:44:22 +08:00
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 (/)
|
|
|
|
# Paths required for prediction.
|
|
library_folder = '' # Where the Github Repo is located.
|
|
structures_folder = library_folder + 'PDB/' # Where pdb/mmCIF structures files are stored.
|
|
predictions_folder = library_folder + 'predictions/' # Output folder.
|
|
model_folder = library_folder + 'models/' # Where the networks as stored as pairs of files (.h5,.data).
|
|
|
|
# Additional paths required for prediction with evolutionary information.
|
|
MSA_folder = library_folder + 'MSA/' # Where multiple sequence alignments are stored.
|
|
path2hhblits = None # Path to hhblits binary. Not required if using ScanNet_noMSA networks.
|
|
path2sequence_database = None # Path to sequence database Not required if using ScanNet_noMSA networks. Example:
|
|
|
|
# path2hhblits = '/path/to/hh-suite/build/bin/hhblits' # Path to hhblits binary. Not required if using ScanNet_noMSA networks.
|
|
# path2sequence_database = '/path/to/uniclust30_2018_08/uniclust30_2018_08' # Path to sequence database Not required if using ScanNet_noMSA networks.
|
|
|
|
# Additional paths required for training models.
|
|
pipeline_folder = library_folder + 'pipelines/' # Where preprocessed datasets are stored.
|
|
initial_values_folder = model_folder + 'initial_values/' # Where initial values of the parameters for the gaussian kernels and residue-residue graph edges are stored.
|
|
|
|
# Path to visualizations folder.
|
|
visualization_folder = library_folder + 'visualizations/'
|
|
|
|
# Additional paths for reproducing baselines.
|
|
path_to_dssp = '/path/to/mkdssp' # Path to dssp binary. Only for reproducing handcrafted features baseline performance.
|
|
path_to_msms = '/path/to/msms.x86_64Linux2.2.6.1' # Path to msms binary. Only for reproducing handcrafted features baseline performance.
|
|
|
|
path_to_multiprot = library_folder + 'baselines/homology/' + 'multiprot.Linux' # Path to multiprot executable. Only relevant for homology baseline.
|
|
homology_folder = library_folder + 'baselines/homology/' # Where files are stored for homology baseline. |