Usage: python3 main.py aligned_pdbs=</path/to/folder> aligned_fasta=</path/to/file> output=</path/to/folder> [options]
Example: python3 main.py aligned_pdbs=./input_pdbs aligned_fasta=./input.fasta output=./output
Mandatory input parameters:
===========================
aligned_pdbs=<string> # Path to folder with aligned protein 3D-structures as separate files in the PDB format (each file should represent one chain)
aligned_fasta=<string> # Path to the corresponding sequence representation of the alignment in the FASTA format
output=<string> # Path to folder to store results
Utilization of computing resources:
===================================
cpu_threads=<int> # Number of parallel CPU threads to utilize (the default is "all" physically available)
Cluster analysis methods:
=========================
method=hdbscan # Use HDBSCAN automatic method (default)
method=optics # Use OPTICS automatic method
method=dbscan eps=<float> # Use DBSCAN method for manual fine-tuning of the results by specifying the ‘eps’ value (eps > 0)
Cluster size:
=========================
min_samples=<int> # The 'min_samples' parameter of HDBSCAN, OPTICS, and DBSCAN (the number of points in a neighborhood
for a point to be considered as the cluster core)
min_cluster_size=<int> # The HDBSCAN 'min_cluster_size' parameter to regulate the minimal size of a cluster
Selection of common core positions:
===================================
max_content_of_gaps=<int> # Define the allowed gap content in alignment column, in % (at most 5%, by default)
max_content_of_mismatch=<int> # Define the allowed 3D-mismatch content in alignment column, in % (at most 5%, by default)
mismatch_threshold=<float> # Define the cut-off value to discriminate spatially aligned from misaligned residues, in angstroms (selected automatically)
Printing result:
===================================
number_of_result_resids=<int> # Number of residues with the greatest score to print in RESULT-files (10, by default)
ref=<string> # Set the reference protein by its name in the FASTA alignment (default is the first protein)
PyMol parameters:
=================
compile_pymol_pse=false # Disable compilation of PyMol sessions with 3D-annotation of results