r=sql_ask_database(conn,f"SELECT structure_id, '_1_', chain_name, '_', CAST(pdb_start AS TEXT), '-', CAST(pdb_end AS TEXT) FROM chain WHERE rfam_acc='{f}' AND issue=0;")
r=sql_ask_database(conn,f"SELECT structure_id, '_1_', chain_name, '_', CAST(pdb_start AS TEXT), '-', CAST(pdb_end AS TEXT) FROM chain WHERE rfam_acc='{f}';")
filelist=sorted([''.join(list(x))+'.cif'forxinr])
r=sql_ask_database(conn,f"SELECT cm_coord FROM align_column WHERE rfam_acc = '{f}' AND index_ali > 0 ORDER BY index_ali ASC;")
cm_coords=[x[0]forxinr]# len(cm_coords) is the number of saved columns. There are many None values in the list.
r=sql_ask_database(conn,f"SELECT pdb_start, pdb_end FROM chain WHERE rfam_acc='{family}' AND structure_id='{structure}' AND chain_name='{chain}' AND issue=0;")
ifnotlen(r):
# there is no chain named like this and mapped to this family
returnNone
iflen(r)>1:
warn(f"Several entries found for structure {structure}-{chain} ({family}) : {len(r)} entries")
@@ -1301,14 +1353,17 @@ if __name__ == "__main__":
print()
print("-r 20.0 [ --resolution=20.0 ]\tCompute statistics using chains of resolution 20.0A or better.")
print("--3d-folder=…\t\t\tPath to a folder containing the 3D data files. Required subfolders should be:"
"\n\t\t\t\t\tdatapoints/\t\tFinal results in CSV file format.")
"\n\t\t\t\t\tdatapoints/\t\tFinal results in CSV file format."
"\n\t\t\t\t\trna_mapped_to_Rfam/\tmmCIF files produced by RNANet (using --extract)."
"\n\t\t\t\t\trna_only/\t\tmmCIF files produced by RNANet in no-homology mode.")
print("--seq-folder=…\t\t\tPath to a folder containing the sequence and alignment files. Required subfolder:"
"\n\t\t\t\t\trealigned/\t\tSequences, covariance models, and alignments by family")
print("--from-scratch\t\t\tDo not use precomputed results from past runs, recompute everything")
print("--distance-matrices\t\tCompute average distance between nucleotide pairs for each family.")
print("--non-redundant\t\t\tIn distance matrix computation, only use the equivalence class representatives.\n\t\t\t\t Does not apply to rRNAs, where the option is always True.")
print("--wadley\t\t\tReproduce Wadley & al 2007 clustering of pseudotorsions.")
print("--hire-rna\t\t\tCompute distances between atoms and torsion angles for HiRE-RNA model, and plot GMMs on the data.")
print("--rescan-nmodes\t\tDo not assume the number of modes in distances and angles distributions, measure it.")
print("--hire-rna\t\t\tCompute distances between atoms and torsion angles for HiRE-RNA model,\n\t\t\t\t and plot GMMs on the data.")
print("--rescan-nmodes\t\t\tDo not assume the number of modes in distances and angles distributions, measure it.")