name_to_code_dict = name_to_code(spec_dict, "c") # "c" stands for common name # Read the db fasta... db_fasta = "gpcrdb.9cat.alignment.fasta" frame_dict = pr.fasta.read(db_fasta) # Read the fasta to process... proc_fasta = "step2.interest.fasta" proc_dict = pr.fasta.read(proc_fasta) # Test the concept of fetching sequence alignment # Specify chains to process... fl_xlsx = "gpcrdb.all.xlsx" sheet = "total" lines = load_gpcrdb_xlsx(fl_xlsx, sheet = sheet) drc = "pdb" drc_input = "psa.i" drc_export = "psa.o" if False: for line in lines[:]: # Unpack parameters uniprot = line[1].lower() spec = line[5].lower() pdb = line[7].lower() chain = line[10].upper() # Form entry name... entry = f"{pdb}_{chain}"
seq_dict = pr.fasta.read(fl_aln) # The default ones are not good enough nseqi = 616 cseqi = 1248 # Define atoms used for distance matrix analysis... backbone = ["N", "CA", "C", "O"] len_res = len(backbone) len_seq = (cseqi - nseqi + 1) * len_res # [[[ LOAD DATABASE ]]] # Specify chains to process... fl_chain = "gpcrdb.all.xlsx" sheet = f"{job_name}" lines = load_gpcrdb_xlsx(fl_chain, sheet=sheet, splitchain=True) drc = "pdb" # Define atoms used for structural alignment... backbone = ["N", "CA", "C", "O"] # Specify the backbone atoms to select... backbone_select = "name " + "+".join(backbone) # Specify the rigid framework... fl_fwk = 'fwk.dat' fwk = pr.utils.read_file(fl_fwk) fwk = [[int(i) // 4, int(j) // 4] for i, j in fwk] # Pick a PDB... pdb, chain = "6PS6", "A"
#!/usr/bin/env python3 # -*- coding: utf-8 -*- import pyrotein as pr from loaddata import load_gpcrdb_xlsx import pymolPy3 # Launch pymol without GUI... pm = pymolPy3.pymolPy3(0) if False: # Specify chains to process... fl_chain = "gpcrdb.all.xlsx" lines = load_gpcrdb_xlsx(fl_chain, sheet="total", splitchain=True) drc = "pdb" # Flatten the list entries = [i[7] for i in lines] else: drc = "pdb.refine" fl_dat = "pdb.refine.dat" lines = pr.utils.read_file(fl_dat) entries = [i[0] for i in lines] # Fetching... pm(f"cd {drc}") for i in entries: pdb = i.lower() pm(f"load {pdb}.pdb") pm(f"save {pdb}.fasta")