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")
