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import glob
import ssbio.utils
import subprocess
import ssbio
import os.path as op
from add_3Dalignment import *
import os
from pathlib import Path
import gzip
import shutil
import streamlit as st
def run_freesasa(infile, outfile, include_hetatms=True, outdir=None, force_rerun=False, file_type = 'gzip'):
if not outdir:
outdir = ''
outfile = op.join(outdir, outfile)
if file_type == 'pdb':
if ssbio.utils.force_rerun(flag=force_rerun, outfile=outfile):
if include_hetatms:
shell_command = 'freesasa --format=rsa --hetatm {} -o {}'.format(infile, outfile)
else:
shell_command = 'freesasa --format=rsa {} -o {}'.format(infile, outfile)
command = subprocess.Popen(shell_command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
out, err = command.communicate()
elif file_type == 'gzip':
with gzip.open(infile, 'rb') as f_in:
with open('file_temp.pdb', 'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
infile = 'file_temp.pdb'
if ssbio.utils.force_rerun(flag=force_rerun, outfile=outfile):
if include_hetatms:
shell_command = 'freesasa --format=rsa --hetatm {} -o {}'.format(infile, outfile)
else:
shell_command = 'freesasa --format=rsa {} -o {}'.format(infile, outfile)
command = subprocess.Popen(shell_command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
out, err = command.communicate()
return outfile
def calculate_freesasa(ID, model_num, existing_free_sasa, path_to_input,path_to_output_files, file_type = 'gzip'):
print('Calculating surface area...\n')
file_base = str(Path(path_to_input / '*'))
file_str = glob.glob(file_base)[0].split('-')[-1].split('.')[0]
if file_type == 'gzip':
if ID not in existing_free_sasa:
fullID = f'AF-{ID}-F{model_num}-{file_str }.pdb.gz'
run_freesasa(Path(path_to_input / fullID),
Path(path_to_output_files / f'freesasa_files/{fullID}.txt'), include_hetatms=True,
outdir=None, force_rerun=False)
elif file_type == 'pdb':
if ID not in existing_free_sasa:
fullID = f'AF-{ID}-F{model_num}-model_v1.pdb'
run_freesasa(Path(path_to_input / fullID),
Path(path_to_output_files / f'freesasa_files/{fullID}.txt'), include_hetatms=True,
outdir=None, force_rerun=False)
def sasa(source, pdbID, uniprotID, sasa_pos, wt, mode, path_to_output_files,file_type = 'gzip'):
if mode == 1:
sasa = 'nan'
for filename in list(Path(path_to_output_files / 'freesasa_files').glob("*")):
if source == 'PDB':
fname = str(filename).split('.')[0].split('/')[-1].upper()
elif source == 'MODBASE':
fname = str(filename).split('.')[0].split('/')[-1]
elif source == 'SWISSSMODEL':
fname = str(filename).split('_')[2]
if pdbID == fname:
files = open(filename, 'r')
file = files.readlines()
for k in file:
if k.strip()[10:13] == sasa_pos:
residue = str(k[4:7].strip())
if wt == threeToOne(residue):
sasa = str(k[22:28]).strip('\n')
return (sasa)
elif wt != threeToOne(residue):
sasa = str(k[22:28]).strip('\n') + '*'
return (sasa)
else:
return 'nan' #######
if mode == 2:
if sasa_pos != np.NaN:
sasa = 'nan'
if file_type == 'pdb':
for filename in list(Path(path_to_output_files / 'freesasa_files').glob("*")):
fname = list(filter(None, filename.split('.'))).split('/')[-1].upper()
if uniprotID == fname:
files = open(filename, 'r')
file = files.readlines()
for k in file:
if k.strip()[10:13] == sasa_pos:
residue = str(k[4:7].strip())
if wt == threeToOne(residue):
sasa = str(k[22:28]).strip('\n')
elif wt != threeToOne(residue):
sasa = str(k[22:28]).strip('\n') + '*'
return sasa
elif file_type == 'gzip':
for filename in list(Path(path_to_output_files / 'freesasa_files').glob("*")):
fname = list(filter(None, str(filename).split('.')))[0].split('/')[-1].split('-')[1].upper()
if uniprotID == fname:
files = open(filename, 'r')
file = files.readlines()
for k in file:
if str(k.strip()[10:13]) == str(sasa_pos):
residue = str(k[4:7].strip())
if wt == threeToOne(residue):
sasa = str(k[22:28]).strip('\n')
elif wt != threeToOne(residue):
sasa = str(k[22:28]).strip('\n') + '*'
else:
sasa = 'nan'
return sasa
else:
sasa = 'nan'
return sasa |