Spaces:
Sleeping
Sleeping
File size: 5,892 Bytes
c2a02c6 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 |
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 |