Delete code/add_sasa_alphafold.py

code/add_sasa_alphafold.py

@@ -1,129 +0,0 @@
-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