Create add_sasa.py

code/add_sasa.py

@@ -0,0 +1,119 @@
+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(uniprotID, sasa_pos, wt, mode, filename, path_to_output_files, file_type = 'gzip'):
+    if mode == 1:
+        files = open(filename, 'r')
+        file = files.readlines()
+        for k in file:
+            if str(k.strip()[10:13].strip()) == str(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]).strip() == 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