Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -214,14 +214,13 @@ def get_coords(annot, alignments, coords, resnums_for_sasa, mode):
             return np.NaN, np.NaN, np.NaN
 
 
-def get_alignments_3D(identifier, model_num, pdbSequence, source, chain, pdbID, mode,file_format = 'gzip'):
+def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chain, pdbID, mode, path_3D_alignment,file_format = 'gzip'):
     print('In Function')
     pdbSequence = convert_non_standard_amino_acids(pdbSequence)
     print(pdbSequence)
     print(mode, source)
     if mode == 1:
-        if source != 'MODBASE':
-            print('I am here')
+        if source == 'PDB':
             # Step 1: Fetch the PDB file
             pdb_url = f"https://files.rcsb.org/download/{pdbID}.pdb"
             response = requests.get(pdb_url)
@@ -236,18 +235,10 @@ def get_alignments_3D(identifier, model_num, pdbSequence, source, chain, pdbID,
             resnums_for_sasa = [i[5] for i in atoms]
 
         else:
-            pdb_url = f"https://files.rcsb.org/download/{pdbID}.pdb"
-            
-            response = requests.get(pdbID)
-            response.raise_for_status()  # Check for a successful response
-            
-            # Step 2: Parse the PDB file from memory
-            atoms = [i for i in response.text.split('\n') if i.startswith('ATOM')]
-            atoms = [i.split() for i in atoms]
-            atoms = [i for i in atoms if i[2] == 'CA']
-            atomSequence = ''.join([three_to_one(i[3]) for i in atoms])
-            coords = [[i[6] ,i[7] ,i[8]] for i in atoms]
-            resnums_for_sasa = [i[5] for i in atoms]
+            if line[0:7].strip() == 'ATOM' and line[13:15].strip() == 'CA':
+                atomSequence += threeToOne(line[17:20].strip())
+                coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
+                resnums_for_sasa.append(line[22:26].strip())
             
         """
         atomSequence = ''