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Upload get carbon-alpha only atoms from pdb structures script as per request

Author: nabingiri

preprocessing/get_ca_from_pdb.py

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+"""
+
+@author: nabin
+
+This script extracts carbon-alpha only atoms from protein structure (.pdb) and saves it.
+python3 get_ca_labels.py <input protein structure path> <output protein only ca structure path>
+
+"""
+
+from Bio import PDB
+import os
+import sys
+
+def save(x, y, z, count, amino_name, chain_id, true_ca_path):
+    atom = 'CA'
+    residue_name = amino_name
+    with open(true_ca_path, 'a') as fi:
+        fi.write('ATOM')
+        fi.write('  ')
+        fi.write(str(count).rjust(5))
+        fi.write('  ')
+        fi.write(atom.ljust(4))
+        fi.write(residue_name.rjust(3))
+        fi.write(' ')
+        fi.write(chain_id)  
+        fi.write(str(count).rjust(4))
+        fi.write('    ')
+        fi.write(str(x).rjust(8))
+        fi.write(str(y).rjust(8))
+        fi.write(str(z).rjust(8))
+        fi.write(str(1.00).rjust(5))
+        fi.write(str(0.00).rjust(5))
+        fi.write('           ')
+        fi.write(atom[0:1].rjust(1))
+        fi.write('  ')
+        fi.write('\n')
+
+
+def label_mask(pdb_path, true_ca_path):
+    count = 0
+
+    parser = PDB.PDBParser(QUIET=True)
+    pdb_map = pdb_path
+    struct = parser.get_structure("CA", pdb_map)
+    for model in struct:
+        for chain in model:
+            for residue in chain:
+                for atom in residue:
+                    if atom.get_name() == "CA":
+                        x, y, z = atom.get_coord()
+                        amino_name = residue.resname
+                        chain_id = chain.id
+                        save(x, y, z, count, amino_name, chain_id, true_ca_path)
+                        count += 1
+
+
+if __name__ == "__main__":
+
+    input_pdb = sys.argv[1]
+    true_ca_pdb = sys.argv[2]
+    if os.path.exists(true_ca_pdb):
+            os.remove(true_ca_pdb)
+    label_mask(input_pdb, true_ca_pdb)
+    print("########## NG: get_ca_labels: DONE ##########")
+