--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BioPDB_align_and_rmsd.py	Thu Jun 06 07:09:14 2024 +0000
@@ -0,0 +1,107 @@
+#!/usr/bin/env python3
+
+# The MIT License
+#
+# Copyright (c) 2010-2016 Anders S. Christensen
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+import argparse
+
+import Bio.PDB
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Residues to be aligned')
+    parser.add_argument(
+                        '--start_residue', default=None,
+                        help='start residue')
+    parser.add_argument(
+                        '--end_residue', default=None,
+                        help='end residue')
+    parser.add_argument(
+                        '--ref_structure', default=None,
+                        help='reference structure')
+    parser.add_argument(
+                        '--model', default=None,
+                        help='model structure')
+    parser.add_argument(
+                        '--aligned_structure', default=None,
+                        help='aligned structure')
+    parser.add_argument(
+                        '--rmsd', default=None,
+                        help='rmsd')
+    args = parser.parse_args()
+
+    # Select what residues numbers you wish to align
+    # and put them in a list
+    start_id = int(args.start_residue)
+    end_id = int(args.end_residue)
+    atoms_to_be_aligned = range(start_id, end_id + 1)
+
+    # Start the parser
+    pdb_parser = Bio.PDB.PDBParser(QUIET=True)
+
+    # Get the structures
+    ref_structure = pdb_parser.get_structure("reference", args.ref_structure)
+    sample_structure = pdb_parser.get_structure("sample", args.model)
+
+    # Use the first model in the pdb-files for alignment
+    # Change the number 0 if you want to align to another structure
+    ref_model = ref_structure[0]
+    sample_model = sample_structure[0]
+
+    # Make a list of the atoms (in the structures) you wish to align.
+    # In this case we use CA atoms whose index is in the specified range
+    ref_atoms = []
+    sample_atoms = []
+
+    # Iterate of all chains in the model in order to find all residues
+    for ref_chain in ref_model:
+        # Iterate of all residues in each model in order to find proper atoms
+        for ref_res in ref_chain:
+            # Check if residue number ( .get_id() ) is in the list
+            if ref_res.get_id()[1] in atoms_to_be_aligned:
+                # Append CA atom to list
+                ref_atoms.append(ref_res['CA'])
+
+    # Do the same for the sample structure
+    for sample_chain in sample_model:
+        for sample_res in sample_chain:
+            if sample_res.get_id()[1] in atoms_to_be_aligned:
+                sample_atoms.append(sample_res['CA'])
+
+    # Now we initiate the superimposer:
+    super_imposer = Bio.PDB.Superimposer()
+    super_imposer.set_atoms(ref_atoms, sample_atoms)
+    super_imposer.apply(sample_model.get_atoms())
+
+    # Save RMSD into an output file:
+    with open(args.rmsd, 'w') as rmsd_out:
+        rmsd_out.write(str(super_imposer.rms))
+
+    # Save aligned coordinates of the model:
+    io = Bio.PDB.PDBIO()
+    io.set_structure(sample_structure)
+    io.save(args.aligned_structure)
+
+
+if __name__ == "__main__":
+    __main__()