From faf6373be7291b0cccfbbc4ac638f626950716ae Mon Sep 17 00:00:00 2001
From: mmagnus <mag_dex@o2.pl>
Date: Wed, 25 Sep 2024 22:10:41 -0400
Subject: [PATCH] cif2pdb fancy way

---
 rna_tools/rna_pdb_tools.py | 63 +++++++++++++++++++++++---------------
 1 file changed, 39 insertions(+), 24 deletions(-)

diff --git a/rna_tools/rna_pdb_tools.py b/rna_tools/rna_pdb_tools.py
index 444160799..a7447ac53 100755
--- a/rna_tools/rna_pdb_tools.py
+++ b/rna_tools/rna_pdb_tools.py
@@ -1219,12 +1219,24 @@ def get_parser():
             structure = parser.get_structure("structure_id", cif_file)
             pdb_file = cif_file.replace('.cif', '_fCIF.pdb')
 
-            remarks = []
+
             try:
                 # Save to PDB format
                 io = PDBIO()
                 io.set_structure(structure)
                 io.save(pdb_file)
+
+                print(f'saved: {pdb_file}')
+                # open a file add remarks
+                new_file = ''
+                with open(pdb_file, 'r') as f:
+                    if not args.no_hr:
+                        new_file += add_header(version) + '\n'
+                    new_file += f.read()
+
+                with open(pdb_file, 'w') as f:
+                    f.write(new_file)
+
             except TypeError as e:
                 print('Warning: some of the chains in this mmCIF file has chain names with more char than 1, e.g. AB, and the PDB format needs single-letter code, e.g. A.')
 
@@ -1262,14 +1274,14 @@ def has_high_rna_content(chain, threshold=0.8):
                 import string
                 letters = list(string.ascii_uppercase)
 
-                # New structure
-                new_structure = Structure.Structure("new_structure")
-                new_model = Model.Model(0)  # Create a new model
-                new_structure.add(new_model)  # Add the new model to the new structure
-
                 for model in structure:
                     for chain in model:
                         if has_high_rna_content(chain):
+                            # New structure
+                            new_structure = Structure.Structure("new_structure")
+                            new_model = Model.Model(0)  # Create a new model
+                            new_structure.add(new_model)  # Add the new model to the new structure
+
                             chain_id_new = letters.pop(0)
                             chain_id = chain.get_id()
 
@@ -1277,28 +1289,31 @@ def has_high_rna_content(chain, threshold=0.8):
                             for residue in chain:
                                   for atom in residue:
                                        atom_count += 1
-                            print(f'rna chain {chain.id} -> {chain_id_new} # of atoms: {atom_count}')
+
+                            remarks = []
                             remarks.append(f'REMARK rna chain {chain.id} -> {chain_id_new}')
+
                             chain.id = chain_id_new
                             new_model.add(chain)
 
-                io = PDBIO()
-                io.set_structure(new_structure)
-                io.save(pdb_file)
-
-            print(f'saved: {pdb_file}')
-
-            # open a file add remarks
-            new_file = ''
-            with open(pdb_file, 'r') as f:
-                if not args.no_hr:
-                    new_file += add_header(version) + '\n'
-                if remarks:
-                    new_file += '\n'.join(remarks) + '\n'
-                new_file += f.read()
-
-            with open(pdb_file, 'w') as f:
-                f.write(new_file)
+                            pdb_file = cif_file.replace('.cif', f'_{chain_id}_n{chain_id_new}_fCIF.pdb')
+   
+                            io = PDBIO()
+                            io.set_structure(new_structure)
+                            
+                            io.save(pdb_file)
+                            print(f'rna chain {chain.id} -> {chain_id_new} # of atoms: {atom_count} {pdb_file}')
+                            # open a file add remarks
+                            new_file = ''
+                            with open(pdb_file, 'r') as f:
+                                if not args.no_hr:
+                                    new_file += add_header(version) + '\n'
+                                if remarks:
+                                    new_file += '\n'.join(remarks) + '\n'
+                                new_file += f.read()
+
+                            with open(pdb_file, 'w') as f:
+                                f.write(new_file)
 
     if args.pdb2cif:
         try: