rna_mmcif2pdb.py: add

rna_tools/rna_mmcif2pdb.py

@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+
+"""
+from __future__ import print_function
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+
+from rna_tools.rna_tools_lib import edit_pdb, add_header, get_version
+import os
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    version = os.path.basename(os.path.dirname(os.path.abspath(__file__))), get_version(__file__)
+    version = version[1].strip()
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+
+    parser.add_argument('--version', help='', action='version', version=version)
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument('--no-hr', help='do not insert the header into files',
+                        action='store_true')
+    parser.add_argument("file", help="", default="") # nargs='+')
+    return parser, version
+
+
+if __name__ == '__main__':
+    parser, version = get_parser()
+    args = parser.parse_args()
+
+    if list != type(args.file):
+        args.file = [args.file]
+
+    for cif_file in args.file:
+        from Bio.PDB import MMCIFParser, PDBIO
+        parser = MMCIFParser()
+        structure = parser.get_structure("structure_id", cif_file)
+        pdb_file = cif_file.replace('.cif', '_fCIF.pdb')
+
+        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:
+            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.')
+            def has_high_rna_content(chain, threshold=0.8):
+                # RNA nucleotides: A, C, G, U, and X (you can modify as needed)
+                rna_nucleotides = ['A', 'C', 'G', 'U', 'X']
+                total_residues = 0
+                rna_residues = 0
+
+                # Count the total number of residues and RNA-like residues
+                for residue in chain:
+                    total_residues += 1
+                    if residue.get_resname().strip() in rna_nucleotides:
+                        rna_residues += 1
+
+                # Calculate the proportion of RNA residues
+                if total_residues == 0:
+                    return False  # Avoid division by zero if chain has no residues
+
+                rna_percentage = rna_residues / total_residues
+
+                # Check if the percentage of RNA residues is greater than or equal to the threshold (80% by default)
+                return rna_percentage >= threshold
+
+            from Bio.PDB.MMCIFParser import MMCIFParser
+            from Bio.PDB import MMCIFParser, Structure, Model, Chain
+
+            # Initialize the parser
+            parser = MMCIFParser()
+
+            # Parse the structure
+            structure = parser.get_structure("structure", cif_file)
+
+            # Create a list of single-letter chain identifiers
+            import string
+            letters = list(string.ascii_uppercase)
+
+            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()
+
+                        atom_count = 0
+                        for residue in chain:
+                              for atom in residue:
+                                   atom_count += 1
+
+                        remarks = []
+                        remarks.append(f'REMARK rna chain {chain.id} -> {chain_id_new}')
+
+                        pdb_file = cif_file.replace('.cif', f'_{chain_id}_n{chain_id_new}_fCIF.pdb')
+                        print(f'rna chain {chain.id} -> {chain_id_new} {pdb_file} # of atoms: {atom_count}')
+
+                        chain.id = chain_id_new
+                        new_model.add(chain)
+
+                        io = PDBIO()
+                        io.set_structure(new_structure)
+
+                        io.save(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)

setup.py

@@ -18,7 +18,8 @@
              'rna_tools/rna_pdb_replace.py',
              'rna_tools/rna_standardize.py',
              'rna_tools/rna_pdb_inspect.py',
-
+             'rna_tools/rna_mmcif2pdb.py',
+
              'rna_tools/tools/misc/rna_tools_which.py',
              'rna_tools/tools/misc/rna_tools_demo.py',