pdb_renumber script

add useful script

scripts/pdb_renumber.py

@@ -0,0 +1,69 @@
+import os
+import sys
+
+
+
+def renumber_res(pdb_input, output_dir, start_res=1):
+
+    ##get all chainIDs from the pdb file
+    chainIDs = []
+    with open(pdb_input, 'r') as f:
+        for line in f:
+            if line.startswith('ATOM'):
+                chainID = line[21]
+                if chainID not in chainIDs:
+                    chainIDs.append(chainID)
+
+    ## split the chain in the pdb file with pdb_splitchain
+    os.system(f'pdb_splitchain {pdb_input}')
+
+    #get the current working directory
+    cwd = os.getcwd()
+
+    #renumber all the chains:
+    all_outputs = []
+    chains = []
+    for chainID in chainIDs:
+        chain = os.path.join(cwd, os.path.basename(pdb_input).replace('.pdb', f'_{chainID}.pdb'))
+        output = chain.replace('.pdb', '_renumbered.pdb')
+        all_outputs.append(output)
+        os.system(f'pdb_reres -{start_res} {chain} > {output}')
+        chains.append(chain)
+
+    #merge all chains into one file 
+    out_name = os.path.basename(pdb_input).replace('.pdb', '_merged.pdb')
+    output = os.path.join(output_dir, out_name)
+
+    #sort the outputs
+    sorted_outputs = sorted(all_outputs)
+    #combine items in the list to a string
+    command = 'pdb_merge ' + ' '.join(sorted_outputs) + ' > ' + output
+    os.system(command)
+
+    #remove all the middle files
+    middle_file = all_outputs + chains
+    os.system(f'rm {" ".join(middle_file)}')
+
+
+def show_help():
+    print("""
+    Usage: python script_name.py PDB_INPUT_FILE START_RESIDUE_NUMBER
+
+    Description:
+    This script renumbers the residue IDs in a PDB file starting from a specified residue number.
+
+    Example:
+    python script_name.py input.pdb 100 . 
+
+    This will renumber the residues in 'input.pdb' starting from residue number 100 in the current dir
+    """)
+
+
+if __name__ == '__main__':
+    if len(sys.argv) != 4:
+        show_help()
+    else:
+        pdb_input = sys.argv[1]
+        start_res = int(sys.argv[2])
+        output_dir = sys.argv[3]
+        renumber_res(pdb_input, output_dir, start_res)