Split NMR-style multiple model pdb files into individual models: Difference between revisions

Split NMR-style multiple model pdb files into individual models (edit)

1,216 bytes added , 22 October 2014

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added Python version

6

edits

@@ Line 39: / Line 39: @@
    if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"}
    }
+== Python script ==
+For this kludgy version using Python 2.x, you need to paste the entire PDB file into the script where it says "PASTE YOUR PDB FILE TEXT HERE".</br>
+You can fork [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py the code here at Github].</br> (Eventually, I hope to have a more full-featured version there that you can just point at your file using an argument at the command line, and after that a web-hosted service to do it for you right on a web page.)
+  PDB_text = """
+  PASTE YOUR PDB FILE TEXT HERE
+  """
+  model_number = 1
+  new_file_text = ""
+  for line in filter(None, PDB_text.splitlines()):
+      line = line.strip () #for better control of ends of lines
+      if line == "ENDMDL":
+          # save file with file number in name
+          output_file = open("model_" + str(model_number) + ".pdb", "w")
+          output_file.write(new_file_text.rstrip('\r\n')) #rstrip to remove trailing newline
+          output_file.close()
+          # reset everything for next model
+          model_number += 1
+          new_file_text = ''
+      elif not line.startswith("MODEL"):
+          new_file_text += line + '\n'
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