adding and saving files

2021-02-09 18:30:47 +00:00 · 2021-02-09 18:30:47 +00:00 · 4f25acfa35
commit 4f25acfa35
parent d77491b507
3 changed files with 240086 additions and 0 deletions
--- a/scripts/add_chains_pdb.py
+++ b/scripts/add_chains_pdb.py
@ -0,0 +1,118 @@
+#! /usr/bin/env python
+#  Filename: rename_pdb_for_chimera.py
+# http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000476.html
+
+######################################################################
+#                                                                    #
+# Created: Maximilian N. Andrews, July 18, 2005                      #
+#  Ciamician, Bologna University                                     #
+#                                                                    #
+# Function:                                                          #
+#                                                                    #
+#  This script adds a chain ID to all the subunits (column 22) in    #
+#  the PDB file.                                                     #
+#  The chains are named 'A','B','C',etc. until all of the subunits   #
+#  have been labeled.                                                #
+#                                                                    #
+#  For the subunits to be renamed properly the PDB must contain a    #
+#  line beginning with TER after each subunit, for example:          #
+#  ...                                                               #
+#  ATOM   1570  OXT HIE   103      24.590  -9.249  30.054            #
+#  TER                                                               #
+#  ATOM   1571  N   SER   104      16.936   7.767  30.236            #
+#  ...                                                               #
+#                                                                    #
+# Notes:                                                             #
+#                                                                    #
+#  The original file is first read by the script, then copied to a   #
+#  backup file - with the same name, but with "~" added at the end   #
+#  of it - and then it is renamed and saved with the original name.  #
+#                                                                    #
+# Usage:                                                             #
+#                                                                    #
+#  rename_pdb.py arg1 arg2                                           #
+#  arg1 is the the number of chains that have to be renamed;         #
+#  arg2 is the name of the input file;                               #
+#  example: rename_pdb.py 4 MY_PDB.pdb                               #
+#                                                                    #
+######################################################################
+
+
+import sys
+import os
+
+def BAILING_OUT(N_ARG):
+     """ The srcipt needs two arguments:
+     [int] The number of subunits to be renamed;
+     [str] The name of the PDB file to be renamed.
+
+     The correct use of this script is:
+
+     rename_pdb.py arg1 arg2
+
+     arg1 is the number of chains in the protein;
+     arg2 is the name of the input file;
+
+     example: rename_pdb.py 4 MY_PDB.pdb
+     """
+     if N_ARG != 3:
+             print( BAILING_OUT.__doc__)
+             sys.exit()
+     else:
+         return
+
+BAILING_OUT(len(sys.argv))
+
+NUMBER_CHAINS = sys.argv[1]
+PDB_IN = sys.argv[2]
+
+print('Number of chains is: ',sys.argv[1])
+print('The PDB file to rename is: ',sys.argv[2])
+PDB_OUT = PDB_IN
+PDB_BAK = PDB_IN+'~'
+f = open(PDB_IN,'r')
+lines = f.readlines()
+f.close()
+
+print('Making backup file '+ PDB_BAK+'...')
+os.rename(PDB_IN,PDB_BAK)
+print('...done!')
+
+print('Renaming ' + PDB_IN + '...')
+CHAIN = 65 # this is the integer that corrisponds to the character "A"
+MAX_CHAIN = int(NUMBER_CHAINS) + CHAIN
+LETTER = chr(CHAIN)
+NEW_PDB = []
+
+for i in range(len(lines)):
+     line = lines[i]
+     if line.startswith('TER'):
+         CHAIN = CHAIN + 1
+
+     if CHAIN < MAX_CHAIN:
+             LETTER = chr(CHAIN)
+     else:
+             LETTER = ' '
+
+     if line.startswith('ATOM'):
+          newline=line[0:21]+LETTER+line[22:]
+          NEW_PDB.append(newline)
+
+     elif line.startswith('TER') and len(line) > 21: # just in case there
+    #is a chain identifier in the "TER" line... (the condition len 
+    #(line) is added just in case the TER line is a just few characters  
+    #long... i.e. it would add a blank space at the start of the following  
+    #line)
+         newline=line[0:21]+' '+line[22:]
+         NEW_PDB.append(newline)
+     else: # if line doesn't start with either ATOM or TER, it will print it as is
+         NEW_PDB.append(line)
+
+print('...done!')
+
+print('Writing renamed file '+ PDB_OUT +'...')
+f = open(PDB_OUT,'w')
+for i in range(len(NEW_PDB)):
+     f.write(NEW_PDB[i])
+f.close()
+print('...done!')